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Why are the protagonists generally seated by the window?
I've noticed that in some anime the protagonist is seated by the window in the classroom. More specifically, the protagonist is generally on the second seat from the back (or sometimes on the very last seat).
I don't know if this happens in every anime, but it seems to happen on at least some.

Top: Tomoko from Watamote (left), Touma from Index (right). Bottom: Light from Death Note (left), Tenma from School Rumble (right).
Why does this happen?
Does it have something to do with character conception or mood setting?
Is it a plot device or something else?

This does seem to happen disproportionately often. Probably, it's just so that they can waste a few extra scenes with the protagonist looking out the window pensively or watching other characters doing outdoor activities, but there may be more to it than that.

Back of the class, next to the window... away from the teacher and can day-dream?

Oh really, I wanted to ask that question this morning but had no images :| +1

I'll just point out that, as with everything, Sakamoto does this best.

How else are they going to meet Haruhi?

Related question: Is there a reason the windows seem to always be on the left hand side of the classroom (while facing forward)?

Related: https://i.imgur.com/DGirrGk.jpg

It's definitely a plot device. There more interesting scenarios if the character has access to a window (sees what's going on outside), 3 neighbors, and isn't overly distracted by the teacher..

TAMNI! I was really hoping to see that here, since that was the first thing that came into my mind when I saw this question.

@Bobson, most people are right-handed, so when windows is on the left, hand will not obstruct light when writing. Most classrooms in real world have windows on the left for this reason.

@WGH - That makes a lot of sense.

It is a way (probably easiest) to describe the character that he/she is bored. And I think it also has a feel-good moment for the viewers which is basically one of main objectives of most of the animes. If I remember correctly they talk about this in the first episode of Handa-kun.

From my experiences, there's culture that 'cool' kids sit next to the window seat among countries in East Asia. It could be that this culture is influenced by anime (reverse causality), but it's a good hypothesis that cool protagonists sit next to the window to reflect this culture. For example, if the student was bullied in the class, he will not be able to sit on those window seats.

While backbenchers are common throughout the world, windows seats are similarly favoured by just about everybody in most situations. People want and prefer window seats be they in classrooms, trains, or aeroplanes. In anime, these seats additionally facilitate a few things (some of which have been covered in other answers):

The character can look out of the window to act bored.
The character can look out of the window to see other characters outside.
The character can easily exit the classroom by way of the window.
The character can easily enter the classroom by way of the window.
It reduces some of the artwork. When focussing on the character, the artist will not need to bother drawing and animating additional characters on either side. He can simply focus on the main character and draw a window or a wall as background. This saves time and money.

That said, I think that there's a mild case of confirmation bias in the question. There are plenty of anime where the protagonist is not seated by the window. Offhand, I can name Makunouchi Ippo in Hajime no Ippo, most characters in Lucky Star, the characters in Hidamari Sketch, and so on.

+1 for the remark about confirmation bias. This makes me feel the need to collect some real data to validate or refute it.

Although I understand your remark on confirmation bias, the bias is not intentional. I've only watched a few anime that have scenes in classrooms, and in all of them the protagonist is seated by the window. Since I saw a pattern, I thought it was significant enough to check for its significance.

@JNat It rarely is intentional :) Have you seen any of the anime I've noted in my answer? In any event, I think that the question is a good one.

@coleopterist I have not seen those, no. Congrats on your 2k :)

This answer was based on a valid criticism of the question in the answer by coleopterist. It does not seek to answer any of the questions posed in the OP, which in my opinion are already satisfactorily answered in several of the other answers, and should ideally be viewed as an extended comment on that answer.
The following are preliminary statistics, based solely on the anime I currently have access to. There is much to criticize, but I believe it is good enough for now. I intend to do a more detailed study of this in the future; please see the Future Work section below.

Description
The goal of this study is to gather statistics to attempt to confirm or invalidate the proposition that anime protagonists disproportionately sit near windows in classrooms. It was also found interesting to consider how far back in the room these characters sat.
In what follows, the term "column" will be used for a line of desks parallel to the window, and "row" will be used to mention lines of desks perpendicular to the window.
Methodology
Play the first episode of all anime currently available in which the protagonist is a student. There were no cases where the protagonist was not obvious. Attempt to locate the protagonist's seat by playing through the video at 8x normal speed, pausing when necessary. If the protagonist's seat can be located, note it, otherwise mark it as undetermined. In order to save time, multiple videos were played concurrently in many cases.
Data Set
The 34 anime series I currently have access to in which the protagonist is a student at or below high-school level. This is by no means a representative sample, given that they are disproportionately recent anime. A fairer method will be used in future studies.
Results
Of the 34 anime included, in 18 cases the protagonist's seat could not be determined. In the remaining 16 cases, 7 were next to a window, and 6 of those 7 were in the back two seats of that column. Of the remaining 9, 3 were in the back two seats in some column other than the column closest to the window. 4 were in the front row, and 2 were somewhere else (in one of these cases the classroom had no windows). In most cases, there were 5 or more seats per column, and at least 4 columns. It was not uncommon for one or more other significant characters to be seated in the immediate vicinity of the protagonist, and the reason that the back two seats were counted rather than just the back one was specifically for the cases where another character is sitting directly behind the protagonist.
Conclusions
It appears that both being near the window and being towards the back of the classroom are both disproportionately common based on this limited sample. These accounted for, respectively, 7/16 (43.8%) and 9/16 (56.3%), while the expected rate for both of these for random data would be well below 50%, especially in the former case. The results are not very significant statistically, suggesting that more data is in order.
Future Work
There are issues with the methodology which merit further work. In particular, the sample is by no means representative. It is prone to my own biases, which aren't easily measurable, so a more controlled experiment is needed. Rather than a self-selected sample, a better to choose a representative sample in some way which is less biased. Possible options include looking at a list of most popular anime or all recent TV anime. Either of these is expected to increase the amount of time required. The various merits and issues with each of these options will be weighed.
Another issue is that the first episode may not be sufficient. It would be good to go through enough of each anime to be sure that the correct seat is chosen, though this may prove difficult. Whatever method is used, it must be unbiased to avoid confirmation bias. This is expected to increase the time required for future studies.
A third issue is that the sample sizes are insufficient for detailed study, or even to make any real conclusions extending beyond the sample itself. In some sense this is a fundamental issue, as it will always be time consuming to locate the seat of any character in anime. Even a sample size of 34 took a significant amount of time, and the modifications in the above paragraphs are likely to increase that significantly. A sample size of 100 seems like the largest practically feasible number. The considerations of this paragraph and the above two will need to be balanced against the time of the study, which is expected to be significant (indeed, even this preliminary study proved more time-consuming than I would have liked).
While the primary goal of future studies should be establishing to a higher degree of accuracy whether this effect is truly present (and if so how large of an effect it is), there are other interesting things to look at in the long term. A few are presented here:
Correlations between the seat choice and the genre would be interesting to look at, but are likely to require significantly more statistics than are feasible. This is mentioned as a possible long-term project, but it's unlikely to be completed. The more pressing goal. In addition, it would be interesting to do a similar study for other media, but this is likely to be less trivial as most other media are less uniform in presentation than anime. Finally, a historical survey, studying how common this was in different periods, would be very interesting but is probably too ambitious.

tl;dr: Yes, this does seem to be a real thing, at least preliminarily. It's certainly not always the case, but it happens frequently enough to be interesting. However, the data I have aren't good enough to make any solid conclusions beyond "yes, this happens more often than one would expect". More data will be needed to determine to what degree this is due to biases and statistical variation in the sample, and to what degree this actually happens.

If you admit this is not an answer then why did you post it as an answer? Wouldn't it be better to put it on a dropbox or pastebin and link it?

@atlantiza While this doesn't directly answer any of the three questions raised, it is still closely related to the original question, since the OP implicitly assumes that this is true. That is to say, this is answering a question that probably should have been asked, but wasn't. Of course, it would be a valid answer to say that "actually, this is not statistically unusual," and equally well in my opinion it should be valid to post an answer confirming that it is statistically significant.

Plus, I'm certainly not going to go through several hours of work just to dump it in a link in a comment somewhere and have it disappear. I think the other answers so far answer the questions raised in the OP fairly well, so this is focusing on one thing which wasn't explicitly mentioned there, but should have been.

I just asked a related question in the comments to the OP, and you might be able to answer it with this data set.  What's the frequency of windows on the left hand side of the classroom compared to the right hand side?

@Bobson I didn't bother to note that, but in my experience it does seem like windows are more commonly on the left side. However, that could be influenced by the fact that all four of the chosen screenshots in the OP have windows on the left though, so I'm wary of making a conclusion without looking back at the data. If/when I do collect better data, I'll be sure to include this.

The results are not very significant statistically. You could say that :P The results can be explained by sampling bias.

Very nice study =D

I assume you ended up never finding the time to run this study/trial thing?

I have never noticed that before, but it sounds quite logical to me considering these points.

The character can look to the outside world giving more freedom to new plot lines.
Less background students make it easier to draw focus on the important characters, especially during class hours, when the seats must be taken.
Maybe just personal preference, but I think it is nicer to have pictures with some contrast (window-landscape on one side, tables on the other), than just a dull matrix of tables.

Another reason could also be that the proximity of the window allows different light settings on the character.
A brighter light make the character 'shine' compared to the others that are in the darker part of the room.

I noticed this as well and it is not even just about where the student sits.  In most cases that I've seen, the camera angle is facing the windows (lunch periods, random talking around a desk, etc.)
My theory is that the windows allow for multiple benefits.  First, many shows are not just about the school, so looking out the window can be a bit of a waiting-for-school-to-end-so-we-can-play type thing.
Also, having the window in the background gives much more freedom to set the scene.  You can easily notice the current weather (oh look, it's raining) or the season.  It can also show foreshadowing events (dark clouds on the horizon).
Another possible reason, it allows for the character to feel more like a loner all by themselves in the back corner.  If the character is going to be popular, the back row tends to allow more space for others to stand as opposed to the middle of the classroom.
Besides, looking at the other walls is not very exciting and in the end the show is for entertainment purposes.

