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 rejoindre forces to save humanity from the ambitions of Apocalypse.
Despite rescuing Professor X, the bigotry towards mutants still exists as our Heroes return to Bayville High, scorned and verbally abused par their human classmates, including their mutant-hating Principal Edward Kelly.