The X-Men and the Brotherhood rally after the mansion's destruction, and they try to find Xavier and the captured X-Men.
Cylops leads the X-Men in a search for the missing Xavier and Wolverine.
The mutants' existence is no longer a secret, so Xavier has the X-Men and the Brotherhood return to school, but Principal Kelly has a surprise plan for the mutant students.
The Brotherhood are expelled from school, and Magneto asks Gambit to bring them to him. He then sends them to rescue Wanda's brother from jail.
The destroyed Institute is restored by the X-Men; Mystique escapes and sets a trap for Cyclops.
Spyke gets hold of sports drink that harms mutants. Meanwhile, Kitty learns to drive, which terrifies her friends.
Wanda searches for Magneto while Toad steals Nightcrawler's holo-image inducer, hoping that, if he changes his appearance, he'll win over the Scarlet Witch.
Rogue has no control over her powers, and the powers of others that she has absorbed surface, including those of Sabretooth, and the X-Men must find a way to help her.
Mesmero returns and uses Gambit's powers to free Apocalypse.
Wolverine learns that he's been cloned by HYDRA scientists, and the clone targets Logan.
Mesmero tries to free Apocalypse once again and uses Rogue to help him, while the X-Men join forces with Magneto and the Acolytes to stop him.
Mesmero releases Apocalypse from his tomb and the X-Men, Brotherhood and Acolytes rush to the tomb to fight him.
The X-Men go on a cruise, then travel to an island when vacationers resent their abilities. But they face danger when the island's volcano erupts.