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 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.

Magneto destroys a chemical plant in order to attract Professor X. Cyclops, Rogue, Storm, and Professor X proceed to the chemical plant, while Jubilee is left to guard Sabretooth. Professor X enters the chemical plant to confront Magneto. Just as Magneto appears to beat Professor X, Professor X telepathically forces Magneto to recall his younger years. Magneto retreats in panic. Back at the X-Mansion Sabretooth growls in disgust at the senator on television and Jubilee notices a problem with his wrist bindings. Jubilee loosens the restraints, and Sabretooth captures Jubilee, but Wolverine leaps from the shadows and attacks him. Their battle is interrupted with the return of Professor X and the other X-Men.

A group of mutants called Morlocks capture Jean and Cyclops when they go out. The Morlocks leader Callisto kidnapped Cyclops so that he would rule the Morlocks beside her. Jean uses her telepathic powers and tells the Professor that they have been captured. Wolverine, Gambit, Rogue, and Storm go to search for them. When the X-Men find Jean and Cyclops, Storm challenges Callisto for leadership of the Morlocks to save Cyclops and Jean. Callisto has no choice but to accept the challenge. After a brief fight, Storm defeats Callisto and becomes the new Morlocks' leader, but having saved Jean and Cyclops, she makes Callisto the leader in her absence.

Wolverine flees to Canada to seek solitude in the Canadian wilderness. He finds peace among a group of Baffin Island Inuit, only to discover Sabertooth has been stalking him and has taken the people of the village captive, and plans to kill them all. Wolverine is able to defeat Sabertooth and rescue the villagers. Back at the X-Mansion, Gambit tells the X-Men he heard the people at Genosha welcome mutants and he wants the team to vacation there. Professor Xavier sends Storm, Gambit, and Jubilee to Genosha as tourists. While in Genosha, Storm, Gambit and Jubilee are attacked and captured by a Sentinel.