Something else to add to the other answers is lighting from the window, at least from those examples. That way you can focus on the art of only the important characters while the other students can have less detail since they're in the dark. Plus, it adds more opportunities for interesting shading and light play.

Can't answer for the reasoning behind this trope.
But it seems pretty frequent, so much that BlogSuki's Jason calls it the First Modern Law of Anime:

“All major characters will have their desk window side towards the back. Sub Law: If a romantic interest occupy the same classroom, that character would be within one desk of this desk.”
source

(the sub law seems to work with rivals too)

The visual aids that windows provide are to highlight a character. They do so either by special illumination or attracting the eyes: objects placed next to bright windows tend to get noticed first.
Scene bottom-left: Light Yagami is highlighted by being illuminated sharply, the other two (convieniently!) have postures that avert their bodies from illumination. Here the illumination is used exclusively, no red laser eyes, fang-baring grins or dramatic name-writing are involved.
Scene top-left: Tomoko is in color and is illuminated not by one, but two beams of light.
Scene top-right: Three individuals get noticed by being close to the viewer and being in an illuminated area.
Scene bottom-right: Tenma attracts attention first by being next to a featureless glowing window and having the most discernible face.

Also, looking out of windows signifies contemplative moods. If my teachers noticed me daydreaming, they would seat me in the front of the class. Japanese school teachers do a poor job of catching students contemplating bloodbaths at the back of their classes.
Would love to see a scene that goes contrary to both explanations.

Rather than looking at the scene to try and find metaphorical reasons for this phenomenon, I suggest a possible financial reason.
It's cheaper to re-use stock background and animation.  All anime studios will have cells or digital information from previous anime that are available to them.  Rather than re-inventing the wheel for possibly dozens of anime series that they carry they re-use parts some parts that have common themes and then touch them up to add "uniqueness" to the setting.
Not saying this is the case, but considering how most anime high schools look exactly the same, it'd be a safe bet to say this is the reason.

I also saw this a lot, it really is a good question. ^_^
In my opinion this happens when they are in a bad mood or lonely. When you see your main character sitting at the corner on the last seat looking at the window, it will transfer you the sorrow and sadness he/she has: you gain their feelings.
I think it is for transferring us their mood.


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What is the actual reason behind the Nine Tails attack?
In the anime, the nine tails were summoned by Madara/Tobi during Naruto's birth and made to attack Konoha. Later Minato saved the village. For what reason the nine tails was made to attack Konoha?

The answer to this question will contain manga spoilers. Proceed with care.

Madara/Tobi had taken control of the Nine-Tails, but during his battle with Minato, Minato removed the Nine-Tails from the control of Tobi. Then Tobi escapes from the battle.
This is where the Nine-Tails was summoned by Madara/Tobi in Konoha (chapter 502):

This is when Minato removes the Nine-Tails from the control of Madara/Tobi (chapter 503):

This is when Madara/Tobi escapes:

Now, since no one was present to control the Nine-Tails, he went on a rampage and thus attacked the village.
Initially, Madara/Tobi wanted to keep control of the Nine-Tails and use its power for himself, and destroy Konoha. But now the Nine-Tails was a loose canon destroying Konoha on its own free will.

 After Rin, who was someone very special to Obito, was killed, he was taken by hatred towards the Ninja world. Uchiha Madara had for long contained hatred for the Senju clan. After his defeat in the hands of the First Hokage - Hashirama Senju, had made the destruction of Konoha his vendetta. Madara saped into this hatred of Obito and toned Obito's thoughts to suit his own needs. When Madara/Tobi learned that Kushina is about to deliver a child, they made their move, as the time of delivering the child is when the seal is the weakest for a Jinchuruki. Having a Tailed Beast in his disposal would have been a great advantage for Madara, as he was already planning something that concerned the Bijuus.

Thus Madara/Tobi attacks Konoha, and in turn the Nine-Tails attacks Konoha.

Inorder to find the snapshots for the answer, I went through the chapter of Kushina and Naruto conversing. And now I'm nostalgic..

But this doesn't answer the question. He already knows how the attack was performed, but he wants to know why.

The reason why the Nine tails attacked has been coverd, but does he wants to know why Tobi attacked konoha too?

Can someone please teach me how to maintain paragraphs inside a spoiler block. I use the >! to start the spoiler, after hitting a double enter for a para break the ! appears for each paragraph. No matter how many times i try it is the same result.

@Debal. Madara Uchiha is right. I saw the attack in the Anime. I want to know why he wanted to attack Konoha using the nine tails.

@Please check the spoiler part. I have included it.

@MadaraUchiha Perhaps there is a way to sort questions where it only contains manga or anime. That way spoilers can be less of a problem.

@MadaraUchiha we could include a new tag of "manga" and "anime" that can be used by other story lines too

@debal: Not really new, these tags used to exist and are now blacklisted because they were misused (for every question that was about "manga" or about "anime"). If you want an anime-only answer, just state so in your question.

The question here is not the actual reason of the Nine Tails attack to Konoha, but the actual reason of the Masked Man attack to Konoha.
The attack of the Nine-Tailed Demon Fox, coincided with Kushina Uzumaki, the Nine-Tails' second jinchūriki, giving birth to Naruto on the night of October 10th. During a female jinchūriki's pregnancy, the energy used to maintain the seal has to be redirected to the growing child in her womb — whether consciously done or not. As a result, the seal used on the beast weakens in direct proportion, and as such special preparations have to be made when a female jinchūriki is about to give birth as the seal may break entirely (Naruto Episode 500 Pages 8-9).

However, the childbirth's location was eventually discovered by Tobi, who learned the information by observing Kakashi at the Konoha Cemetery.

Making his way to the site, Tobi killed the ANBU stationed outside and later Biwako and Taji after the child had been born(Naruto Episode 500 Pages 13-17).

Holding the newborn Naruto at ransom, he forces Minato to leave the cave via his Flying Thunder God Technique when he sets off the explosive tags he had placed on the newborn's blanket.

Taking advantage of Minato's absence, Tobi forcibly extracted the Nine-Tails from a visibly exhausted Kushina while noting that the Four Symbols Seal also carried the Flying Thunder God Technique seal as a security measure which would enable Minato to teleport to his wife's aid at any time(Naruto Episode 501 Pages 1-6).
As the Nine-Tails finally emerged from the seal, Tobi used his Sharingan to gain control of the tailed beast and commands it to destroy Konoha.
My analysis:
The main reason however is notably clear. Tobi/Madara took advantage of the weakened seal because of Kushina's child birth and to take control over the Kyuubi. The attack to Konoha is just a secondary effect from Tobi taking control of the Kyuubi. The attack was merely a prerequisite of his main plan of collecting the Kyuubi. We knew that the Eye of the Moon Plan requires all the tailed beast in order to form the Bijuu; and the very root of these plan is to fill the empty hole in the heart of Obito(Naruto Episode 530 "What can fill the hole" Pages 4-5).

Yes Kurama did attack Konoha but this was only because he was controlled by Madara’s Sharingan and was forced to attack the hidden leaf. If Karuma wasn’t controlled by Madara/“Tobi” He would’ve destroyed destroyed them first than the leaf village

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How do the 3 sannin know about using Five Elements Seal on Naruto?
In the Anime, during the Chunnin exams, Orochimaru attacks Sasuke inside the Forest of Death. When Naruto came to rescue, Orochimaru identified that he was the nine tails and places the Five Elements  seal on Naruto. Later it was unsealed by Jiraiya. In the Search for Tsunade arc, Orochimaru tells Kabuto that the seal can be placed or removed only by the 3rd Hokage and the sannin. Were the 3 sannin taught about this by the 3rd Hokage?

I'd just like to point out that saying "3 sannin" is incorrect. Sannin in itself means 3 people, with the explicit understanding that they're 3 ninja. See the comments below this answer for more info. That would mean that saying "3 sannin" is the same as saying "3 3 (ninja) persons".

Apparently so. It's possible that other people were able to use the seal (for instance, Kushina, who was a sealing expert, or the Second and First Hokages, who knew advanced sealing techniques, but passed away).
It's possible that they referred to only living shinobi for that purpose (it makes sense, because they were trying to figure out who unsealed it).
I believe the technique was passed down to (or invented by) the Third, and he in turn taught it to his disciples.
Note that Minato never used the Five Element Seal.

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Where did the ninja clans other then Senju and Uchiha originate from?
In the anime, it is shown that the Senju and Uchiha clans originated from the Sage of Six Paths who is the God of Shinobi. Where did the other clans like Sarutobi, Nara, Inuzuka, clans from other countries originate from?

If you've watched the latest episodes, you would see different villages and empires of the past. I would assume that has something to do with it.

Recall that the Sage of the Six Paths discovered the existence of chakra and used it to create jutsu. The direct descendants of him became Senju and Uchiha, where their powers were split between body and eye.
Other ninja clans were not descendents, however they were able to learn how to use chakra as well in different forms of jutsus. Of course there are some clans, like the Hyuuga where the series notions the possibility of them deriving from the Uchiha.
Clans like Sarutobi, Nara, and Inuzuka clans are not related to the Sage of Six Paths though. On the other hand, Uzumaki is blood related to Senju.

Just to clarify any misconceptions, there were already people living on earth before Otsutsuki Kaguya made her move to steal the chakra of the Divine Tree. Its actually not like the Otsutsuki clan populated earth in its entirety. Just like someone said in the comments, there were villages and empires belonging to different settlements at that time. And so to answer your question, all those other clans originated on earth just like normal families do. However, everyone was greatly influenced by the Otsutsuki clan.
Longer version:
The people who lived in The land of the Ancestors, welcomed Kaguya because they saw her as a Goddess and she bore 2 children with Tenji, the Emperor of the land (Hagoromo and Hamura).
Hamura Otsutsuki, the younger one, later on became the ancestor of the Hyuuga Clan, after which he went to the Moon to guard the Juubi's Husk.
The elder brother, Hagoromo Otsutsuki became known as the Sage of Six Paths, because he founded and taught everyone about Ninjutsu which was originally called Ninshuu. All other clans must have learned thier various Jutsus from any number of thier Ancestors who was a follower of Hagoromo (or a follower of a follower of Hagoromo, kinda like that).
Apart from the Hyuuga, Uchiha, Senjuu and Uzumaki clan (all of whom inherited specific chakra and traits of the Otsutsuki Clan), all other clans learned Jutsu's indirectly from the Sage of six paths teachings.


