The remaining X-Men and Brotherhood members deal with the aftermath of the exposure of mutants and go to Area 51 to save their captive members. The X-Men are now alone in a world which shuns them.

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 are allowed back in school on a trial basis, provided they do not use their powers on campus. This proves not an easy task with Principal Kelly secretly orchestrating trouble for them, including a showdown with the Brotherhood.

The Scarlet Witch wants to find out where her father Magneto is, so she enlists Caliban for help. She then goes to her brother Quicksilver for information. When he refuses, Wanda delivers him to the police to try drawing Magneto out.

Jean is about to confess her love to Scott when Mystique abducts Scott and abandons him in the desert in Mexico. Jean, who has vivid telepathic visions of him in peril, tracks him down, but Mystique is determined to kill both of them.

Spyke joins a skateboarding contest sponsored by "Pow-R 8" soda. However, Pow-R 8 is harmful to mutants, and when Spyke drinks a swig, it causes serious side effects to his mutation. The mysterious Morlocks, step in to help him.

The Scarlet Witch finally tracks down Magneto to his Acolyte headquarters. While, Kurt is spending time with Amanda Sefton and meeting her parents. In a bid to win the Scarlet Witch's affections, Toad steals Nightcrawler's Image Inducer.

Rogue has absorbed so many thoughts, memories and personalities of other people that she can no longer contain or control them. She becomes completely overwhelmed when she accidentally touches Risty and learns the truth about her identity.

Angel spots Gambit stealing a mysterious artifact, but when he tries to stop him, Mesmero fights him off. When the Acolytes want to steal another artifact, the X-Men fight them and discover there is a bigger plan happening.

A mysterious female assassin attacks the X-Mansion, knocking out the X-Men one by one. Wolverine finds out that the assassin is his clone, designation "X-23", created by the Dr. Deborah Risman and raised without love to be a living weapon.

Rogue falls under the mind control of Mesmero and is used as a weapon to absorb the mutant abilities of every X-Man, Brotherhood, and Acolyte member. Mesmero wants Rogue to give all of her stolen abilities to Apocalypse to awaken him.

The X-Men, Brotherhood, and Acolytes continue their battle against Mesmero. The heroes and villains track down Apocalypse to Egypt, but only to come face-to-face with him and having failed to prevent Apocalypse from coming back to life.

Taking a break from superhero duty, the X-Men take a pleasure cruise. However, Magma becomes violently ill, literally suffering from earth withdrawal. When Boom Boom and Iceman take her to an island, she accidentally triggers a volcano.