After the events on Liberty Island, everyone at Xaviers School for Gifted Youngsters are settling in. Magneto is locked up in a plastic cell, Rogue and Bobby Drake have finally got together, and Wolverine has set off to find the origins of where he came from. But it wont stay quiet for long. After
a mutant attack on the President, everyone starts to fear any type of mutant. William Stryker who plans to stop all mutants, takes over the school, causing Wolverine and his team of mutants to go into hiding. Stryker has managed to capture Xavier and will use him to create another version of Cerebro. Wolverine and the team must now team up with their enemy, Magneto to stop Stryker before its too late.