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Is "Phantom Rouge" story canon?
Simply that: did the events of Hunter x Hunter: Phantom Rouge really happen (with respect to HxH story, of course)? At least the timeline is credible (between Yorknew City and Greed Island arcs).

It's a part-canon side-story.
AniDB:

The premise of the movie is based off a manuscript of the Yorknew City arc written by Togashi Yoshihiro that he eventually ended up scrapping.

WP:

The film is based on an unpublished story manga creator Yoshihiro Togashi wrote around 10 years ago.

Since it's based off his own work, Phantom Rouge presumably has Togashi's blessings.

I think it is, it hasn't been confirmed by the mangaka but there is a manga chapter about Kurapika's past that is shown in the movie.


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What technology/jutsu do the Akatsuki members use to communicate with each other?
In the anime, it is shown that the Akatsuki members communicate with each other from the place they were currently present. What is that technology or jutsu?

I guess it will be form of telepathy or sort of and pein also have ability to manipulate certain objects remotely like antennas

Or maybe they just use "stick-to-the-plan" technique. =)

They also use Zetsu to communicate as well.

This would be the Magic Lantern Body Technique

...The Akatsuki members sit down and send out "thought waves" (思念波, shinenha), converted into chakra. These thought waves are then picked up by Pain, acting as a kind of control tower. This technique amplifies the thought waves and broadcasts them to a specific location through illusionary bodies. The illusionary bodies differ from being mere reflections. While Pain is relaying the members' thoughts, they can have conversation and use varying techniques...

From Nagato's wiki page under Ninjutsu

While acting through the Deva Path, Nagato displayed a wide range of techniques. Nagato was responsible for Akatsuki's meetings by using a technique that allowed him to pick up their thought waves and broadcast them in the form of an astral projection to a specific location.

Accorrding to this, Pain "has a telepathy-like ability that allows Akatsuki members to communicate with each other through astral projection wherever they are located."


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The Tree of Life in Fullmetal Alchemist
I've noticed references to the Kabbalah in a couple of anime I've watched.  One of them is Fullmetal Alchemist.
Fullmetal Alchemist has the Tree of Life on the Gate:

So, my question is, Is there any deeper meaning to the use of the Kabbalistic tree of life, or is it just used because it looks cool?

The fact that this engraving with the Tree of Life only appears to Ed may also be noteworthy. As can be read here, the gate's appearance differs from character to character, and only Ed sees the Sephirothic Tree of Life.

The Tree of Life is one of the most important symbolism in western alchemy.
The spiritual nature was especially highlighted among early practitioners of alchemy, but I would say that it was more Hermetic occultism than religious Judaism/Christianity. (Therefore, some people might spell it Qabalah rather than Kabbalah.)
The 10 emanations/attributes and the paths in the Tree were associated with the alchemical metals, elements, and planets that govern the alchemical process. The image below shows the tree with astrological planetary symbols associated. In alchemy, these planets were associated with various metals and elements. Therefore, an emanation might correspond to the sun and hence gold, and so on.

Therefore, it is only natural that it would make an appearance in an anime about alchemists.
For reference, you can find a giant essay here, although I haven't gone through all of it: "Secret Fire: The Relationship Between Kundalini, Kabbalah, and Alchemy"

(Originally split from this answer)
The actual mythology of the show involving alchemy has a closer tie to religious symbolism than something like Evangelion (which was mainly to look cool). Within the Full Metal Alchemist show, historical in-universe events are tied to real world symbolism, like the Tree of Life, The Flamel (named after the real-life French alchemist), the Homunculi and the seven deadly sins, etc.
There's been several analysis of the religious symbolism in FMA:

http://chrisqu.hubpages.com/hub/Fullmetal-Alchemist-Brotherhood-Religious-Symbolism-and-Discourse
https://gargarstegosaurus.wordpress.com/2008/10/25/the-curious-case-of-religion-in-fullmetal-alchemist/

Unlike with Evangelion, I don't know of any statements made by the staff to address the use of religious symbolism in the show, but I think it's pretty clear that it's more internally consistent than simply to look cool.

In Fullmetal Alchemist: Brotherhood, two gates were shown instead of just one as in the original. Both of the gates have pictures of a tree on them. As you have already said, one of them is the tree of life.
To uncover the identity of the other gate, we have to bring to light the book of Genesis, which is where I personally believe the two gates originated from.
If you are familiar with the story of creation, you know that Adam and Eve lived happily in a garden where only one law existed. This law was simply not to eat the fruit which grew from the tree of knowledge of good and evil. Adam and Eve were told that disobedience would lead to death.
We later realize that you would not actually stop breathing and became a cold lifeless shell, but instead, this death refers to dying to the flesh. Dying to the flesh means surrendering your life to your deadliest desires and choosing to never obtain fulfillment. Pretty dismal, right? Anyway, Adam and Eve decided to rebel and eat the fruit after being promised by the devil that such consumption would unfold the truth and enable them to understand the ways of God.
Back to the universe of Fullmetal Alchemist, alchemy was a powerful science that brought happiness to both those using its powers for good and those receiving aid from alchemists. A rule was given with this great gift: do not perform human transmutation. Ed and Al had repeatedly heard that death followed after a human transmutation.
Against better judgment, the two brothers gave into their deadliest desire to have their deceased mother be by their sides once again. Immediately following the human transmutation, Ed and Al passed through a gate with picture of a tree where they uncovered truth, both good and evil knowledge that governed alchemy and even the world itself. Because of the boys' disobedience, Al lost his entire body and could not be entirely happy or fulfilled without it. He died to the flesh... LITERALLY!
For these reasons, I am led to believe that the tree on the gate resembles Adam and Eve's tree of knowledge of good and evil found in the Bible.

I'm unsure about this explanation. Where do Ed and Al hear that "death followed after a human transmutation"? I only recall it being stated numerous times that it was forbidden; the cost of the transmutation appears to not have been made apparent until later in the manga.

Note also that it is only Alphonse who loses his body; Ed and Izumi do not. Also, is there a precedent for this interpretation of Genesis? I would associate "surrendering your life to your deadliest desires and choosing to never obtain fulfillment" with dying spiritually, not "to the flesh". It is true that Eve and Adam do not die right after they consume the fruit, but I always assumed that (God perhaps being merciful to them) it meant that they would die later. (I also don't know if these concepts "translate" to Japanese or from classical Hebrew, but perhaps that's a lesser problem.)


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How come Donyatsu can stand in the rain?
In chapter 3, Donyatsu gets attacked by the Machumaro, and they take a bit from his back:

With this, we know that (at least) a superficial layer of his body is composed of some kind of pastry, which is even edible.
We also know that Donyatsu needs to eat, which means he somehow has a digestive system.
In chapter 13, however, Donyatsu is seen standing in the rain:

How can he stand in the rain and not melt (he has a sugar coating) or get soaked (since he's made of pastry)?
Furthermore, how exactly does his body (and of the bodies of the rest of his gang) really work, physiologically?

The same way nyan cat flies through space and poops rainbows (in space).


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Does the Rinnegan eye put more strain on the user?
In the anime, it is shown that over usage of Byakugan and Sharingan eyes will cause the user to strain. Does that happen with a Rinnegan user?

It's not mentioned anywhere that it does.

In Naruto, Byakugan and Sharingan strain are slightly different though. Byakugan strain is just temporary while Sharingan users actually start going (permanently) blind from too much usage. I'm pretty sure Rinnegan causes no strain as people like Pain were constantly using it. On the other hand, people like Tobi turned off his Sharingan quite often.

Only overuse of Mangekyu leads to blindness I think. Normal Sharingan does not.

They never mention strain of the Rinnegan in the manga so the following is conjecture
Nagato (and his puppets) seems to have the Rinnegan up 24/7. In flashbacks to the Sage of Six Paths he has Rinnegan up so I believe it does not cause strain like the other ocular powers

All eye techniques use up a lot of chakra.
Clan users can use the techniques for longer periods of time as compared to non clan users (like Kakashi). But even then there is a limit to which the doujutsu can be used, and that is dependent on the chakra level of the user.
Now to which extent the Rinnegan can be used has not been explicitly defined in the manga, so it can only be a guess. But surely it should cause strain to the user on over usage.

While I agree all ocular techniques use chakra, that doesn't necessarily mean they cause strain. Sasuke could probably keep on his normal 3 tomoe sharingan for the whole day and while it may consume chakra, I doubt it will strain his eyes. At this point, only using the mangekyou seem to do that. It seems pretty normal to always have rinnegan on, where as sharingan and byukagan get turned off, so it might cause no strain. This is all just speculation though.


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Why did the "until we graduate" provision enter into the ending of OreImo?
In the last episode of Ore no Imouto ga Konna ni Kawaii Wake ga Nai (season 2, episode 16 / OVA episode 3), we learn that Kirino and Kyousuke agreed to the following:

 Kirino and Kyousuke will be boyfriend and girlfriend starting on Christmas Eve (when Kyousuke confesses to Kirino that he loves her), and ending when they both graduate (Kirino from middle school and Kyousuke from high school).

This is kind of weird, since:

 That's just 4-5 months. It's fairly clear that they're in love with one another, and Kyousuke goes so far as to reject all the other girls that are basically throwing themselves at him. Why would they cut it off after so little time?

