Spanish conquest of Peru

Beginning of the conflict

The civil war between Atahualpa and Huascar weakened the empire immediately prior to its struggle with the Spanish. Historians are unsure of whether a united Inca Empire could have defeated the Spanish in the long term due to factors such as the high mortality from disease and its related social disruption, and the superior military technology of the conquistadors, who possessed horses, dogs, metal armor, swords, cannons, and primitive, but effective, firearms. Atahualpa appeared to be more popular with the people than his brother, and he was certainly more valued by the army, the core of which was based in the recently conquered northern province of Quitu.
At the outset of the conflict, each brother controlled his respective domains, with Atahualpa secure in the north, and Huáscar controlling the capital of Cuzco and the large territory to the south, including the area around Lake Titicaca. This region had supplied large numbers of troops for Huáscar's forces. After a period of diplomatic posturing and jockeying for position, open warfare broke out. Huáscar seemed poised to bring the war to a rapid conclusion, as troops loyal to him took Atahualpa prisoner, while he was attending a festival in the city of Tumibamba. However, Atahualpa quickly escaped and returned to Quitu. There, he was able to amass what is estimated to be at least 30,000 soldiers. While Huáscar managed to muster about the same number of soldiers, they were less experienced.
Atahualpa sent his forces south under the command of two of his leading generals, Challcuchima and Quisquis, who won an uninterrupted series of victories that soon brought them to the very gates of Cuzco. On the first day of the battle for Cuzco, the forces loyal to Huáscar gained an early advantage. However, on the second day, Huáscar personally led an ill-advised "surprise" attack, of which the generals Challcuchima and Quisquis had advance knowledge. In the ensuing battle, Huáscar was captured, and resistance completely collapsed. The victorious generals sent word north by chasqui messenger to Atahualpa, who had moved south from Quitu to the royal resort springs outside Cajamarca. The messenger arrived with news of the final victory on the same day that Pizarro and his small band of adventurers, together with some indigenous allies, descended from the Andes into the town of Cajamarca.

