The X-Men saves Storm from the Shadow King. Gambit steals something from the X-Men and Wolverine must get it back. Nightcrawler fights pirates and falls in love with Scarlet Witch. Wolverine has a rematch with the Hulk. The X-Men attempt to stop the destruction of Genosha forewarned by Xavier. The team tries to find Master Mold. Meanwhile in the future Xavier forms a new X-Men team. Nightcrawler discovers that Magneto's paradise is not all it seems as he is holding several mutants in an underground dungeon. Mystique breaks into the Mansion and captures Nightcrawler. Wolverine recovers part of his past from Weapon X and encounters Sabretooth. Warren Worthington Jr. discovers a "cure" for mutants.
Cyclops lets Emma enter his mind to erase his memories of Jean only to discover the cause of the explosion. The reason is Jean Grey, who became the Phoenix. Emma finds that the Hellfire Club knew about Phoenix and sides with the X-Men against them. They find her without memories at a hospital. The X-Men convince Magneto and Kelly to reach an agreement. However, Magneto uses Mystique to start a war by having Sentinels attack Genosha, then reprogramming them to attack humans. Magneto is defeated and banished from Genosha, while Emma seemingly sacrifices herself to stop the Phoenix. From the future Xavier informs the X-Men that the first dystopian future has been erased only to be replaced by another.