In an interview, FUSHIMI Tsukasa (the author of the light novels) was asked for his comments on the following:

12巻は全体的に美少女ゲーム（ギャルゲー）を意識した構成になっていて、原点に帰った印象を受けます。
I felt that volume 12 [the last volume] was written in a manner informed by galges. It felt like a return to the way it originally was.

Fushimi responded:

そうですね。狙って１巻っぽいシーンを書いています。すべてに決着をつけて禁断の道に突っ込むという痛快な物語は、電撃文庫で、直接描くのは、とても難しいですし、桐乃を幸せにするエンドにしようと決めた以上、彼女の今後には、可能な限り良いレールを敷いてやらなくてはいけないし……非常に悩みました。結果は、読んでいただいたとおりなのですが、再読する方向けに、蛇足ながらコメントさせていただくと、
・「完全なる桐乃エンド」
・「最初の人生相談と同じように、兄妹は、二人だけの秘密を抱えて終わる」
１２巻は、そんなお話です。
I guess so. I wrote so that it would have scenes that felt like those in volume 1. With Dengeki Bunko [Fushimi's publisher], it was very difficult to write a thrilling story in which they settle everything and head down a forbidden path. I was sure I would give Kirino a happy ending, so I did my best to set up as good a situation for her as possible, for the sake of her future. I found it very difficult to do so. It ended up the way you read it [in volume 12], but if I were to add a few unnecessary comments for those readers who are reading it for a second time, I would say:
"A Completely Kirino Ending"
"The story ends with the two siblings sharing a secret, the same way their first life-advice-talk [jinsei soudan] began."
That's basically what volume 12 was about.

In another interview, Fushimi was asked:

すでに最終巻を読まれた読者には既知の結末になるんですが、エンディングに向けての展開はどういう風に決めていったんですか？
The ending [of the anime] will probably come as a bit of deja vu to those who have already read the novel. How did you decide how the story would reach its end?

Excerpted from Fushimi's reply:

[...]桐乃の想いが完全に報われる結末が[...]ひとつもなかったんです。普段表には出さないし、いろいろな事情があって、分かりやすい形で書いてあげることもできないけれど、彼女がとても主人公のことを想っているのを、僕は知っていたので、何とかしてやりたかった。[...]
In the main story [as contrasted with the PSP game], I couldn't write an ending where Kirino's affection is truly and entirely rewarded. Various circumstances prevented me from plainly writing that sort of ending. Nonetheless, I realized that she cared deeply for [Kyousuke], and so I felt I had to do something for her.

Fushimi's comments strongly suggest that he wanted to write a different ending - presumably a more "taboo" one in which Kirino and Kyousuke remain in a relationship - but was prevented from doing so by his publishers. Hence the "until we graduate" provision.


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How is the voice quality of a seiyuu classified?
Considering the extreme popularity of voice acting and voice acting schools in Japan, I'm curious to know if the industry actually classifies the quality of each voice. I'm not talking about things like age, gender, etc. Rather I'm interested in the tonal quality of the voice.
Personally, I'm particularly taken by the tonal quality of Mizuhara Kaoru, the seiyuu who voiced Kusakabe Misao in Lucky Star. Kusakabe's voice has got a thick, musical quality to it and sounds ... double-layered.
(I'm not the only one enamoured with Kusakabe's voice:

Her character Misao Kusakabe in Lucky ☆ Star gained a cult following in fans and spawned internet memes due to her own addition of a nonsensical "vuah" (ヴァ) at the end of her sentence.("if it's picked up within 5 seconds, the germs don't get attached" 五秒以内だったら、菌がつかないんだってヴァ) This began in the 18th episode of the anime where her character Misao was nervous and embarrassed after eating food that has been dropped on the ground in front of others. The popularity was substantial enough to have a 13th Lucky Star character album featuring Misao released four months after the originally planned twelve albums were released even when her character already shared a duet character album as the 9th album.

This is at around the 18 minute mark of the 18th episode.)

Well I don´t think they actually classify the quality of each voice. Why do I think so?
Most seiyuu are picked after they either send in some records or do a vocal audition, or they have done voice overs/acting before and are scouted this way.
When a company wants some voice acting done, they usually keep in mind the characters that have to be voiced. Most of the time characters have a specific personality and they want a voice to best represent this personality. For example, let's look at Mizuhara Kaoru, the seiyuu who voiced Kusakabe Misao in Lucky Star. She has a melodic yet playful voice which can represent the character as one of the best. To even better grasp this concept, think of Naruto being voiced with Kusakabe Misao's voice. This would not match the personality the character has to represent.
So if there were to be a classification for seiyuu, it would differ per character. So there are no known "standard classifications" for seiyuu.


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Is there some deeper meaning associated with all the religious symbolism in Evangelion?
It just seems like they put all those symbolism for no reason, and it sounds and looks pretty stupid IMO. The series would have been a lot better without all the nonsense.

Possible duplicate: http://anime.stackexchange.com/a/4786/49

Your question a bit vague and overly broad. Anno putting in references to Christianity while being from a predominantly Shinto society is like the Americans doing a series on Norse mythology, more so on mystique than symbolic meaning. That aside, there are a lot of theories on the subject, but they're mostly just other people's opinions and interpretations. Anno himself even admitted that there's no deeper meaning behind the symbolism.

In a few interviews:
Hiroyuki Yamaga: May 1998 issue of "Evangelion":

On the reasons for use of Judeo-Christian symbology in Eva
YAMAGA: I don’t know exactly why. I suspect that Mr. Anno may have read some book on it, and there was some thoughts he wanted to express on it. I personally am glad that, rather than Christianity, he didn’t express some obscure Buddhist theme, because then it would have been linked more with Aum Shinri Kyo. [LAUGHS]

Kazuya Tsurumaki: Q&A from "Amusing Himself to Death":

Can you explain the symbolism of the cross in Evangelion?
Kazuya Tsurumaki: There are a lot of giant robot shows in Japan, and we did want our story to have a religious theme to help distinguish us. Because Christianity is an uncommon religion in Japan we thought it would be mysterious. None of the staff who worked on Eva are Christians. There is no actual Christian meaning to the show, we just thought the visual symbols of Christianity look cool. If we had known the show would get distributed in the US and Europe we might have rethought that choice.

and from an NHK special "Extra Curricular Lesson with Hideaki Anno", a student asks:

"Why is that robot-looking thing called an Evangelion"?
Anno: "It is a Christian word meaning Fukuin or Gospel and it's supposed to bring blessings. Actually, it's a Greek word. I used it because it sounds complicated"

So it seems the creators didn't mean for there to be any deeper religious meaning from all the religious symbolism. That doesn't mean that there isn't in-universe meaning to the show. For example, the name of the Angels correspond to their features (e.g. "Gaghiel" = "Fish", "Israfel" = "Music", "Sahaquiel" = "Sky", etc), and the symbols themselves aren't haphazardly placed. There could very well be an in-universe explanation for why the symbolism is there at all, possibly inherited from the Angels themselves or created by Seele.
Additionally, there could be meaning derived from the symbolism beyond what the creators originally intended.


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Is there any alchemy-based transportation in FMA?
In FMA, cars and trains are shown, but they seem to be regular early 1900s cars and trains, similar to those that existed in the real world at that time. I was wondering if there are any forms of transportation that are shown to take alchemy, either in the construction or in the actually running of them?

There is no official word one way or another on this, as far as I can tell.
That said, there is significant evidence that the alchemists outside of the military are not as talented as the ones we've seen. In general, the military tends to pick up extraordinarily talented alchemists for their own purposes. (You can see scenes such as Al fixing the radio, Ed's little parade around town fixing everything, and even Ed fixing up the town after alchemy stopped working for a while; in each of these scenarios, the townspeople are astounded at their skill level.) Alchemists who do not join the military (Izumi, Hawkeye's father) tend to live more secluded lives and devote their time to research or other science.
From this, we can conclude that there are probably few alchemists who are willing to take their time and contribute to an industry (transportation manufacturing) that does not take advantage of their scientific understanding or level of skill the same way being in the military would. Not only that, but the military grants lots of time for personal research as well as huge grants to State Alchemists.
Given all that, it's tough to say that any alchemists would find themselves in the manufacturing industry; this doesn't mean there aren't any able to, though. We've seen Ed able to completely transform the exterior of a car.

However, as I said, since there is no official word on this, we can only assume that the alchemists outside of the military likely do not have the skill nor motivation to participate in the manufacturing of transport vehicles.
In terms of alchemy actually being used for transportation, this is essentially unheard of. The only time this actually happens is when people move between reality and non-reality. (This happens when they are deconstructed and taken into the Gate, or when Ed and Ling escape from Gluttony.)

All that I could come up with transportation wise was when Ed used pillars of earth to travel skywards in The Conqueror of Shamballa.


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Is anime popularity growing outside of Japan despite declining profits?
http://www.japantimes.co.jp/news/2013/03/23/national/to-survive-anime-must-adapt-but-not-too-much/
I thought that they would make more money now that many streaming sites buy licenses from anime producers.

Can you clarify what you are looking for?

I don't know what your question is, but streaming licenses don't really make producers much money. Their business model is selling DVDs/Blu-rays. Streaming is viewed as little more than an advertisement, so streaming licenses are cheap and produce little money. Home video licenses are costly and net almost all of the profits for producers. That may change in the future, but right now that's the business model.


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Why does Touma care if other people learn that magic exists?
There are multiple scenes in the Index movie (The Miracle of Endymion) where Touma cuts Index off when she's about to say something to Arisa about magic or magicians or whatnot.
Why does Touma have an interest in preventing Arisa (or anyone) from learning that magic exists? It doesn't seem like other people knowing about magic would have any adverse effects on him.

Probably to prevent them from stepping into the world of science-magic conflict that he has experienced so far?

