X2: X-Men United (2003)

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? - X-Men (2000)

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

Having returned from the north after finding nothing, Wolverine/Logan watches over the school students for a night as Charles Xavier visits Magneto in his plastic confinement prison, and Storm and Jean Grey search for a teleporter mutant known as Nightcrawler who attempted to assassinate the President. Things become deadly as William Stryker, a scientist who has experimented on mutants, leads a siege on Xavier's mansion, few mutants escape. With the school no longer safe, Magneto out of prison, and forming a temporary alliance with the X-Men, and Professor Xavier in the hands of Stryker, the mutants team up to stop Stryker's plans to wipe the mutants off the face of the Earth. - commanderblue