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.
A strange phenomena occurs in the wake of Apocalypse: A jungle-covered Mayan pyramid takes on a technological appearance and an impenetrable force shield surrounds it, even down into the ground underneath.
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.
Rogue witnesses her infatuated crush, Scott, date Jean. She is consoled by her British friend, Risty, but when she accidentally touches and absorbs everything from her at a concert, she finds out that she was Mystique all along in disguise.
Despite rescuing Professor X, the bigotry towards mutants still exists as our heroes return to Bayville High, scorned and verbally abused by their human classmates, including their mutant-hating Principal Edward Kelly.