I personally think he might want to avoid of those conflict between Science and Magic ( since It is already happened and happen along with anime )

Ultimately, Touma doesn't want everyone to know about the truth of Academy City, where corruption prevails and everyone is just a test subject. If everyone knows the truth, all chaos would break loose.
And once people learn about magic, the domino effect happens.
People learn about magic -> People learn about the struggle of power (Science vs Magic) -> People learn that Academy City is corrupted beyond belief in every aspect possible -> A big war ensues where everyone chooses a side
Just think about the magic side as a gang that is trying to take control of the government. The government (Academy City) has been sweeping their own dirty deeds under the rug, as well as concealing their opponents. Learning about magic opens the door to everything.


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What's the character in the poster hanging on the wall supposed to be?
In the beginning of Urusei Yatsura - Beautiful Dreamer, the class is setting up their classroom to be the "Third Reich Decadent Coffee Shop", and in a panning shot of the classroom, there's a poster of a red guy that is obviously supposed to be dressed up as Adolf Hitler. But what's the character supposed to be? Is it a reference to some bit of popular culture or from another show?


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Is there a religion in Amestris?
Occasionally, especially when talking about human transmutations, Amestrians mention God, mainly with the idea of human transmutations being a transgression against God. An example of this is when Olivier Armstrong is talking about the three tenets for state alchemists and is answering the question of why human transmutations are forbidden.
It doesn't seem to me like this is a reference to "Truth", seeing as very few people seem to know about "Truth", who is essentially the God within the gate. Is there some specific religion's God that this is reference to, or it is a sort of generic God=nature? Is there a stated religion within Amestris?

Do you mean "believers of a God" or an entity called "God" apart of Truth?

Would the Leto-Cult count here?

"Believers in God", because they all seem to reference God in the same way that religious people now do, but presumably virtually nobody knows about Truth-as-God.

As I consider a more complete answer, I will just remind anyone reading that there is the Ishvalan belief system (very similar to Judaism) present in their portion of Amestris, even after the war.

also possibly interesting is the belief in the sage of the west.

Don't know if it matters, but the Sage of the West is Van Hohenheim.

There appear to be a few religions in Amestris (or potentially a few views or denominations belonging to a single religion), and we can see actions from several people that denote a religious following.
Truth and God

Ironically, the being who is canonically referred to God seems to have little to no religion based around it (the same for Truth). They are essentially all-powerful beings of nature, but garner little attention from those outside alchemy (who are generally atheists).
Letoism

In the town of Lior, a priest, Father Cornello, has been given a Philosopher's Stone by an at-the-time undisclosed party. Leaving his fellow Lior citizens unaware of this, he manages to garner a lot of attention through miracles (smaller ones in Brotherhood, though much more effective and large ones in the 2003 anime). These miracles, according to Cornello, are from the Sun God, Leto, around whom the religion is based.
In Brotherhood, after Cornello is debunked, Letoism disappears. The 2003 anime handles it differently, and one could say that the religion lingers on.
Ishvala

Among the Ishvalans (those who remain, and their society prior to the war), there is a common belief in the Earth God Ishvala, who is said to be the one true creator, much like you could consider a typical god in a monotheistic religion. His teachings prohibit the use of alchemy, though some of his followers have stepped around this teaching and, in some cases, broken it entirely.
A note: The Ishvalan religion borrows many traits from Judaism, but I won't go into detail here.
Other religions

In the 2003 anime, Ed and Al end up in Aquroya, where they meet a woman named Clara. There are signs later that she is not fully committed to this religion (though her churchgoers are), and not much is said about it, except that (according to Clara) Ed and Al's bickering "goes against God's will."
There appear to be few mentions of religion outside of Letoism, Ishvala, and this small religion in Aquroya; I would wager a guess that any other mentions of "God" (by non-alchemists) belong to this same unnamed religion. It appears to borrow traits from Catholicism (or Christianity as a whole), which would line up with early 1900s in Germany, if I recall correctly.
The Eastern Sage and the Sage of the West are also regarded somewhat as religious figures, the latter described as being a man of gold (his hair and eyes, and also a reference to alchemy's properties with regard to gold).
In Xing, a religion similar to Buddhism has developed, it would seem, which talks about chi and the flow of energy in the earth (referred to as the Dragon's Pulse). Likely, being a monarchy, there is also a god atop their structure, though I don't believe he is ever mentioned.

Very good compilation! Here have some fake internet points!


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In episode 1 of Hyouka, what was the topic of the essay Houtarou has to rewrite?
In episode 1 of Hyouka, Houtarou is forced to stay after school one day to rewrite an essay that he accidentally left at home. What is the essay about?

The full title of the essay (partially obscured in the image above) is:

「入学一ヶ月の実感と今後の抱負」
"My experiences during the first month of school, and my ambitions for the future"

In the essay, he writes about his desire to do his very best to promote culture at his school (via his participation in the classic literature club), adding that this won't interfere with his academic pursuits, as befits a student attending the finest high school in Kamiyama.
Interestingly, when this scene appears in the Kotenbu series (on which Hyouka is based), it appears much later, chronologically (in volume 4), and does not include the text of the essay. His internal monologue in the novel does suggest, however, that he's basically making this up as he goes along to get it over and done with.


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What book is Houtarou reading in episode 2 of Hyouka?
In episode 2 of Hyouka, Houtarou is shown reading a book throughout the episode. What book is it?

Houtarou is reading On Decadence (堕落論 = Daraku-ron, sometimes also translated Discourse on Decadence), by Ango SAKAGUCHI.

(image source: this blog)
Sakaguchi was a novelist, essayist, and critic who lived from 1906-1955. He gained immense popularity in the immediate post-war period with his 1946 essay On Decadence, which criticized pre-war Japan as too heavily steeped in bushido culture, and argued that though post-war Japan was decadent, it was better than what came before.
On Decadence is not mentioned in the Kotenbu series of novels on which Hyouka is based.
In an amusing connection, the anime Un-Go (written アンゴ = ango in Japanese and hence pronounced identically to Sakaguchi's given name) was based on one of Sakaguchi's period novels - Meiji Kaika Ango Torimono-chou, loosely "Ango's Tales of Detectives from the Dawn of the Meiji Period".


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Why is katakana used for the onomatopoeia/sounds in the background?
In Japanese, katakana is used for loan words/foreign words, but it shows up a lot in backgrounds of manga as what seems to be onomatopoeia. Is this manga-specific, and where did it originate?

The center white katakana on the bottom panel seem to be "fuaaaaa", for instance.

You would probably get better answers by asking this on http://japanese.stackexchange.com/.

This question appears to be off-topic because it is about the Japanese language (which already has a SE), not something specific to anime/manga.

Using onomatopoeia to stress sound effects in literature is not manga-specific or even comic-specific. For example, 1966's Batman TV series or even Nickelodeon's The Fairly OddParents had readily available audio to match their onscreen text with emphasis. But several cultures have their own origins. Tracing back when this particular artistic/literary device caught on would be pretty exhaustive, if even credible at all.


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How come only certain animals can talk?
In Naruto, some animals can talk, like the toads of Mount Myōboku, Kakashi's ninja dogs, Manda, and Katsuyu. Some of them have ever used hand signs.  Yet Akamaru can't even talk. Is the ability to talk given to certain animals at random, or can they all talk when they have enough chakra or do they just simply have to learn how?

I think it was mentioned in one of the databooks, that Kakashi's Dogs can only talk because they are clever enough. I'm not sure, however.

Are you indirectly saying Akamaru isn't clever?

relevant: http://anime.stackexchange.com/questions/4161/why-cant-inuzuka-clans-dogs-use-human-language/

@Vogel612 So the animals that can talk are spirts? But they can breed

@TAAPSogeking why should they not? as far as i recall they are also growing old... furthermore "spirits" is maybe the wrong expression... they are moreover the "animal Species" representatives

@looper they are summons... not surprising they can talk. even the fckin snail can talk..


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What does the title of the anime "K" mean?
In 2012, there was an anime titled K (or sometimes K Project). Does the title mean anything in the context of the anime?
(cf. C, which was titled for the word "Control", and X, which was supposedly titled after the use of the letter "x" as a variable).

I would say it stands for "Kings".

I would say it is for King

There are two possibilities for what the "K" refers to.
The first is Adolf K. Weismann, who is the original person that became Yashiro Isana, the main character of the show.
The second is "King". The leader of each clan is its King, who controls the members of the clan.  Weismann is a King.
KINGS is also the first opening theme of the show.

J/C, any reason for the quote block there? Doesn't seem necessary.

@Eric It was an accident, which I have now fixed. Thanks.

The K in K project stands for König which is aprecciated to be engraved on the slate. This is for König project, the main project carried in the second war by Adolf K Weismann which translated into english is King project.

I'll put together @poop's and @kuwaly's answers.
The two possibilities are are "K" for "King" or for Adolf "K" Weismann. However, the second for Weismann is incorrect. Wiki: http://k-project.wikia.com/wiki/Yashiro_Isana
After a bit of research as well as a search through the K-Project wiki, I found that Adolf's middle name isn't actually revealed in either the anime or any sources. Due to his middle name not being known, we can see that it is of little importance to the anime.
Now let's jump to the title of the last episode title, "King." We can piece the title of the anime together with the title of the final episode as the anime was leading up to the final episode, uniquely named, "King." "King," is the most likely of the two options since the plot line, use of the word "King" and the name of the final episode all relate to the one word, "King."
So the title of the anime would be, "King-Project," or "King."

I've watched a talkshow. In that talkshow, the creator told that K means "Kizuna" or bonds. So, it means every character has a complex bond that bind 'em each other.

Do you maybe have a source? Like the actual talk show, maybe a transcript or such. Without the actual source to cite, this answer is of a very low quality.


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What are these pixeled-out places from the Endymion special?
In the Index-tan special for the Toaru Majutsu no Index: Endymion no Kiseki movie, the following two images appear, pixelated-out, during a conversation about landmarks in Tokyo:

What are these places?

How come they are blurred out?

@krikara Presumably the same reason that pop-culture references to things like brand-name goods get pixelated out. I don't really know what the reason for that is, though. Conventional wisdom is that this happens to avoid trademark infringment and so forth, but I don't know what the actual answer is.