Capture of Atahualpa

After his victory and the death of his brother Huáscar, Atahualpa was fasting in the Inca baths outside Cajamarca. Pizarro and his men reached that city on 15 November 1532.
Pizarro sent Hernando de Soto and Hernando Pizarro to the Inca leader's camp. Hernando Pizarro and De Soto explained they were emissaries of Emperor Charles I of Spain, to offer their services, and "impart to him the doctrines of the true faith."  Additionally, they invited the Incan leader to visit Pizarro at his quarters along the Cajamarca plaza. Atahualpa replied that his fast would end the next day, when he would visit Pizarro. When De Soto noticed Atahualpa's interest in his horse, he put on a display of "excellent horsemanship" in close proximity. Atahualpa displayed hospitality by serving refreshments.
The next morning, Pizarro had arranged an ambuscade around the Cajamarca plaza, where they were to meet. When Atahualpa arrived with about 6,000 unarmed followers, Friar Vincente de Valverde and Felipillo met them and proceeded to "expound the doctrines of the true faith" and seek his tribute as a vassal of King Charles.  The unskilled translator likely contributed to problems in communication. The friar offered Atahualpa the Bible as the authority of what he had just stated. Atahualpa stated, "I will be no man's tributary."
The friar urged attack, starting the Battle of Cajamarca on 16 November 1532. Though the historical accounts relating to these circumstances vary, the true Spanish motives for the attack seemed to be a desire for loot and flat-out impatience. The Inca likely did not adequately understand the conquistadors' demands.
At the signal to attack, the Spaniards unleashed volleys of gunfire at the vulnerable mass of Incas and surged forward in a concerted action. The effect was devastating, the shocked Incas offered such feeble resistance that the battle has often been labeled a massacre, with the Inca losing 2,000 dead. Pizarro also used cavalry charges against the Inca forces, which stunned them in combination with gunfire.
The majority of Atahualpa's troops were in the Cuzco region along with Quisquis and Challcuchima, the two generals he trusted the most. This was a major disadvantage for the Inca. Their undoing also resulted from a lack of self-confidence, and a desire to make public demonstration of fearlessness and godlike command of situation. The main view is that the Inca were eventually defeated due to inferior weapons, 'open battle' tactics, disease, internal unrest, the bold tactics of the Spanish, and the capture of their emperor. While Spanish armour was very effective against most of the Andean weapons, it was not impenetrable to maces, clubs, or slings. However, ensuing hostilities such as the Mixtón Rebellion, Chichimeca War, and Arauco War would require that the conquistadors ally with friendly tribes in these later expeditions.
The battle began with a shot from a cannon and the battle cry "Santiago!" Many of the guns used by the Spaniards were hard to use in the frequent close-combat situations. Most natives adapted in 'guerrilla fashion' by only shooting at the legs of the conquistadors if they happened to be unarmored.
During Atahualpa's captivity, the Spanish, although greatly outnumbered, forced him to order his generals to back down by threatening to kill him if he did not. According to the Spanish envoy's demands, Atahualpa offered to fill a large room with gold and promised the Spanish twice that amount in silver. While Pizarro ostensibly accepted this offer and allowed the gold to pile up, he had no intention of releasing the Inca; he needed Atahualpa's influence over his generals and the people in order to maintain the peace.
When Atahualpa was captured at the massacre at Cajamarca, he was treated with respect, allowed his wives to join him, and the Spanish soldiers taught him the game of chess. 
Francisco Pizarro sent his brother Hernando to gather gold and silver from the temples in Pachacamac in January 1533, and on his return in March, captured Chalcuchimac in the Jauja Valley.  Francisco Pizzaro sent a similar expedition to Cuzco, bringing back many gold plates from the Temple of the Sun.  By February 1533, Almagro had joined Pizarro in Cajamarca with an additional 150 men with 50 horses.
Pizarro held Atahualpa for a ransom of gold and silver; the treasure began to be delivered from Cuzco on 20 December 1532 and flowed steadily from then on. By 3 May 1533 Pizarro received all the treasure he had requested; it was melted, refined, and made into bars.
The question eventually came up of what to do with Atahualpa; both Pizarro and Soto were against killing him, but the other Spaniards were loud in their demands for death. False interpretations from the interpreter Felipillo made the Spaniards paranoid. They were told that Atahualpa had ordered secret attacks and his warriors were hidden in the surrounding area. Soto went with a small army to look for the hidden army, but a trial for Atahualpa was held in his absence. Among the charges were polygamy, incestuous marriage, and idolatry, all frowned upon in Catholicism but common in Inca culture and religion.
The men who were against Atahualpa's conviction and murder argued that he should be judged by King Charles since he was the sovereign prince. Atahualpa agreed to accept baptism to avoid being burned at the stake and in the hopes of one day rejoining his army and killing the Spanish; he was baptized as Francisco. On 29 August 1533 Atahualpa was garrotted and died a Christian. He was buried with Christian rites in the church of San Francisco at Cajamarca, but was soon disinterred. His body was taken, probably at his prior request, to its final resting place in Quito. Upon de Soto's return, he was furious; he had found no evidence of any secret gathering of Atahualpa's warriors.
Pizarro advanced with his army of 500 Spaniards toward Cuzco, accompanied by Chalcuchimac. The latter was burned alive in the Jauja Valley, accused of secret communication with Quizquiz, and organizing resistance. Manco Inca Yupanqui joined Pizarro after the death of Túpac Huallpa.  Pizarro's force entered the heart of the Tawantinsuyu on 15 November 1533.
Benalcázar, Pizarro's lieutenant and fellow Extremaduran, had already departed from San Miguel with 140-foot soldiers and a few horses on his conquering mission to Ecuador. At the foot of Mount Chimborazo, near the modern city of Riobamba (Ecuador) he met and defeated the forces of the great Inca warrior Rumiñawi with the aid of Cañari tribesmen who served as guides and allies to the conquering Spaniards. Rumiñahui fell back to Quito, and, while in pursuit of the Inca army, Benalcázar was joined by five hundred men led by Guatemalan Governor Pedro de Alvarado. Greedy for gold, Alvarado had set sail for the south without the crown's authorization, landed on the Ecuadorian coast, and marched inland to the Sierra. Finding Quito empty of its treasures, Alvarado soon joined the combined Spanish force.  Alvarado agreed to sell his fleet of twelve ships, his forces, plus arms and ammunition, and returned to Guatemala.

