The X-Men are back! The superhero team led by Professor Charles Xavier are once again called on in the battle between humans and mutants. After a mutant attacks the President, there is again a public outcry for the registration of all mutants. This registration is the first step in a plan by General William Stryker to destroy all mutants. While Storm and Jean Grey search for the assassin, Cyclops and Professor X go to question Magneto about the assassination attempt. While on these separate missions Stryker launches an attack on both the "Xavier School for Gifted Youngsters" and on Professor Xavier himself. Separated and without their leader, the X-Men must reunite and combat the forces seeking to destroy them. The X-Men are joined on their mission by three young mutants that escape the school attack and Nightcrawler who is the mutant that attacked the President. They also find a surprising ally in Magneto and his band of mutants. Together they must work together to stop Stryker save mutants everywhere.