The first place is the Asahi Beer Hall (i.e. the Super Dry Hall, スーパードライホール). (cf. Google Street View)

The second is Saw, Sawing, an art installation by Claes Oldenburg located at the Tokyo International Exhibition Centre (aka Big Sight). (cf. Google Street View)


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How did they know that some Psychobuster still existed?
Saki's parents leave her a letter describing, roughly translated:

Most of the weapons non-cantus-users created to defeat the
  cantus-users have been rendered useless throughout the years. However,
  one of them managed to survive this whole time: the Psychobuster. Here
  is the address of its possible location - if you manage to find it,
  you might be able to stop the demon.

The letter implies that they know (or at least, are fairly sure) that there is some Psychobuster out there that survived those centuries.
Of course, they aren't sure if Saki will be able to find the Psychobuster in the mentioned location, but they ARE sure that there must be one existing somewhere, which is what concerns me. How can they tell that there is still some left?

Personally, I think later in the series the show started going down the drain and they just had to come up with whatever cliche nonsense would help end the story.

They are not sure that there are any weapons left, but the information regarding the existence of the Psychobuster itself is given to them most likely by a False Minoshiro.
As seen in the next episodes, it also helps them navigate to the presumed location of the Psychobuster.
It all about the hope of finding one. Similarly, the Queerats previously attempted to search for weapons to use against the cantus-users, with Kiromaru willing to sacrifice a large part of his expedition.


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Is Diego Carlo from History's Strongest Disciple Kenichi Mexican?
He is a master of Lucha Libre, uses some occasional Spanish words (Rachel Stanley even calls him "maestro"), and his name sounds vaguely Hispanic. I don't know if it has been stated explicitly on the Manga or somewhere else.

I don't know anything about the show, but "maestro" is Italian, not Spanish.

@kuwaly It's also Spanish http://www.spanishdict.com/translate/maestro

I think so, he use some words in spanish and Lucha libre is a mexican fight and his name is a spanish (mexican) kind. But i dont remender of any dialog in manga about it.


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Why and how is it that Yoruichi can transform into a cat?
I have heard different theories like her mother was a cat demon, she has a kudo no one else has, or the cat is a really advanced gigai. I would really like to know if any of these are true and if not what is the real explanation for it?

Another theory: the cat form is her bankai. :P

I heard from my super anime otaku friend that in an interview Tite Kubo said that Yoruichi's mother was a cat demon so that is where she got her ability, but since it is "from the grapevine" I didn't know the validity of it.

Another theory: the cat form is her bankai Bankai obtained in years of training... imagine if ichigo's transformation bankai is kon.

There is no definitive answer to this and any attempts at an to answer this would be speculative at most. It was never explained in neither the manga nor the anime.
From the wiki:

...While it is unknown how she obtained her cat transformation, she appears to prefer spending most of her time in it....

It is never told why she can do this. But it has something to do with her leaving the Soul Society. It might have been the only way she was able to get out. She was the form of a cat for 100 years. She is the only known one to be able to do this.
Hope this helped!

The part about leaving SS in that form kinda makes sense but still speculation at most.


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How powerful are Koharu Utatane and Homura Mitokado now?
Right now in Naruto universe, Koharu Utatane and Homura Mitokado are members of Konoha Council.

They joined the council after Hiruzen becomes The Third Hokage. According to naruto Wiki:

When Hiruzen became the Third Hokage, Homura and Koharu became his
  councillors. With their years of experience and knowledge and their
  unending effort to make Konohagakure a better place, they eventually
  gained similar respect and social status as the Hokage himself.

But it is known that before that, they're member of Team Tobirama, that also included Sarutobi Hizuren and Tobirama himself. They fought together during the First Shinobi War. So in this time their power could be compared to Hiruzen?

So, How strong are they now? Have they ever fought again after team Tobirama was dissolved?

They could be having a bunch of Sharingans and Hashirama's cells in their arms, lol. But seriously, it doesn't look likely that Kishimoto has any further role for them in the story. Good question though.

Indeed a good question but I think nothing from the manga explained or mentioned anything about their abilities. The answers could be merely speculations.

They are powerful politically, but have no impact in combat.

Both of them were trained along with Hiruzen (the third hokage) by the first and second Hokage (Hashirama and Tobirama) so we can assume them to be quite powerful considering that they participated in the First Shinobi War as well. As of now, they weren't shown in combat at all, not when Kyubi attacked the village or not when Pain eradicated the village. I believe it'll be safe to assume that they have technical skill and experience that they have gained over the years but since unlike lady Chiyo, they don't use puppets or any other tool to help them in combat, they're pretty much off the floor.

They're probably reasonably powerful, but it seems unlikely that they'd even be as powerful as Danzo was, and right now compared to the god-like power of Naruto, Sasuke, the Hokages, the Sage and his mum, their power is most likely basically insignificant.

Years and years later...
Well, in my humble opinion they must be quite powerful. But, they must be "old school" shinobi. Some elemental jutsu, shurikenjutsu and overall ninja field skills. Danzo himself was, not taking his implants.
They being Councilors doesn't make them inoperable in field, actually. By their old age, maybe. But in their younger years, not probably. You see, by the series standards shinobi at their 50ies are still in "action". Orochi, Tsuna, Jiraiya are Databook recordists, stronger even than Kakashi at his 30ies, at least in their "total". Also, in the series, shinobi starts getting crampled in their physical stats at 65+. Like Chiyo and Hiruzen. Yet, both of them remained very skilled technicaly.
In my view, at their prime, Homura and Koharu must have been Top-level Jonin from Konohagakure, while Danzo and Hiruzen were Kage-material - actually Hiruzen had unprecedent talent and is a powerhouse shinobi even today. Also, they were elected by the Second Hokage to partake in his Escort Unite, said to be comprised only by Elite Ninja. Also, at the Nine-Tails attack, they were combat ready in the frontlines along Hiruzen and survived the ordeal, while many younger Jonin died at the claws of the fox.
Kagami Uchiha, said to be an exceptionally strong shinobi from the Uchiha clan died in the First Shinobi World War, with 25 years... not long after the mission we saw in Danzo's flashback.

Welcome to Anime & Manga! While this is an interesting perspective, we prefer answers to cite sources to back-up the information rather than subjection opinions


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What book is Akihito reading in episode 5 of Kyoukai no Kanata?
In episode 5 of Kyoukai no Kanata, Akihito is reading a book while he skips school:

What is this book?

Though it's a little bit difficult to read since his fingers are covering the spine, this book looks like Two Billion Light-Years of Solitude (or 二十億光年の孤独), by Shuntarou TANIKAWA.

Two Billion Light-Years of Solitude is a collection of poetry - in fact, Tanikawa's first publication, published in 1952.


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How does Zoro speak with a sword in his mouth?
When using Santoryu (Three Swords style), Zoro holds a sword in his mouth. How is he able to speak normally, without the sword falling?

anything can be achieved through practise :P

Have you never see a ventriloquist? It's not the official answer but it is totally consistant.

The official explanation given by the author, Oda Eiichiro, in his SBS1 column, is that it is Zoro's heart speaking. This may not sound any more convincing than Artistic License, but One Piece regularly relies on such unusual logic, so it is not entirely out of place.

1 SBS (Shitsumon wo Boshū Suru, roughly meaning "I'm Taking Questions") is a Q&A column in which Eiichiro Oda answers questions sent in by his fans.

I guess yes, it can be done. You know the words won't behaving so much clarity but yes, if you hold the sword hilt with your teeth, you are able to speak out.

I hate how people always ask this question...
Okay, put a pen in your mouth, try speaking
You will be able to speak, despite the pen being in your mouth. Sure, your voice sounds muffled, but Zoro's voice is also muffled when he speaks with a sword in his mouth
You don't need to move your teeth in order to talk, just your tongue, which I'm pretty sure isn't wrapped around Zoro's sword.
I hope I answered your question.

You know those techinique things? Zoro's "three sword style" technique require him to have a third sword, enableing him to perform that technique

The question is how can he speak with a sword in his mouth. Your answer does not seem to answer this question.


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What is Hiro'omi reading at the beginning of episode 6 of Kyoukai no Kanata?
Around the 03:00-mark of episode 6 of Kyoukai no Kanata, Hiro'omi is shown reading a book:

What book is this?

A brief search into some of the text displayed in the screenshot reveals that this page contains part of the text of "Eiketsu no Asa" (永訣の朝; roughly "The Morning of a Final Farewell"; text; a reading), a poem by Kenji MIYAZAWA1. "Eiketsu no Asa" is part of his first published collection, Haru to Shura (春と修羅; Spring and Asura).
In what may prove to be a bit of foreshadowing, "Eiketsu no Asa" was written on the occasion of the untimely death of Kenji's younger sister, Toshi.

1 Miyazawa may be better-known to Western audiences for his novel Night on the Galactic Railroad, which was made into an anime film back in 1985.


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What happened to Bon Clay after the Impel Down arc?
SPOILER ALERT: Contains spoilers for those who have not read or watched the end of Impel Down arc.
In the anime episode 451, Bon Clay disguises himself as Magellan to help Luffy and the prisoners escape on the Marine ship. Magellan gets very angry when he finds out, and attacks Bon Clay.

The episode ends after a few seconds, and the subsequent episodes do not show what happened next. Does it imply that Bon Clay was killed offscreen, or is this left as a suspense?

Bon Clay did not get killed. He somehow survived the fight against Magellan, and escaped to the Level 5.5 (Newkamaland), where he has become the new "Queen". Many of the Newkama prisoners who escaped during the Impel Down arc have reoccupied it.
The canonical evidence is on the cover page of Chapter 666. It is not yet known how Bon Clay escaped from Magellan, or how and why the Newkama prisoners returned to Impel Down.

You should at least wait for someone to answer. LOL

@NixR.Eyes I wanted to share this information with the community. Since SE works only in Q&A mode (there's no "blog" option), I had to post it in a "Answer Your Own Question" format.

