A mysterious huge explosion destroys the X-Mansion at the moment that Wolverine was leaving. Professor X and Jean Grey are mysteriously missing, and perhaps gone for good, causing the X-Men to disband. Beast is examining the remains of the explosion and finds out that Professor X was the target. However, one year later, an anti-mutant government agency called the Mutant Response Division (or M.R.D. for short) hunt Wolverine and arrest a family that helped him. This causes him to go after them with the help of Beast. Inside the jail, they free all the mutants, including Dust, Boom Boom, and Pyro. In the end, Wolverine decides to find the other X-Men and fight the MRD.

With help from Angel, the X-Men are able to move back into the rebuilt mansion. Forge has been brought to the team to repair Cerebro and the Blackbird. The telepathic Emma Frost, the beautiful former headmistress of the Massachusetts Academy, requests to join the X-Men in order to help find Professor X. Wolverine is suspicious at in the beginning but reluctantly agrees, believing that Emma only has intentions to take control of Cerebro. Emma Frost is able to locate Professor X in Magneto's controlled mutant nation of Genosha. Now with Cyclops back in action, Wolverine leads the X-Men on a mission into the enemy territory in order to retrieve their lost mentor.