Rebellion and reconquest

After Atahualpa's execution, Pizarro installed Atahualpa's brother, Túpac Huallpa, as a puppet Inca ruler, but he soon died unexpectedly, leaving Manco Inca Yupanqui in power. He began his rule as an ally of the Spanish and was respected in the southern regions of the empire, but there was still much unrest in the north near Quito where Atahualpa's generals were amassing troops. Atahualpa's death meant that there was no hostage left to deter these northern armies from attacking the invaders. Led by Atahualpa's generals Rumiñahui, Zope-Zupahua and Quisquis, the native armies were finally defeated, effectively ending any organized rebellion in the north of the empire.
Manco Inca initially had good relations with Francisco Pizarro and several other Spanish conquistadors. However, in 1535 he was left in Cuzco under the control of Pizarro's brothers, Juan and Gonzalo, who so mistreated Manco Inca that he ultimately rebelled. Under the pretense of recovering a statue of pure gold in the nearby Yucay valley, Manco was able to escape Cuzco.
Manco Inca hoped to use the disagreement between Almagro and Pizarro to his advantage and attempted the recapture of Cuzco starting in April 1536. The siege of Cuzco was waged until the following spring, and during that time Manco's armies managed to wipe out four relief columns sent from Lima, but was ultimately unsuccessful in its goal of routing the Spaniards from the city. The Inca leadership did not have the full support of all its subject peoples and furthermore, the degrading state of Inca morale coupled with the superior Spanish siege weapons soon made Manco Inca realize his hope of recapturing Cuzco was failing. Manco Inca eventually withdrew to Tambo.
Archaeological evidence of the rebellion incident exists. The remains of about 70 men, women, and adolescents were found in the path of a planned expressway near Lima in 2007. Forensic evidence suggests that the natives were killed by European weapons, probably during the uprising in 1536.
After the Spanish regained control of Cuzco, Manco Inca and his armies retreated to the fortress at Ollantaytambo where he, for a time, successfully launched attacks against Pizarro based at Cuzco and even managed to defeat the Spanish in an open battle.
When it became clear that defeat was imminent, Manco Inca retreated further to the mountainous region of Vilcabamba and established the small Neo-Inca State, where Manco Inca and his successors continued to hold some power for several more decades. His son, Túpac Amaru, was the last Inca. After deadly confrontations, he was murdered by the Spanish in 1572.
In total, the conquest took about forty years to complete. Many Inca attempts to regain the empire had occurred, but none had been successful. Thus the Spanish conquest was achieved through relentless force, and deception, aided by factors like smallpox and a great communication and cultural divide. The Spaniards destroyed much of the Incan culture and introduced the Spanish culture to the native population.

Aftermath

A struggle for power resulted in a long civil war between Francisco Pizarro and Diego de Almagro in which Almagro was killed. Almagro's loyal followers and his descendants later avenged his death by killing Pizarro in 1541.  This was done inside the palace of Francisco Pizarro in a fight to the death by these assassins, most of which were former soldiers of Diego de Almagro who were stripped of title and belongings after his death.
Despite the war, the Spaniards did not neglect the colonizing process. Spanish royal authority on these territories was consolidated by the creation of an Audiencia Real, a type of appellate court. In January 1535, Lima was founded, from which the political and administrative institutions were to be organized. In 1542, the Spanish created the Viceroyalty of New Castile, that shortly after would be called Viceroyalty of Peru. Nevertheless, the Viceroyalty of Peru was not organized until the arrival of a later Viceroy Francisco de Toledo in 1572. Toledo ended the indigenous Neo-Inca State in Vilcabamba, executing the Inca Túpac Amaru. He promoted economic development using commercial monopoly and built up the extraction from the silver mines of Potosí, using slavery based on the Inca institution of forced labor for mandatory public service called mita.
The integration of Spanish culture into Peru was carried out not only by Pizarro and his other captains, but also by the many Spanish who also came to Peru to exploit its riches and inhabit its land.  These included many different kinds of immigrants such as Spanish merchants, peasants, artisans, and Spanish women. Another element that the Spanish brought with them were African slaves to work alongside captive Incas for use in labor with things such as agriculture and mining for silver. These people all brought with them their own pieces of Spanish culture to integrate into Peruvian society.
The arrival of the Spanish also had an unexpected impact on the land itself, recent research points out that Spanish conquest of the Inca altered Peru’s shoreline. Before the Spaniards arrived, inhabitants of the arid northern Peruvian coast clad massive sand dune–like ridges with a -likely- accidental form of “armor”, millions of discarded mollusk shells, which protected the ridges from erosion for nearly 4700 years prior to the Spanish arrival, and produced a vast corrugated landscape that is visible from space. This incidental landscape protection came to a swift end, however, after diseases brought by Spanish colonists decimated the local population and after colonial officials resettled the survivors inland, without humans to create the protective covering, newly formed beach ridges simply eroded and vanished. According to Archaeologist Torben Rick, parts of the northern coast of Peru may look completely natural and pristine, “but if you rewind the clock a couple of millennia, you see that people were actively shaping this land by creating beach ridge systems".
Almost nothing was left of the Inca civilizations after the conquest by the Spanish, as culture was not as significant as gold to the new conquerors.  The unique indigenous road and communications systems were essentially lost.  The only things that persisted of the original culture are the very few artifacts that remained and the minute cultural aspects, such as language, that was left behind by the small percentage of Incas who persisted. (survived)

