In 1986, 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 Warren Worthington II discovers his son is a mutant as he 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. Magneto 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, Magneto recruits Callisto and several other mutants. They attack the mobile prison holding Mystique to free her, also freeing Multiple Man and Juggernaut. Mystique, shielding Magneto from a cure dart, is hit by it and loses her mutant abilities. Magneto abandons her as a result.
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 Logan and Storm return to the X-Mansion, Xavier explains to Logan that when Jean sacrificed herself to save them, she also freed the "Phoenix", a dark and extremely powerful alternate personality which Xavier had telepathically repressed, aware of the Phoenix's godlike 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.
Magneto learns of Jean's resurrection through Callisto, and the X-Men arrive at the Grey home at the same time as the Brotherhood. Magneto and Xavier go in, and both vie for Jean's loyalty until the Phoenix resurfaces. She destroys the house and disintegrates Xavier before Magneto and Logan can stop her. Jean leaves with Magneto. After interrogating a depowered Mystique, the FBI discover Magneto's base in the woods. However, the life forms in the camp are all decoy copies of Multiple Man. Magneto and the Brotherhood have gone to storm Alcatraz by using his magnetic manipulation powers to reroute the Golden Gate Bridge. 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 by Magneto. Logan has Colossus throw him at Magneto and distract him long enough for Hank McCoy to inject Magneto with the "cure" and thus nullify his powers. Army reinforcements arrive and shoot at Jean just as Logan had calmed her down. The Phoenix is awakened by the attack and disintegrates the troops in retaliation. The Phoenix then begins to destroy Alcatraz and anyone within range of her powers. Logan realizes that only he can stop the Phoenix due to his healing factor and adamantium skeleton. When Logan approaches her, Jean momentarily gains control and begs him to save her, and everyone else, by killing her. Logan fatally stabs Jean, killing the Phoenix, but mourns 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, Magneto sits at a chessboard in San Francisco, seemingly human and weak. As Magneto gestures toward a metal chess piece, it wobbles slightly. Elsewhere, Moira MacTaggert checks on a comatose patient[a] who greets her with Xavier's voice, leaving her startled.
Hugh Jackman as Logan / Wolverine:
Halle Berry as Ororo Munroe / Storm:
Ian McKellen as Erik Lehnsherr / Magneto:
Patrick Stewart as Professor Charles Xavier:
Famke Janssen as Jean Grey / Phoenix
Haley Ramm as young Jean Grey
Anna Paquin as Marie / Rogue:
Kelsey Grammer as Dr. Henry "Hank" McCoy / Beast
James Marsden as Scott Summers / Cyclops
Rebecca Romijn as Raven Darkholme / Mystique
Shawn Ashmore as Bobby Drake / Iceman
Aaron Stanford as John Allerdyce / Pyro
Vinnie Jones as Cain Marko / Juggernaut
Elliot Page[b] as Kitty Pryde
Daniel Cudmore as Peter Rasputin / Colossus
Ben Foster as Warren Worthington III / Angel
Cayden Boyd as young Angel
Michael Murphy as Warren Worthington II
Dania Ramirez as Callisto
Shohreh Aghdashloo as Dr. Kavita Rao
Josef Sommer as the President
Bill Duke as Trask
Eric Dane as Multiple Man
also marketed as X3 or X-Men 3
based on the X-Men superhero team introduced in Marvel Comics.
the sequel to 2003's X2, as well as the third installment in the X-Men film series