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 Beast stands trial for the break-in, a powerful mutant "Master of magnetism" attempts to break him from prison. Professor Xavier recognizes his age-old foe Magneto, a maverick who aims to start a mutant war against humanity.

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.

Wolverine leaves the X-Men to seek solitude in the Canadian wilderness. He finds peace among a group of Baffin Island Eskimos, only to discover that Sabretooth has been stalking him all this time.