Twenty years in the past, Professor Charles Xavier and Erik Lehnsherr meet young Jean Grey at her parents’ house to invite her to join their school, the X-Mansion. Ten years later, the industrialist father of Warren Worthington III discovers his son is a mutant as Warren tries to cut off his wings.
In the present, Worthington Labs announces it has developed an inoculation to suppress the X-gene that gives mutants their abilities, and offer the “cure” to any mutant who wants it. The cure is created from the genome of a young mutant named Jimmy, who lives at the Worthington facility on Alcatraz Island. While some mutants are interested in the cure, including the X-Men’s Rogue, many others are horrified by the announcement. Lehnsherr re-establishes his Brotherhood of Mutants with those who oppose the cure, warning his followers that the cure will be forcefully used to exterminate the mutant race.
With help from Pyro, Lehnsherr recruits Callisto, and several other mutants. They attack the mobile prison holding Mystique to free her, also freeing Juggernaut and Multiple Man. Mystique saves Lehnsherr by taking a shot of the mutant cure aimed at him, rendering her human. Hateful of humans, Lehnsherr abandons Mystique, much to her shock. Meanwhile, Scott Summers, still distraught over the loss of his fiancée, Jean Grey, drives to her resting location at Alkali Lake. Jean appears to Summers but, as the two kiss, Jean kills him. Sensing trouble, Xavier sends Logan and Storm to investigate. When they arrive, they find only telekinetically floating rocks, Summers’ glasses, and an unconscious Jean.
When they return to the X-Mansion, Xavier explains to Logan that when Jean sacrificed herself, she also freed the “Phoenix”, a dark and powerful alternate personality which Xavier had telepathically repressed, fearing the Phoenix’s destructive potential. Logan is disgusted to learn of this psychic tampering with Jean’s mind but, once she awakens, he discovers that she killed Summers and is not the Jean Grey he once knew. The Phoenix emerges, knocks out Logan, and escapes to her childhood home.