Taking a break from superhero duty, the X-Men (without Rogue and Berzerker) take a pleasure cruise.

The X-Men, Brotherhood, and Acolytes track Apocalypse to Egypt, but fail to prevent him from coming back to life.

Rogue falls under the mind control of Mesmero and is used as a weapon to absorb the mutant powers of every X-Man, Brotherhood, and Acolyte member.

A mysterious female assassin terrorizes the X-Mansion, knocking out the X-Men one by one. Wolverine finds out that it is his clone, created by the Dr. Deborah Risman and raised without love by HYDRA, and she wants to kill him because she holds him responsible for her miserable life. Wolverine and X-23, as she is called, square off in a battle that Wolverine does not want to win.

The Acolytes and the X-Men face a spider-like being which is virtually unstoppable.

Rogue appears to have problems with her powers, as the residual impressions of everyone she has touched start flashing through her mind and body.

Wanda receives a clue from one of Magneto's minions, Pyro, directing her to a ski resort. Meanwhile, Kurt is meeting Amanda's parents for the first time, and the Toad believes he can use Kurt's holo-inducer to disguise himself and win Wanda's love.

Evan enters an extreme Skateboarding competition, and puts his skills to the test. But something is wrong: A mysterious woman is watching and following him during the competition.

Mystique escapes from imprisonment while the X-Men repair and rebuild the Institute. Disguised as Alex, she lures Scott into a trap - leaving him stranded in the middle of the Mexican desert without his glasses.

Wanda goes searching for Pietro. Meanwhile the brotherhood's members are expelled from school, much to Lance's dismay.

During the rebuilding of the manor, Kitty and Kurt intercept a bunch of graffiti artists disguised as monsters. The older students get to go back to Bayville High for one day before attending a hearing to determine their ultimate fate, while they are banned from using their powers.

While Storm and Beast step in front of the Senate to try curbing the rampant anti-mutant crowd, the rest of the X-Men have to stop Juggernaut, who has been unleashed by Mystique and is threatening to destroy a dam.

The X-Men and Brotherhood deal with the after math of the world finding out about mutants. Mystique, diguised as Professor X, manages to blow up the Insitute. Some of the X-Men and Brotherhood were captured, leaving the mutants that escaped to find them and the Professor.