When Jean has nightmares about huge circus clowns, a mysterious hypnotist kidnaps some of the X-Men including Jean Grey, Nightcrawler, Spyke, and Shadowcat, and brainwashes them into committing crimes for him.
The Bayville High Sadie Hawkins dance arrives, and everybody is scrambling for dates. While, Forge constructs a device to greatly improve Nightcrawler's teleportation abilities, which has a dangerous side effect on his portals.
In order to help a depressive Beast out of his slump, Shadowcat arranges a field trip with the New Mutants. However, hunters catch Beast, thinking him to be Bigfoot, and the young mutants must save their teacher from life in captivity.
The female X-Men are fed up with playing second fiddle, and form a vigilante crime-fighting group called the Bayville Sirens. Scott and Kurt try to figure out what they are up to until an old enemy crosses the Sirens' path.
Nick Fury informs Wolverine that Magneto has stolen a device once used to create Captain America. Wolverine, Rogue and Nightcrawler go to recover it. Meanwhile, Logan reminisces about his history with Captain America during World War II.
Mystique returns to the Brotherhood with a mentally unstable, but immensely powerful mutant named Wanda Maximoff who was abducted from a mental institution, much to the horror of her twin brother Pietro.
Anti-mutant activist Bolivar Trask abducts Wolverine and introduces him to his newest invention, the Sentinels. Meanwhile, the X-Men and the Brotherhood members team up to face Magneto who summons his Acolytes to create mayhem.
The X-Men and Brotherhood teams arrive to stop Magneto and end up facing his Acolytes, as he has other plans for them to reveal the existence of mutants to the world but then, a shocking twist reveals that nothing was as it seemed to be.
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.