When anti-mutant Colonel William Stryker kidnaps Professor X and attacks his school, the X-Men must ally with their archenemy Magneto to stop him.
Several months have passed since the X-Men defeated Magneto and imprisoned him in a seemingly impregnable plastic chamber. One day, a mutant by the name of Nightcrawler infiltrates the White House and attempts to assassinate the President, setting off a chain reaction of anti-mutant measures by the government. Meanwhile, Logan is trying to discover his past. As scientist named William Stryker discovers Professor X's secret school and Cerebro, Magneto's partner, Mystique, is planning to break her leader out of prison. But when Professor X's school is attacked by Stryker's forces, Logan, Rogue, Iceman, and a few are lucky to escape. Those who remain meet in Boston, where they form an uneasy alliance with Magneto to stop Stryker and rescue Professor X.—John Wiggins
After the events on Liberty Island, everyone at Xavier's School for Gifted Youngsters is settling in. Magneto is locked up in a plastic cell, Rogue and Bobby Drake have finally gotten together, and Wolverine has set off to find his origins. But it won't stay quiet for long. After a mutant attack on the President, everyone starts to fear any type of mutant. William Stryker, who plans to stop all mutants, takes over the school, causing Wolverine and his team of mutants to go into hiding. Stryker has managed to capture Xavier and will use him to create another version of Cerebro. Wolverine and the team must now team up with their enemy, Magneto, to stop Stryker before it's too late.—Film_Fan
After Magneto's bitter defeat in X-Men (2000), the indoctrinated teleporter, Nightcrawler, wreaks havoc in the heavily guarded Oval Office, triggering an all-out military assault at Professor Xavier's school for mutants. Bent on annihilating all meta-humans, the religious fanatic and scientist, Colonel William Stryker, abducts the leader of the X-Men, in high hopes of using his brain in conjunction with the powerful mutant-detecting device, the Cerebro, to seek and destroy every superhuman. Now, as Professor X's life is in danger, the remaining X-Men have no other choice but to join forces with their imprisoned arch-enemy, Magneto, to have a fighting chance to survive. Can the united X-Men defeat Stryker?—Nick Riganas
Already living in a society that mistrusts them, the mutants are faced with even more discrimination after an unforeseen enemy, who may be a mutant with extraordinary powers, launches a devastating attack. The news of the assault causes a public outcry against the mutants, including renewed support for the Mutant Registration Act, and Colonel William Stryker, a military leader rumored to have experimented on mutants (possibly including Wolverine), is amongst the most vocal supporters of the legislation. Stryker puts into motion a plan to eradicate the mutants and begins an offensive on the X-Men mansion and school. Magneto, having escaped from his plastic prison, forms an unlikely alliance with Professor Xavier to stop Stryker. Meanwhile, Wolverine heads north to investigate his past.—Uber Minion
Nightcrawler, a Teleporting mutant, attempts to assassinate the President of the United States in the White House, but he fails and escapes after being shot by a Secret Service agent. Wolverine heads to Alkali Lake but finds nothing left of the base. Logan returns to the school, reunited with Rogue, her boyfriend Iceman, Cyclops, Storm, and Jean Grey. He is requested by Professor Xavier to watch over the children at the school, while Storm and Jean find Nightcrawler with the help of the professor and Cerebro.
Cyclops and the Professor visit Magneto in his plastic prison to see if he had any part in the attack on the President. Reading Magneto's mind, the Professor discovers that a covert government operative, William Stryker, has been extracting information from Magneto. A trap is sprung, and Cyclops and the Professor are captured by Stryker and his assistant Yuriko Oyama. A military raid of the X-Mansion begins, with the soldiers sedating every student they find. However, the plan backfires when Wolverine strikes back and kills a large number of Stryker's men, while Colossus, Rogue, Iceman, Pyro, and most of the students escape through a series of hidden tunnels in the school. Wolverine confronts Stryker, who fails to shed any light to his past. Iceman returns, saves Wolverine by creating a wall of ice between him and Stryker, and they both escape through one of the tunnels. Stryker's soldiers had already succeeded in sedating six students and managed to break inside Cerebro.
Impersonating Senator Robert Kelly and Yuriko, Mystique gains information about Magneto's prison and provides a means for him to escape. Wolverine, along with Rogue, Iceman and Pyro head to Iceman's (Bobby Drake's) parents' home in Boston. After a 9-1-1 call from Bobby's brother Ronny, the police arrive just as the group is about to leave. Pyro uses his fire manipulation powers to fend off the police but gets carried away and is prevented from causing further damage by Rogue. The X-Jet arrives to pick them up, and they are quickly targeted by two Air Force fighter jets. They manage to force the pilots to eject with the help of Storm and Jean Grey; however, they are hit by a missile which threatens to crash them. Only due to the sudden interference of Magneto do they survive. The X-Men then team up with Magneto and Mystique.
Magneto has learned Stryker orchestrated the attack on the President and has been experimenting on mutants, using a drug injected directly into the back of the neck to control them. Jean reads Nightcrawler's mind and determines that Stryker's base is located at Alkali Lake, inside the dam where he plans to kill the world's mutants by building a second Cerebro.
Through his son, Jason, Stryker gains control over the Professor. His son is able to project powerful visions in the mind, blinding a person to reality, and through this the Professor is brainwashed to use Cerebro to find and kill all mutants. Mystique is able to infiltrate Stryker's base by impersonating Wolverine as the X-Men followed. Storm and Nightcrawler search for the kidnapped students. Jean, Magneto, and Mystique are attacked by a brainwashed Cyclops while trying to rescue the Professor and in the process caused damage to the generators that keep the dam from collapsing. The force of Jean's telekinetic blast awakens Cyclops from his brainwashing, and Wolverine simultaneously finds Stryker in an Adamantium smelting room along with Yuriko, who is revealed to be Lady Deathstrike. Wolverine manages to defeat Deathstrike and then finds Stryker on a landing pad, where Stryker attempts to bargain Wolverine for his life with stories of his past.
Storm and Nightcrawler find the children and break them out of their cell. Magneto and Mystique managed to kill the rest of Stryker's men by setting off their grenades, which causes a leak in the dam, and Magneto stops Jason and the Professor before the mutants are killed. While disguised as Stryker, Mystique uses Jason to convince the Professor to kill all humans; she and Magneto, along with their new initiate, Pyro, then use Stryker's helicopter to escape Alkali Lake, chaining Stryker to concrete rubble. Meanwhile, Nightcrawler Teleports Storm inside of Cerebro where she creates a snowstorm to free the Professor from his telepathic illusion.
They all then flee the base as water engulfs it, only to discover that Magneto, Mystique, and Pyro - who had earlier been convinced by Magneto to join them - had escaped on the helicopter. Fortunately, Iceman and Rogue arrive with the X-Jet and everyone gets on board. The dam bursts completely, flooding the landscape and killing Stryker. A malfunction aboard the X-Jet prevents it from taking off; Jean sacrifices herself by leaving the jet and creating a telekinetic wall as a shield against the flood. She activates the X-Jet's primary engines before releasing the torrent of water down on herself, presumably killing her.
The X-Men are able to supply the President with files from Stryker's private offices. The next scene returns to the school, with Professor Xavier, Cyclops, and Wolverine talking about Jean's past. While they leave, Wolverine tells Cyclops that Jean made a choice and that it was him, which relieves Cyclops a good deal. The film ends with a voice-over by Jean Grey on the process of evolution (a speech originally made by the Professor in the introduction of the first film). The camera floats over Alkali Lake, showing a vague shape of a 'Phoenix' flying above it, hinting at her survival.