Effects of the conquest on the Incan people

The long-term effects of the arrival of the Spanish on the population of South America were simply catastrophic. While this is the case for every group of Native-Americans that encountered Europeans from the fifteenth century onwards, the Incan population suffered a dramatic and quick decline following contact. It is estimated that parts of the empire, notably the Central Andes, suffered a population decline ratio of 58:1 during the years of 1520–1571.
The single greatest cause of the decimation of native populations was infectious disease. Old World Eurasian diseases, which had long been endemic on the Continent, were carried unknowingly by colonists and conquistadors. As these were new to the natives, they had no acquired immunity and suffered very high rates of death. More died of disease than any army or armed conflict. As the Inca did not have as strong a writing tradition as the Aztec or Maya, it is difficult for historians to estimate population decline or any events after conquest. But, it is apparent that the Inca began to contract the diseases several years before the Spanish appeared in the region, as it was likely carried to their empire by traders and travelers. The outbreak, believed to be hemorrhagic smallpox, reached the Andes in 1524. While numbers are unavailable, Spanish records indicate that the population was so devastated by disease that they could hardly resist the foreign forces.
Historians differ as to whether the illness of the 1520s was smallpox; a minority of scholars claim that the epidemic was due to an indigenous illness called Carrion's disease. In any case, a 1981 study by N. D. Cook the shows that the Andes suffered from three separate population declines during colonization. The first was of 30–50 percent during the first outbreak of smallpox. When a measles outbreak occurred, there was another decline of 25–30 percent. Finally, when smallpox and measles epidemics occurred together, which occurred from 1585 to 1591, a decline of 30–60 percent occurred. Collectively these declines amounted to a decline of 93 percent from the pre-contact population in the Andes region. Mortality was particularly high among children, ensuring that the impact of the epidemics would extend to the next generation.
Beyond the devastation of the local populations by disease, they suffered considerable enslavement, pillaging and destruction from warfare. The Spanish took thousands of women from the local natives to use as servants and concubines. As Pizarro and his men took over portions of South America, they plundered and enslaved countless people. Some local populations entered into vassalage willingly, to defeat the Inca. Native groups such as the Huanca, Cañari and Chachapoya fought alongside the Spanish as they opposed Inca rule. The basic policy of the Spanish towards local populations was that voluntary vassalage would yield safety and coexistence, while continued resistance would result in more deaths and destruction.
Another significant effect on the people in South America was the spread of Christianity. As Pizarro and the Spanish subdued the continent and brought it under their control, they forcefully converted many to Christianity, claiming to have educated them in the ways of the "one true religion." With the depopulation of the local populations along with the capitulation of the Inca Empire, the Spanish missionary work after colonization began was able to continue unimpeded. It took just a generation for the entire continent to be under Christian influence.

Quotes

I wish Your Majesty to understand the motive that moves me to make this statement is the peace of my conscience and because of the guilt I share. For we have destroyed by our evil behaviour such a government as was enjoyed by these natives. They were so free of crime and greed, both men and women, that they could leave gold or silver worth a hundred thousand pesos in their open house. So that when they discovered that we were thieves and men who sought to force their wives and daughters to commit sin with them, they despised us. But now things have come to such a pass in offence of God, owing to the bad example we have set them in all things, that these natives from doing no evil have turned into people who can do no good.. I beg God to pardon me, for I am moved to say this, seeing that I am the last to die of the Conquistadors."
— Mansio Serra Leguizamon
When has it ever happened, either in ancient or modern times, that such amazing exploits have been achieved? Over so many climes, across so many seas, over such distances by land, to subdue the unseen and unknown? Whose deeds can be compared with those of Spain? Not even the ancient Greeks and Romans.
— Francisco Xeres, Report on the Discovery of Peru
When I set out to write for the people of today and of the future, about the conquest and discovery that our Spaniards made here in Peru, I could not but reflect that I was dealing with the greatest matters one could possibly write about in all of creation as far as secular history goes. Where have men ever seen the things they have seen here? And to think that God should have permitted something so great to remain hidden from the world for so long in history, unknown to men, and then let it be found, discovered and won all in our own time!
— Pedro Cieza de León, Chronicles of Peru
The houses are more than two hundred paces in length, and very well built, being surrounded by strong walls, three times the height of a man. The roofs are covered with straw and wood, resting on the walls. The interiors are divided into eight rooms, much better built than any we had seen before. Their walls are of very well cut stones and each lodging is surrounded by its masonry wall with doorways, and has its fountain of water in an open court, conveyed from a distance by pipes, for the supply of the house. In front of the plaza, towards the open country, a stone fortress is connected with it by a staircase leading from the square to the fort. Towards the open country there is another small door, with a narrow staircase, all within the outer wall of the plaza. Above the town, on the mountain side, where the houses commence, there is another fort on a hill, the greater part of which is hewn out of the rock. This is larger than the other, and surrounded by three walls, rising spirally.
— Francisco Xeres, Massacre, Gold and Civil War