|- | align="center" | 24 | | align="center" | 2007-03-31 |- | colspan="5" | Crown Thunder takes an old pirate ship and prepares to launch it toward Echo Ridge, but Mega Man and Lyra Note battle together to try to stop the enemy. They discover that the pirate ship is the source of his power, and by attacking it, they're able to defeat him. Then, Luna is devastated when she assumes Mega Man and Lyra Note are involved romantically, causing her anger to show at school. Her friends take her to a Sonia Sky concert to cheer her up, but the FM-ian Ophiuchus targets Luna's devastation and offers her the power to capture Mega Man. (On Toonami Jetstream's website, this episode was listed as "Amusement Gone Awry") |- | colspan="5" bgcolor="#CCCCFF"| |- | align="center" | 25 | | align="center" | "Biggest Fan or Biggest Foe?" | align="center" | 2007-03-31 | align="center" | 2007-12-10 (TJ) |- | colspan="5" | Geo encounters Ophiuchus Queen, the fusion of Luna and Ophiuchus, who knocks him unconscious. This leaves Sonia to take care of the enemy, transforming into Lyra Note to battle. Mega Man later intervenes, and together, they knock Luna out of the fusion. Ophiuchus escapes. Afterwards, Geo recalls his encounters with the FM-ians from the previous 12 episodes, and he questions the connections between his father's disappearance and Omega-Xis's appearance on Earth. |- | colspan="5" bgcolor="#CCCCFF"| |- | align="center" | 26 | | align="center" | N/A | align="center" | 2007-04-07 | align="center" | - |- | colspan="5" | Tom returns to AMAKEN after weeks of absence, but he is completely under Cygnus's control now. He attempts to throw Aaron off a skyscraper, but Mega Man rescues him. After a heated battle with Cygnus Wing, Tom reveals to Geo that Omega-Xis was the one who killed Kelvin. The startling news causes Geo to collapse into a river where he is washed away. |- | colspan="5" bgcolor="#CCCCFF"| |- | align="center" | 27 | | align="center" | N/A | align="center" | 2007-04-14 | align="center" | - |- | colspan="5" | Tom gathers the FM-ians together and gives them the power to mimic their EM Wave Human forms without the aid of the humans they merged with. Meanwhile, Omega-Xis helps Aaron find Geo's body and he is rushed to a hospital. That night, Geo and Omega-Xis reunite for an emotional argument until Omega-Xis leaves Earth completely. |-