@Happy No, I dont mean it that way. It just happens that I love Bon Clay's role in the Impel Down Arc. And it saddened me too that he has to sacrifice himself at the end, then glad to find out that he is alive. =)

@NixR.Eyes Yeah, I love him too. For me, Bon Clay (not Luffy) was the real hero of the Impel Down arc. Don't think Luffy would complain. ;) Many of my friends who only watch anime were depressed that he died, so I thought I should share this to spread some happiness. :)

Wow, even i had no clue about it!
But is he so strong that he could actually survive Magellan!!?

@MärmîkŠhâh May not be strong enough to defeat Magellan, but he is a master of disguise. He might have deceived Magellan again to escape.

Ya, man i would love to see him back in the anime!!

It's just a speculation, but as we know Magellan was defeated by the Blackbeard pirates. With a lucky timing that could be the cause why he survived. But as I said, this is just a speculation.


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Why Ash does not grow up?
In all the series only the dress is changed.
Ash doesn't grow up or does his maturity changes.
What is the reason?

Probably because it would drastically change the demographic of the show. In Digimon, they introduced new kids and aged out the old ones, whereas Pokemon thought keeping the original character was probably a better idea.


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What does "Fullmetal" mean?
The title is obviously the State Alchemist name of Edward Elric, but what does the word "Fullmetal" mean? I watched both series with dub in my mother language, and in that, Ed was referred as "Steel Alchemist". (translated to English)

"Steel Alchemist" is in fact the literal translation of Edward Elric's title. The term "Fullmetal" is most likely a reference to Stanley Kubrick classic war-is-hell film Full Metal Jacket.
The "jacket" of a full metal jacketed bullet is usually made of steel. Sometimes you hear these bullets called steel jacketed in English, and in many other languages, a translation of this second name is much more common. In many countries outside the US, FMJ was retitled to reflect the most common local name for the bullets, in order to preserve that reference. I don't know if Japan did this: IMDB doesn't list the Japanese title for some reason.
But if Japan did retitle the movie, then the title "Steel Alchemist" may have been intended all along to reflect the title of the "Steel Jacketed" movie. Many translations of FMA actually do use a title that reflects the way FMJ was titled in the translation's own language, and so it's possible that "Fullmetal Alchemist" is just another application of that practice.

A quick Wikipedia check shows that Japan didn't retitle the movie (and that even when referencing actual bullets, "full metal jacket" is loan word/phrase).


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Why do Killua's and Gon's skin tones change in episode 45 and 46 Huncyclopedia?
At the end of the 2011 Hunter × Hunter (episodes 27 through 58), there is a little short "Huncyclopedia", which is Gon and Killua talking about some character or element in the series.
From episodes 37 through 44, the two have a "Whale Island" theme, which shows them in shorts and out in the wild rather than in a classroom. However, in the two episodes following this, their skin tone is significantly darker. Oddly enough, they are still in their original tones for the intro, as well as when they make animal faces at the end of episode 46.

Is this supposed to be a tan, or is there some other reason for this change?

They probably got tan from being outside for so long. The ones in the intro a probably static cardboard stand-ins. Also Whale Island is probably Gon's backyard. Note sure about why they changed back to their original colors to do the cat nd dog faces. Maybe since it's all non-canon they were just like: poof and we're back.

What @Krazer said is pretty much the answer. Such "interesting" logic is often seen in omake sections, which are meant to be lighthearted anyway.

As you guessed this really is only supposed to be a tan. Quite a strong one, but still just a tan.

The last one or two Hunterpedias before their skin changed were done outside, so they got sunburned. There is no official answer, but it was speculated by the community as an animation error.


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Are there any slugs besides Katsuyu in the Naruto universe?
The Legendary sannin Jiraiya, Orochimaru, and Tsunade have summoning contracts with toads, snakes and slugs respectively. While Jiraiya and Orochimaru summon different toads and snakes on different occasions, Katsuyu is the only slug that Tsunade has summoned.
Later, their students, Naruto, Sasuke, and Sakura gain their summoning techniques. Naruto and Sasuke summon different toads and snakes. However, when Sakura summons a slug in Chapter 634, it is Katsuyu again.
Are there any slugs besides Katsuyu in the Naruto universe?

As of Chapter 655, Katsuyu is the only slug to have been seen summoned using Kuchiyose no Jutsu, by Tsunade and Sakura.1 The only other character known that could count as a slug is Saiken, also known as Rokubi (Six Tails).

Kishimoto has also drawn three other slugs on the cover pages of Chapter 4, Chapter 153, and Chapter 162.

1 While we have seen toads at Myoboku Mountain, and the White Snake Sage at Ryuchi Cave, the Shikkotsu Forest where slugs reside has not been shown yet.


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Is there an official statement about Detective Conan's ending?
Currently, Detective Conan series is now on it's 721 (source) and probably still counting. Is there any statement from the production if they have any plans on having this anime series end? If there is, what is their plan on doing so? Will Conan be able to revert back to Shinichi and have the Black Organization behind bars or something like that? Or do they want this to be open-ended?

Nothing has been put about about this lately. All your questions can probably be answered by the mangaka himself. As far as anime is concerned, its going pretty well so i don't think they'll stop it. The manga is about a 100 chapters ahead of episode 721!!
So its kind of difficult to tell.

neither the anime nor manga seems like it's headed towards a conclusion any time soon...

There hasn't been any official announcement related to the end of the manga or the anime, but here's an interview with Aoyama Gosho which took place in 2011.

I really didn't expect it to last this long. I thought it might end after the first volume. Also, about the name "Conan," initially the editor-in-chief told me to change it to Detective Doyle because there was already an anime called Conan, The Boy in Future (directed by Miyazaki Hayao), but I said “I'd overtake The Boy in Future!” and it finally got through. But the new serialization's announcement said Tantei Shonen Conan/Detective Boy Conan, and I thought no way, this is pretty bad (laughs). However, about 10 years ago, someone from Ghibli* said to me, “when you talk about Conan now you'd be referring to the detective,” and I thought “Yes, I did it!”

This should clear most of your questions.

This doesn't seem to answer any of my questions though.


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What does being a saint mean?
In Toaru Majutsu no Index, there are currently about 20 saints

 as of before the Acqua of the Back-Arc.

So far I've read until the arc named in the spoiler and I'm wondering, how you become a saint and what makes a saint?

 Kanzaki mentions that she was born with that ability, so it's most likely that it's a trait that one has all his life. But it seemed to me, that Acqua of the Back wasn't a saint back when he worked for England; Is this wrong or did he become a saint when he became a part of Gods right Seat?
 It also seems, that a life of a saint doesn't depend on being a saint, because Acqua comes back later.

Are saints just extremely powerful? Or do they have another special trait?

Kaori Kanzaki is so powerful she can survive (and fight) in the vacuum of space AND survive reentry. All in ripped jeans and a t-shirt.


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What is the complete form of Izanagi?
In Chapter 510, while Tobi explains the Izanagi to Konan, he remarks about those who could use an "incomplete form" of Izanagi, referring to Danzo, and implying that he (or someone else) could use a "complete form" of Izanagi. What is this complete form of Izanagi?

Good question.=)

It doesn't seem like Obito has much a future left, so let's get cracking.
Tobi uses Izanagi against Konan (Page 10)
Tobi's Izanagi lasted for 10 minutes (Page 3)
Tobi was definitely referring to himself using the complete form of Izanagi. Recall that Danzou had 10 eyes and each eye had a 1 minute duration of Izanagi. Tobi is able to use at least 10 minutes worth for an eye sacrifice.
We also know that with each eye Danzou used, his chakra dropped significantly according to Karin. His huge chakra loss is due to the fact that he is not an Uchiha. While this was not  specifically stated in chapters 510 or 479, we know that a non-Uchiha using Sharingan consumes a lot of chakra (ie Kakashi).
Now Tobi stated that Danzou didn't have full control over Hashirama's powers (Page 12), so this is why his Izanagi had a time restriction (of 1 minute). Tobi goes on to explain how Orochimaru realized this as well, thus implanting 10 eyes to lengthen the duration of Izanagi for Danzou.
The complete form of Izanagi requires full control over both the Uchiha DNA (Sharingan) and the Senju DNA (Hashirama cells). With this, one can use Izanagi without a timelimit per se, but rather a chakra limit. Tobi needs to use chakra to use Izanagi, so the duration of the doujutsu is directly proportional to the amount of chakra that he uses. Once Tobi runs out of chakra, he can no longer use Izanagi.

Of course, people can argue that Tobi's Izanagi might have a defined time limit. We will never know. However, given that Tobi stated his Izanagi was a completed form and proving that his Izanagi can last at least 10 minutes, it is safe to assume that his Izanagi wasn't based on time. If you master a jutsu, the duration of your jutsu should only have a chakra constraint and not a time constraint.


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Aren't players required to choose a subclass?
Most of the characters (at least up to episode 5, since I haven't gone any further) seem to have both class and subclass:

Akatsuki: Class - Assassin; Subclass - Tracker
Shiroe: Class - Enchanter; Subclass - Scribe
Nyanta: Class - Swashbuckler; Subclass - Chef
Serara: Class - Druid; Subclass - Maid

However, Naotsugu (whose Class is Guardian) appears to not have a Subclass.
From the Classes and the Subclasses page on Log Horizon Wiki, one can tell that once a player starts playing Elder Tale he has to choose a Class, which cannot be changed again. However, one also gathers that Subclasses, on the other hand, are changeable, but the site says nothing about whether or not a player is required to have one.
Does this mean that Subclasses are not required?
Or was Naotsugu's class just not yet revealed/unknown?

Naotsugu's subclass is 辺境巡視 (Border Patrol/Frontier Guard).

Is that revealed later on the Anime? Or on the Novel or Manga?

It is mentioned in the web novel at least.

The wiki page you referenced for Naotsugu has been updated saying that he has the Border Patrol Subclass.
On a side note if Elder Tale is anything like most MMORPGs a subclass is not chosen until you have gained a couple levels and there is no advantage for not having one. So it would make sense that most players would pick a subclass to start leveling it right away.


