When a cure is found to treat mutations, lines are drawn amongst the X-Men, led by Professor Charles Xavier, and the Brotherhood, a band of powerful mutants organized under Xavier's former ally, Magneto. It has been several months since The X-Men stopped William Stryker, but that victory came at a price: they have lost Jean Grey when she tried to save them from the collapsed reservoir. Scott Summers (Cyclops) is still grieving about her loss. One day, he comes out to the place where Jean Grey sacrificed herself. Jean Grey appears right in front of him. Meanwhile, the rift between humans and mutants has finally reached the boiling point. Humans have discovered what causes humans to mutate and have found a cure for the mutation. The X-Men are appalled at this idea. When news about the cure comes to Magneto, he decides to organize an army of mutants and wage his war against the humans. When Jean Grey evolves into the Phoenix, her new mutant powers are so strong that she can not control her own body. Then, she kills off Professor X with her new powers. Now, The X-Men must stop Magneto again and put an end to the war against the humans, as well as stop Jean Grey's Phoenix powers.