Several months had passed since The X-Men defeated Magneto and imprisoned him in a plastic chamber. One day, a mutant going by the name of ``Nightcrawler`` infiltrates The White House and attempts to assassinate The President. Meanwhile, Logan is trying to discover his past, and wonder why he became a mutant. However, the friction between the humans and mutants is grinding much harder. As a scientist named William Stryker is assigned to discover about Professor X’s secret school and his chamber called ``Cerebro``. Meanwhile, Magneto’s partner, Mystique, is planning to break her leader out of prison. Then, Professor X’s school is attacked by Stryker’s forces. Logan, Rougue, Iceman and others escaped. The rest of The X-Men meet in Boston along with Magneto, who escaped from prison. They must work together to stop Stryker and rescue Professor X.