A mysterious explosion destroys the X-Mansion right on the moment Wolverine was leaving. Professor X and Jean Grey are missing and perhaps gone for good causing the X-Men to disband. However, one year later, Anti-Mutant hunts Wolverine, and arrest a family that helped him, making him 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 others X-Men and fight the Anti-Mutants.

To regain his honor, Silver Samurai captures the X-Men and attacks Wolverine.

The Inner Circle manage to draw the Phoenix out of Jean Grey but it proves to be more powerful than anyone could have imagined. Now Cyclops, Emma Frost and the rest of the X-Men must find a way to stop it before it destroys the world! Plus, the future X-Men begin their assault on Mastermold and the Sentinels!