A strange phenomena occurs in the wake of Apocalypse, and the X-Men receive permission from the government to study it. Meanwhile, Nightcrawler tries to revive his mother Mystique who is still trapped in stone, much to the dismay of Rogue.

The Brotherhood stage accidents in order to make themselves look like heroes and use their new found fame to make the X-men look bad.

Wolverine and his clone, X-23, team up to take on Hydra.

Charles Xavier's son David has been seemingly abducted.

During a wave of anti-mutant violence, Spyke returns, having further mutated as a vigilante and protector of the sewer-dwelling Morlocks.

Gambit, the card playing Cajun mutant abducts Rogue to help him find his kidnapped father.

Kitty befriends Danielle Moonstar, a young mutant girl, but does she really exist?

Apocalypse plans to turn all humans with the dormant X-gene into mutants.

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.