In order to prevent all of humankind from being turned into mutants, the X-Men, the Brotherhood, S.H.I.E.L.D., The Acolytes, Angel, Spyke, Havok, and the New Mutants all join forces to save humanity from the ambitions of Apocalypse.
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 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.
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.
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 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.
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.
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.
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.