X-Men: The Last Stand (2006)

Twenty years before the movie's current events, Professor Charles Xavier and Erik Lensherr meet a young Jean Grey at her parents' house to make her aware of her powers. Ten  years later, a young Warren Worthington III tries to cut off his wings, before his father discovers he is a mutant. The next scene opens with the X-Men in battle against a giant robot in the Danger Room. Kitty Pryde and Colossus have joined the team, although Cyclops is absent. Storm insists on working as a team, but Wolverine has Colossus throw him as he cuts the giant robot's head off. Storm is upset with Wolverine for not working as part of a team. Sometime afterward, the pharmaceutical company Worthington Labs announces it has developed an inoculation to suppress the X-gene that gives mutants their abilities and makes them different from other humans, offering the "cure" to any mutant who wants it. While some mutants are interested in the cure, including the X-Men's Rogue, many others are horrified by the announcement. In response to the news, the X-Men's adversary, Lensherr, now known as Magneto, raises an army, led by him, Pyro, Juggernaut, Arclight, Multiple Man, and Callisto, warning his followers that the "cure" will be forcefully used to exterminate the mutant race. Cyclops, still emotionally distraught about the loss of Jean, returns to Alkali Lake. Jean appears to Cyclops, but as the two romantically kiss, Jean takes on a fearsome appearance. Psychically sensing trouble, Professor X sends Wolverine and Storm to investigate. When they arrive, the two X-Men encounter telekinetically floating rocks, Cyclops' glasses, and an unconscious Jean. Cyclops himself is nowhere to be found. Xavier explains that when Jean sacrificed herself, she unleashed the powerful alternate personality she calls "Phoenix". Wolverine is disgusted to learn that Xavier has kept Jean in check telepathically, but when Jean awakens, he realizes she is not the Jean Grey he knew. Jean pleads with Wolverine to kill her, but when he refuses, the Phoenix surfaces and knocks out Wolverine, before escaping to her childhood home. Magneto, alerted by Callisto to the presence of an immeasurably strong and powerful mutant, realizes that it must be Jean Grey. Magneto and his allies are already at Jean's childhood home when Xavier and his X-Men arrive. The two men vie for Jean's loyalty until the Phoenix resurfaces. She destroys her family's house, disintegrates Xavier, and leaves with Magneto. The X-Men regroup to confront Magneto's army, despite being significantly outnumbered. Magneto has diverted the Golden Gate Bridge to provide access to Alcatraz Island, the location of Worthington Labs facility. The military troops defending the facility are armed with plastic "cure weapons" able to neutralize the attacking mutants, and non-metallic to counter Magneto's powers. Magneto lets the lesser-powered mutants charge ahead, with heavy initial losses, but then they rapidly begin to overwhelm the troops. The X-Men's Wolverine, Storm, Beast, Iceman, Colossus and Kitty Pryde arrive to battle Magneto and his troops. During the fight, Beast injects Magneto with the cure, nullifying his powers. Meanwhile, Kitty has entered the facility to find Jimmy, who is the source of the cure and saves him from the murderous Juggernaut. They escape as Army reinforcements arrive, only to be obliterated by Phoenix, lashing out with her power and destroying everything around her including the lab itself. Wolverine realizes that due to his self-healing power, he is the only one who can approach her. He tells Storm to evacuate everyone and faces Phoenix alone, his power barely neutralizing the destructive nature of her disintegration attack. Jean, momentarily gaining control, begs Wolverine to save her. Telling Jean he loves her, Wolverine forces himself to stab her, killing her, and, in her dying moments, Jean turns back to normal, smiles at him, and dies. Wolverine weeps over her dead body in his arms in the middle of the devastated island. The school continues without Xavier, with Storm now as headmistress and Logan as a teacher. The US president appoints Beast as ambassador to the United Nations, Rogue returns, telling Iceman she has taken the cure and the two hold hands skin-to-skin. In the epilogue, Magneto sits alone at a chessboard in a San Francisco park. He gestures forlornly towards the queen, causing it to tilt slightly.