As the Beast waits for his arraignment in court in front of an anti-mutant public, Magneto tries to break Beast out of jail, only to receive resistance from Beast. An old enemy of Wolverine's pops up, and the X-Men take him in. Magneto then attacks a military base, trying to bring mutants together against the oppression brought upon.
Professor Xavier and Magneto confront each other for the first time in years, meanwhile Wolverine and Sabretooth come face to face. Professor Xavier tries to examine Sabretooth's mind to figure out his rage problem. After his last terrorist action failed, Magneto plots a new one to bring Professor Xavier out into the open. Sabretooth and Wolverine confront each other in the mansion's war room.
Wolverine has strong feeling for Jean Grey, but she's with Cyclops. Storm has a paralyzing case of claustrophobia and must overcome this as the X-Men venture into the New York sewers to rescue Jean Grey and Cyclops from a deformed race of mutants called the Morlocks. Storm confronts the leader of the Morlocks, Callisto, who wants Cyclops to rule beside her as king.
After leaving the X-Men, Wolverine looks for solitude in the arctic, but comes across Sabretooth, who's been tracking him. When the safety of a local tribe is threatened by Sabretooth, Wolverine must defeat him. Meanwhile Jubilee, Storm and Gambit do some investigating at an island resort called Genosha that seems to be a safe haven for mutants.
Senator Kelly has been abducted by Magneto and given the facts about Magneto's goals of superiority of mutants over humans, the X-men's beliefs of peaceful co-existence between both races, and the Sentinel's plans of global domination. And must make a decision of his future plans in politics based on this information.