Twenty years ago, 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 fiancÃ©e, Jean Grey, drives to her resting location at Alkali Lake. Jean appears to Summers but, as the two kiss, Jean disintegrates 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 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.
Lehnsherr learns of Jean's resurrection through Callisto, and the X-Men arrive at the Grey home at the same time as the Brotherhood. Lehnsherr and Xavier go in alone, and both vie for Jean's loyalty until the Phoenix resurfaces. She destroys the house and disintegrates Xavier before leaving with Lehnsherr. The Brotherhood decides to strike Worthington Labs, and the government sends multiple teams to attack the Brotherhood's base in the forest, with information gained from Mystique, furious over Lehnsherr's betrayal. However, the life forms in the camp are all copies of Multiple Man, and Lehnsherr uses his powers to move the Golden Gate Bridge so he and his army can get to Alcatraz and facilitate the attack on Worthington Labs. The remaining X-Men confront the Brotherhood, despite being significantly outnumbered, and arrive just as the military troops who thus far have been neutralizing the attacking mutants are overwhelmed by the Brotherhood.
During the fight, Kitty Pryde saves Jimmy from Juggernaut, who had been sent to kill him. Logan has Colossus throw him at Lehnsherr and distracting him long enough for Hank McCoy to inject Lehnsherr with the "cure" and thus nullifying his powers. Army reinforcements arrive and shoots at Jean just as Logan had calmed her down. Phoenix is awakened by the attack and disintegrates the troops in retaliation. Phoenix begins to destroy Alcatraz and anyone within range of her powers. Logan realizes that only he can stop Phoenix due to his healing factor. Logan approaches her and Jean momentarily gains control and begs him to kill her. Logan fatally stabs Jean (and thus Phoenix) but mourns for her death.
Sometime later, mutant rights are finally obtained and Xavier's school is still operating with Storm as headmistress. The President of the United States appoints McCoy as ambassador to the United Nations. Rogue reveals to Bobby Drake that she has taken the cure, much to his disappointment. Meanwhile, Lehnsherr sits alone at a chessboard in a San Francisco park. As he gestures toward a metal chess piece, it wobbles slightly, suggesting that the effects of the cure might only be temporary.
In a post-credits scene, Dr. Moira MacTaggert checks on a comatose patient[7] who greets her with Xavier's voice, leaving her startled.
What gene has Worthington Labs developed an inoculation to suppress?
X-gene