Jubilee is saved by the X-Men when Sentinels-- giant mutant apprehending robots--attack a shopping mall. The X-Men discover that renegades within the government are using a Mutant Registration Program to track down and eliminate mutants.

The X-Men break into the Mutant Registration Office to destroy their files, but Beast is apprehended while trying to escape. Meanwhile, Gyrich and Trask, the renegades responsible for the Sentinels, kidnap Jubilee, hoping she can lead them to the X-Men.

While Professor Xavier attempts to stop Magneto's reign of destruction, Sabretooth--an old foe of Wolverine's --infiltrates the X-Men headquarters.

Cyclops and Jean are captured by a band of underground-dwelling mutants called the Morlocks. While the X-Men attempt to rescue them, Wolverine must confront his own strong feelings for Jean and his jealousy toward Cyclops.