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Why are the ship names suffixed with "Go"?
The names of all the ships in One Piece are suffixed with Go in Japanese. For example, Going Merry Go, Thousand Sunny Go, Moby Dick Go. However, the English version drops the Go suffix. This suggested it might be a honorific used to address a ship, but I couldn't find any source that says "Go" is a honorific.
There's also no mention of Go on the Japanese ship-naming conventions page on Wikipedia, and I couldn't find anything like this in any other place either.
I don't recall this being explained in the manga. Is there any explanation for this use of "Go", with a reliable source for reference?

The character used for it is 号, is a counting marker. I don't know what that indicates, but it might help. It's also not used for all of the ships. The government ships, at least, don't seem to use that (though I could be wrong).

@kuwaly Well, yeah, but from what I seem to recall, the Marine ships don't have a name per se. They are just called Marine ships, or named after the Captain, such as Vice Admiral Garp's ship.

Probably they mean "go" in english and not in japanese! :P

号 or the -go suffix is normally used to name naval (aka war) ships in Japan. If you want get the equivalent in English, is the same as S.S. Name of the Ship used by the US. One Piece is just following the same naming convencion.

Do you have some kind of reference, or is it some "general knowledge" thing that a Japanese just happens to know? I have also read about this in some forums, but couldn't find any reliable source.

@MaskedMan very late response, but Japanese Wikipedia for 号 mentioned "鉄道・バス・船舶などの乗り物の愛称につける接尾辞" (A suffix for vehicle's nickname; trains, buses, ships, etc)


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Why wasn't Naruto able to sense Black Zetsu?
If Black Zetsu was commanded to be with  Obito while Madara was fighting the 5 kages,
How come, Naruto was not able to sense Black Zetsu in his Kyuubi mode while fighting with Obito??

it's never stated, that naruto didn't sense BZ. your assumptions are wrong. also most of this "i sense evil" is actually anime filler, meaning non-canonical. there is bound to be a loophole ;)

I think Naruto's ability to sense evil is not a filler only since it plays a big part during the war to battle White Zetsu's.

right. and after that it is never even mentioned again.... certainly not filler.. the writers just needed something to get the white Zetsus off the board, and some new special power for naruto was just the right thing for that. still it's never stated naruto didn't sense BZ

Naruto's ability to sense evil is NOT a filler, because Naruto sensed kisame using his evil sensing powers and also during the war the alliance relied on his evil sensing powers heavily. One reason why Naruto did not (rather than could not) sense BZ is beacause he was more worried about fighiting Obito who himself was a "big" evil to worry about. Remember Naruto doesn't think with his brains.. and isn't the best analyser.. :P

Or, the BZ simply did not have any evil intentions at that time. All he was supposed to do was, have an eye on Obito. Why should the BZ even think of going into the offensive mode as Obito was okay by himself till then? Also, I really doubt if there can be a definitive answer for this, as nothing has been spoken about this in the Manga, as of now.

One might be able to look at it from the philosophical point of view that there was no evil to sense.
The rest of this answer may include spoilers

 Black Zetsu is essentially Kaguya's will incarnate. That being said, Kaguya's goals were not inherently evil. Technically, her goal was peace. While it may have been a peace forced upon the entire world, in a manner they did not agree with, in her mind, it was still an act of good. It's true that she did want the power of her chakra back from all those it had been sewn into throughout the centuries. Even still, it is difficult for mere mortals to understand what drives a being that could be consider god-like. Good and Evil being matters of perception, maybe Kaguya truly believed in the good of her actions. Of course, this is all speculation, but one has to wonder, I mean when Kaguya initially thought that Naruto and Sasuke were Hagoromo and Hamura, she wept, so she can't be all bad.

 All that considered, and Black Zetsu being an extension of Kaguya himself, maybe the whole "sensing evil" didn't work because there was no evil intent. But this all hinges on the philosophy of good and evil, and deciding if there is a difference between knowing something is evil and not caring, or not believing something is evil because of the eventual good, it will do.

I think Naruto could sense BZ evil intent, but maybe not his physical body because the Zetsu army and BZ are as close to nature as beings can be. White Zetsu was able to sneak into the Kage summit ffs, even with the Raikage's senser-nin (C) with him. The Zetsu's are all made from the Juubi/Tree, the origins of chakra so I'm assuming they'd be overlooked even if Naruto was in Sage mode because they're purely artificial/organic humanoids.

As we now know Black Zetsu had the will of Kaguya in him. Just as Naruto wasn't able to sense the Ten Tails (episode 363 of the anime) , Kaguya's powers are even greater than the Ten Tails - she stopped the Infinite Tsukuyomi easily. So sensing Kaguya (or Black Zetsu) is out of the question.

I'm not sure that's true. Naruto couldn't sense the Juubi with Kurama's chakra because in that mode he can sense negative emotions (hate, sadness, anger), and the Juubi doesn't have emotions. Black Zetsu and Kaguya are not the same as that.


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Why doesn't Gai use ninjutsu or genjutsu more often?
According to the wiki, Gai is able to use ninjutsu and genjutsu, so why doesn't he use it?

I think it's because he wants to support Lee!

That would be my guess too. But he doesn't use them even when Lee isn't around.

I'd say because they aren't his strengths - clearly Taijutsu is so why should he use something that he isn't great at?
It could also be that he has used them in the past and it, unfortunately, got him into some difficulty so he had to fall back on the tried and tested techniques of his Taijutsu :)

Gai is based off of Bruce Lee, and Bruce Lee was known for his extraordinary fighting skills (taijutsu in this case). Furthermore, Gai is known as the best taijutsu shinobi in Konoha.
Thus, it would only make sense to accentuate Gai's physical prowess and focus less on genjutsu / ninjutsu.


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How do UQ Holder! and Mahou Sensei Negima! relate?
I've been reading UQ Holder! since it started coming out. So far (14 chapters into the series) I've understood everything, and (I think) I have not missed any reference or anything similar.
However, just today I realised that MAL lists UQ Holder! as Mahou Sensei Negima!'s sequel.
How exactly are the two related, and how much do I miss if I haven't read the latter?
Or is it just meant to be a spiritual sequel, and nothing in the story is related?

I think 10 years is how long COMMERCIAL magic is around in UQ Holder's world. Conventional magic (without apps) is shown to be around much longer.

the mc is negi's grandson, and he is trying to save negi while getting stonger with some of the old crew like fate.

My post primarily answers the titled question such that the answer works for people that have read and have not read Mahou Sensei Negima (MSN).
Part 1 (For people who have read MSN. If you have not read MSN, skip to part 2)
Remember Eva from MSN? She is the same person as Yukihime-sensei. Over the years, Eva figured out a way to change her appearance so she could live life more normally - as an adult.
Basically, everyone from MSN presumably died (since ~100 years have passed) except for Eva since she is an immortal vampire.
Chapter 1:

Page 1 - Eva gives her introduction
Page 2 - She shows how the people from MSN are gone now
Page 5 - Shows her current UQ team
Page 70 - Eva reveals her true identity to Touta

Chapter 2:

Page 16 - Eva reverts back to her 10 year old true form. She stays this way until page 38, where she returns back to her older fabricated form.

Part 2
Both UQ and MSN are related through Eva, although MSN followed Negi's journey (main character of MSN). UQ's story is being told by Eva, who is reflecting on the past. Eva plays an important character in both series, as her role is to train the main characters, Negi and Touta.
Also note that Touta Konoe is Negi Springfield's grandson (Ch 1 Pg 18). Given that his surname is Konoe, we can also assume he is related to Konoka Konoe from MSN as well.
While UQ Holder is the sequel to MSN, there is nothing critical that you have missed. In other words, you can read and understand UQ Holder perfectly fine without reading its prequel. There are the occasional references to MSN though, but they do not affect the plot in any way.
A good analogy for this would be the difference between Dragon Ball and Dragon Ball Z. You can pick up Dragon Ball Z and fully understand everything without watching Dragon Ball. And in this case, UQ Holder and MSN have a time skip of 3 generations later, so every character except Yukihime is presumed dead now.

Having been horribly disappointed by Negima's so-called ending, I am thrilled that there is a sequel of sorts. Sad it isn't specifically designed to do the original proper justice. And both that ending and your synopsis makes me wonder: how does Negi even die? He had the same immortality as Eva, yet he gets killed off like any mortal! I hope I find satisfaction in this story...

@zibadawatimmy maybe you are jumping the gun. I would suggest reading UQ Holder further.... (trying to spoil the minimum possible).

There is another more more more obvious link:
Chapter 1 pg 19: Touta Konoe, the main hero, is the grand-son of Negi Springfield, somehow related to Konoka Konoe (his surname is Konoe).

The good thing about UQ Holder is that even if you didn't read MSN, you will still understand the story.  Yes there are some MSN references which UQ Holder dialogues explain thoroughly especially Negi's "Thunder in Heaven, Great Vigor" was explained in the latter chapters.
As for the other characters, some are not yet dead since not all of them are human like Mana, Eva, and Fate.  There are also characters claiming to know and met Negi such as the Demon with many arms (i forgot the name) Touta fought in the Mahora Martial Arts Tournament, Shion Nagumo a blind swordsman that stated Negi's superhuman magic Magia Erebea fighting the demons of the Lifemaker, and Ruin Ishkur.
Basically, go read UQ Holder and you'll still understand everything but it is an advantage if you have a bit background (most especially on the characterns) in MSN.

First not all of the characters are dead and like said above they relate through Eva(who is Yuki). Personally I would read negima because characters from it reaqure in UQ Holder. Plus you need to know most of the background in the manga to experience a more exciting storyline. Especially when previous characters return in this manga.


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How does immortality work?
Can someone explain to me how immortality works in UQ Holder? Specifically about how each type of immortality works and what is required to kill that type?

Chapter 6 explains the types of immortality that exist, but says nothing about what it takes to kill each type. See pages 14, 15, 16 and 17.