After months of being imprisoned at Manticore, Max has resisted powerful attempts at re-programming and breeding and plans her escape from the genetics lab. She is aided in her breakout by the gentle but beast-like Joshua, an early Manticore creation, and together they release all the other Manticore creatures. Max attempts to reunite with Logan, only to discover that he is now number one on Manticore's most wanted list.
After therapy uncovers repressed memories of abuse and fearing her seven-year-old sister is currently being molested, an eighteen-year-old girl brings charges of rape against her father who winds up murdered when those charges are dismissed.
When Scott and Kurt use their powers to save several people from a car crash, the question of how much they're willing to ignore to keep their powers a secret comes up. Professor X maintains that the world is not ready to know about them, however the other mutants, now without Mystique's guidance, have other ideas...