Twenty years ago, Charles Xavier and Erik Lensherr pay a visit to the Grey family to convince Jean’s parents to enroll her in the Xavier Institute. At a young age, Jean wields enormous power, and Xavier wants to help her control it before it controls her.
Ten years ago, Warren Worthington III discovered wings growing out of his back. After finding out about his mutation, his father channels funds into a “cure” for mutation.
In the present day, the X-Men in training (Iceman, Shadowcat, Rogue and Colossus), led by Storm and Wolverine, are training in the Danger Room against the Sentinels. Wolverine takes matters into his own hands when he decides the team isn’t ready for combat. Storm is enraged over his rash behaviour, but Wolverine retaliates that he is only “substituting” for Scott.
Upstairs, a disillusioned Scott keeps hearing Jean call out to him in his head. Downstairs, Rogue and Bobby are having an argument. Scott decides to head out. Logan tries to stop him, telling him to move on with his life. Scott counters, telling Logan “not everybody heals as fast as [him]” and storms out of the mansion.
Recently, Hank McCoy has been named Secretary of Mutant Affairs. He has been called to a meeting with Homeland Security regarding the intended capture of Magneto. They have been tracking him, but only captured Mystique. Hank had been called to view the file on the mutant, Jimmy, held by Worthington Labs, that Mystique stole from the FDA.
Xavier is teaching a class on “mutant ethics” when he is disrupted by the thoughts of a distracted Ororo. She wants to know why they’re still “hiding”, while Xavier is insistent for the safety of his students. He also wishes Ororo to one day take over the Institute from him, after Scott had “changed” since Jean’s death. Ororo is worried about what Xavier might be implying.
Hank pays a visit to the Institute to deliver the bad news about the mutant “cure”. Meanwhile, Worthington Labs announces on live television the successful concoction of a “cure”. Rogue is taken in by the idea of the “cure”.
On the streets, lower level mutants are gathered together to voice their opinions on combating the “cure”. Magneto steps up and offers these mutants a membership into the Brotherhood. Magneto enlists the help of Callisto to locate Mystique.
Hank visits Worthington Labs to examine Jimmy.
Scott travels back to Alkali Lake, hoping that it can help him come to terms with his grief. He lets loose an optic blast into the water, stirring it up, from which Jean arises.
Jean: “I don’t know.” (They embrace.) “I want to see your eyes. Take these off.”
Jean: “Trust me. I can control it now.” (She takes his glasses off.) “Open them. You can’t hurt me.”
They lock lips. Then Jean turns into Dark Phoenix. It is implied that she destroys him. Xavier senses it and sends Wolverine and Storm to Alkali Lake. They find an unconscious Jean, but no Scott.
Back in the mansion, Xavier is trying to restore the “psychic barriers” in Jean’s mind to “cage” the “Phoenix”, the “dormant” dark, “duo personality” of Jean that had been suppressed over the years.
On Alcatraz, Warren Worthington II is about to administer the cure on his son. In the last minute, Warren Worthington III fights back, deciding that he wants to keep his wings and jumps out of the window.
Magneto tracks down Mystique and rescues her from her prison, as well as other mutants such as Multiple Man and the Juggernaut. Mystique takes a shot of the “cure” meant for Magneto from a guard and reverts to her human form. Magneto abandons her on the premise that she’s not a mutant anymore.
Hank resigns from his post after learning that the “cure” had been used as a weapon and returns to the Institute. In the Institute, Logan makes a stupid move, releasing Jean and the Phoenix from her inhibitors. Jean pleads for Logan to kill her while she has control over her body, but Logan refuses, thereby allowing Phoenix to escape.
Callisto informs Magneto of Jean. Magneto goes after her, and so does Xavier. Xavier confronts Jean alone with Magneto, but Phoenix gets angry. Wolverine and Storm battle the Brotherhood to try and get to Xavier, but it is too late as Phoenix obliterates Xavier’s body. Magneto manages to convince Phoenix to join his cause.
The school holds a memorial service for Charles Xavier. In the night, Bobby tries to cheer Kitty up by freezing the pond in the garden so they can ice skate. Rogue catches them together, and in a fit of jealousy, runs away again.
In a forested area, Magneto’s Brotherhood set up camp. Phoenix’s display of power threatens Magneto slightly.
At the Institute, the adults debate on the school’s closure, as suggested by Hank. Storm refuses to see Xavier’s vision die. Warren walks in seeking a safe haven. Bobby goes in search of Rogue but is told by Piotr that she “took off”. Logan hears Jean calling him in his head and goes in search of her alone. Bobby goes in search of Rogue where the “cure” is being administered. He meets his former friend, Pyro, who attacks the centre where they were distributing the “cure”. Magneto announces that there will be subsequent attacks. The president declares this a national threat issue. The military is armed with plastic weapons that carry the “cure”.
In the forest, Wolverine is ambushed by the Brotherhood. He encounters Magneto, who promptly removes Wolverine from his camp.
A depowered Mystique supplies Homeland Security with information on Magneto’s camp, but it turns out to be a decoy as the Brotherhood targets Alcatraz, using the Golden Gate Bridge as a means of allowing the Brotherhood to access Alcatraz.
Wolverine returns to the Institute to warn the X-Men of Magneto’s plan. The new X-Men team is dispatched to stop Magneto’s attack.
Magneto launches an attack on Alcatraz, sending in the “pawns” first. The military frantically unleashes the “cure” weapons on them. They fail to take out Magneto. Arclight is ordered to use her “shockwave” powers to destroy the weapons. The X-Men arrive to battle the Brotherhood. Juggernaut goes for Jimmy, and Shadowcat chases after him and rescues Jimmy. Quill, Arclight and Psylocke go after Warren Worthington II and Dr Rao. After killing Dr Rao, they toss Warren Worthington II over the edge of the building when Warren Worthington III flies in and catches his father in midair and flies him to safety. Callisto is electrocuted by Storm on a chain-link fence. Magneto and Pyro launch burning cars into the air acting as bombs. Iceman deals with Pyro while Wolverine and Beast use the “cure”on Magneto to stop him.
Backup arrives and start shooting at Jean, angering the Phoenix and starts a wave of destruction. Wolverine orders “everyone to safety” while he attempts to stop Phoenix. In a moment of consciousness, Jean gets Wolverine to kill her.
It is a sad day at the Institute as they bury Scott and Jean alongside Charles Xavier, but it is also a day of renewed hope as the Xavier Institute opens for a new school year. Hank is also appointed the new United Nations Ambassador.
In a park elsewhere, Magneto rediscovers his mutant abilities, hinting that the “cure” might not be “permanent”.
Also, Moira MacTaggat makes a startling discovery that Xavier had transferred his consciousness into her patient without a “higher brain function”.
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