A teleporter infiltrates the White House. Just as he is about to asassinate the President, he is shot in the chest and disappears in a puff of purple smoke.
At the Xavier’s School for the Gifted, Bobby and John compare their powers, whether it would be worse to die frozen or burnt. Meanwhile, the staff, Professor Xavier, Scott, Jean and Ororo are concerned about the recent “mutant attack” on the President and the possibility of the re-introduction of the Mutant Registration Act. Scott thinks that Magneto is behind the attack. Xavier has his doubts, but intends to question Lensherr personally to find out.
At the White House, William Stryker demands that the President authorise his “organisation” for a “special” operation. Senator Kelly interrupts them and learns that Stryker has access to Magneto since his “group developed the technology that built [Magneto’s] prison”. Stryker shows the President some “surveillance information” and convinces the later to grant him authorisation.
Later, Stryker visits Magneto to gain more information using special persuasive means.
Back at Xavier’s School, Logan returns to the mansion. Rogue is there to greet him, and Bobby is not too happy. Bobby freezes Logan’s hand upon shaking it. Jean and Ororo follow up on the greeting. Ororo leaves Jean and Logan alone with the excuse of preparing an X-Plane to track down the mutant assassin. Logan is asked to “babysit” the school for the night.
Logan finds Xavier tracking the mutant with Cerebro. Xavier makes a passing mention that he could “kill every mutant on the planet” if he wanted to. Logan wants Xavier to read his mind again because he couldn’t find any answers at Alkali Lake. Xavier tells Logan he’ll deal with him after visiting Magneto with Scott.
Logan watches from the window as Scott and Jean bid farewell, going on their separate missions. A student enters the room to tell Logan that if he’s upset, he could take it out in the Danger Room.
Meanwhile, Mystique, disguised as Stryker’s assistant Yuriko Oyama, enters Stryker’s office to access information that Stryker holds.
Jean and Storm track the mutant down to St. Michael’s Church in Boston. The teleporter, known as Kurt Wagner, tells them that he was captured and “mark[ed]” and made to assassinate the President.
Magneto tells Xavier that he’s had “frequent visits from William Stryker”. Magneto was made to tell Stryker all about Xavier’s school. Xavier realises that his visit was a set up when he sees Scott unconscious outside Magneto’s cell.
In the meantime, the school is being attacked by special operation troops. Most of the students escape as Logan tries to stop the troops. He comes face to face with Stryker, who seems to hold the answers to Logan’s nightmares. Just then, Bobby puts up an ice wall between Logan and Stryker.
At a bar near Magneto’s prison, Mystique makes her move to seduce the prison guard, Laurio, with full access to carry out her plan to break Magneto out of prison.
In the dam at Alkali Lake, Stryker has Xavier captured. Stryker holds a personal grudge against Xavier, when Xavier couldn’t cure his mutant son Jason, and Jason tormented his wife to death. Stryker now makes use of his son’s brain fluids to create mind-controlling substances which he used on the teleporter Kurt to stage the President’s assassination, and now, Xavier.
Logan, Bobby, Rogue and John, along with some students, make their way to Bobby’s home. Bobby’s family doesn’t take well to his revelation that he is a mutant, especially his brother Ronny.
The next time Laurio enters Magneto’s cell was after Mystique had increased the iron levels in his blood. Magneto kills Laurio in the process of extracting the iron from his blood and escapes.
Back at Bobby’s house, Ronny had called the police on Bobby and the students. Logan gets shot in the forehead when he couldn’t put his “knives” down. John shows off how dangerous he can be by setting fire to all the police cars. Suddenly, a storm rains down on them. Storm and Jean arrives in the X-Plane to retrieve the students.
The X-Plane is being pursued by air force fighter jets. One of the latter’s missiles hit the X-Plane and Rogue is flung out of the plane. Kurt teleports Rogue to safety. Flying back to the school, they encounter Magneto and Mystique.
Setting up camp, Magneto discusses his concerns with the X-Men. Stryker has duplicated Cerebro and has captured Xavier to operate it. They immediately head for Alkali Lake. John finds himself drawn to the dark side when he has a talk with Magneto.
Mystique disguises herself as Stryker to gain access into the dam and takes over the control room. Meanwhile, Stryker prepares Xavier to use Cerebro to destroy all mutants.
While Jean, Storm and Magneto make plans to split up, with Storm going to save the children and the others tracking down Xavier and Cerebro, Wolverine had taken off in search of his past. He encounters Yuriko, his female counterpart, right down to the claws and healing powers. They battle until Wolverine electrocutes Yuriko.
Magneto and Mystique carry on their search as Jean confronts Cyclops. Cyclops had been mind-controlled to attack Jean. Using her telekinesis against his optic blasts, they cause an explosion of power, damaging the dam. Suddenly, all the mutants feel mind-seering pain as Xavier proceeds to use Cerebro as instructed. Magneto manages to stop Cerebro and reprogrammes Cerebro to attack humans instead.
Jean and Cyclops reunite with Storm, Kurt and Wolverine. Storm and Kurt teleport into Cerebro to rescue Xavier. Meanwhile, Magneto kills Stryker and takes off in Stryker’s chopper with Mystique and their new recruit, John. Storm and Kurt manage to get Xavier out, but not Jason.
Two days later, Xavier pays the President a visit. Xavier would like the President to know about Stryker’s evil manipulations before delivering a speech “regarding the mutant threat”.
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