The story brings together the X-Men and their nemesis, Magneto, against a common enemy: Colonel William Stryker, who aims to destroy all mutants.

As the story unfolds, the X-Men must confront their own demons and work together to stop Stryker and his plans to eradicate mutants. Along the way, they are joined by new allies, including Nightcrawler (Zack Crummey) and Rogue (Anna Paquin).