The mutants continue to fight against a society that they fear and distrust. Their situation becomes even more desperate when they come under a powerful attack from an unknown enemy with extraordinary abilities.
The surprise attack again causes political and public outcry over the introduction of Universal Registration of Mutants and the formation of an anti-mutant movement led by William Stryker, a former military man who was rumored to be experimenting on mutants.
Stryker's job had something to do with Logan's mysterious past, which he doesn't remember. As soon as Wolverine begins to try to unravel the past, Stryker activates his anti-mutant program, i.e., organizes an attack on Professor Xavier's house.
Fled from a plastic prison, magneto invites the X-Men to unite and fight together against the common ferocious enemy Stryker. This time around, the X-Men are facing the biggest challenge they've ever faced: the fate of not just all mutants, but all of humanity, is now in their hands.