There is an attempted assassination on the President of the United States by a mutant.
Logan goes to the abandoned military camp at Alkali Lake in search of any information about his past but finds nothing.
Meanwhile, the students of the Institute are on a field trip to the Museum of Natural History. The current exhibition discusses the topic of evolution, from the dinosaurs to present day homo sapiens and even mutants. Jean’s telepathy suddenly goes momentarily out of control. Television and computer monitors start flickering. Scott turns his attention from the class watching a cartoon presentation to check on Jean.
Scott: “Jean? You Okay?”
Jean: “Yeah, yeah. I’m fine, it’s just a...just a headache.”
Scott: “It’s not just a headache, is it? Listen, I...I wasn’t really sure how to say this but ever since Liberty Island you’ve been...”
Jean: “Scott I...”
Scott: “You've been different.”
Jean: “My telepathy has been off lately. I can’t seem to focus. I can hear everything.”
Scott: “Jean, it’s not just your telepathy. A month ago you had to concentrate just to levitate a book or a chair across the room and now when you have a nightmare the entire bedroom shakes.”
Jean: “My dreams are getting worse. Scott, I keep feeling something terrible is about to happen.” (Scott moves in to embrace Jean.)
Scott: “I will never let anything happen to you.”
Ororo interrupts them saying that Bobby and Rogue are missing. Using her telepathy, Jean finds them in the food court.
John is approached by two teenagers asking for a light. John taunts them, until one reaches out to snatch his lighter. With a wink of his eye, John causes the lit cigarette to go up in flames, catching the smoker’s shirt sleeve on fire. Bobby puts out the fire immediately with his powers. This display causes a commotion. Suddenly, all the people in the museum freeze, except for the students. Professor Xavier wheels into the scene and reprimands John. News of the assassination on television catches Xavier’s eye before Scott suggest they leave. Xavier wipes the memory of this incident from everyone’s mind.
Back in the Institute, the staff discuss the assassination incident. Scott thinks Magneto could be behind it, but Xavier dismisses it on the grounds that it would be “irrational” of Magneto. Ororo is worried the government might reintroduce the Mutant Registration Act. Xavier has been monitoring the assassin’s “erratic” movements with Cerebro and finally pinpointed his coordinates. Xavier sends Jean and Storm to find him.
Colonel Stryker joins the President in the Oval Office. He inspects the mark on the desk left by the assassin’s dagger. Stryker’s department had been “dealing with the mutant phenomena” before the current President. Senator Kelly (Mystique in disguise) joins them to discuss Stryker’s findings regarding the Xavier Institute. Stryker’s company built Magneto’s plastic prison, giving him access to interrogate Magneto to get information about the Xavier Institute. The President gives Stryker permission to “enter”, “detain” and “interrogate” the Xavier Institute without harming any of the students. Kelly (Mystique) tries to arrange a visit with Magneto with Stryker but is turned down.
Logan returns to the mansion. Rogue is the first to greet him, followed by a cold handshake by Bobby, who isn’t too happy that Logan’s back, given Rogue’s infatuation with Logan. Ororo exchanges hellos with Logan before taking her leave to prepare the X-Jet when Jean comes down the stairs. Scott interrupts Jean and Logan, still harbouring dislike for Logan. Scott kisses Jean on the lips goodbye before exchanging some words with Logan.
Logan approaches Xavier to ask the latter to read his mind again as Alkali Lake provided no answers. They are in Cerebro as Xavier has a lock on the assassin’s final coordinates. Xavier makes a passing mention that he could kill the assassin if he concentrated hard enough. Xavier has a request that Logan look after the students when he and Scott visit Magneto.
Mystique inflitrates Stryker’s office to gain access to Stryker’s information about Magneto. She stumbles upon Stryker’s plans for a reconstruction of Cerebro. In the mean time, Stryker’s assistant, Yuriko makes her way into the office. Mystique disguises herself as the office janitor to fool Yuriko and escape with her printed documents.
Jean and Ororo find the assassin named Kurt Wagner in an abandoned church. They ask him about the assassination but Kurt has no recollection. Ororo inquires about the scarred patterns on Kurt’s skin that Kurt inflicted upon himself. Jean finds an odd scar on the back of his neck.
Awaking from nightmares, Logan roams the Institute. He meets a student watching television who doesn’t sleep. He finds Bobby in the kitchen having a late night snack while looking for beer. Bobby points Logan to soda in the cupboards. Bobby ices Logan’s soda for him. They have a talk. Bobby’s parents do not know about his mutation.
Xavier has gone to talk to Magneto about the assassination. Magneto claims to have nothing to do with the assassination. After a chat, Magento lets slip about Xavier losing his X-Men. Magneto had told Stryker everything regarding the Institute. Xavier is gassed in Magneto’s prison cell as Yuriko enters the metal detection area. Cyclops stuns the guards with his optic blasts but is taken out by Yuriko who recovers quickly from Cyclops’ blast. Both Xavier and Cyclops are captured.
Special Ops forces break into the mansion. A few students are taken captive. Kitty (Shadowcat) escapes phasing through walls and into the escape tunnels. Theresa (Siryn) starts screaming and her sonic screams wake the enter student body. Most of the students are led to safety by the older students like Piotr (Colossus). Bobby and John go back to find Rogue. Logan is holding his own against the troops, killing many in his path. Logan sends the three into the escape path but Rogue wants to go back to help Logan. Logan encounters Stryker but before he can get some answers to his past, Bobby puts up an ice wall between them. They find their way into the garage and take off in Scott’s car headed for Boston.
Stryker has other plans for infiltrating. To obtain Cerebro, enough to recreate his own.
Mystique initiates her plan to free Magneto from his prison. Disguised as a hooker named Grace, she drugs the guard with full access to Magneto’s cell and injects liquid iron into his bloodstream. Magneto extracts the iron from the guard’s bloodstream and kills the latter in the process. With the aid of the iron, Magneto breaks out of prison.
Stryker brings his son with him to visit his captive, Xavier. Stryker has extracted the fluids from his son, Jason’s brain that acts as a “mind-controlling” substance, keeping his mutant troops under control, like Yuriko, and soon, Cyclops. It dawns on Xavier that Stryker arranged the attack on the President. Stryker instructs Jason to bring Xavier under mind-control now that Xavier has on a “neuro-inhibitor”.
Logan, Bobby, Rogue and John make a stop at Bobby’s house. Bobby decides to talk to his parents about his mutation. Bobby’s brother Ronnie is disgusted at Bobby’s display of his powers, and decides to notify the police department about the mutants in his house.
Jean and Storm have persuaded Kurt to come with them. On the X-Jet, Ororo takes a break and goes to talk to Kurt. Jean finds an active “com device”and learns of the whereabouts of Logan, Bobby, Rogue and John. She learns that the Institute was infiltrated, but most of the students escaped unscathed. Xavier and Scott are still unreachable. Jean and Storm make their way to Bobby’s house.
The police surround Bobby’s house. Logan has no intention of fighting them. One officer shoots Logan in the head. John defies police orders to “get down on the ground” and starts throwing fire around, torching cars and burning the officers. Rogue absorbs John’s powers to extinguish the flames as Logan recovers from the gunshot. The X-Jet arrives and they take off immediately.
Jason is successful in controlling Xavier’s mind. He recreates the illusion of Xavier returning to the mansion, finding only a little girl alone. Xavier takes her to Cerebro to find the other students. Stryker instructs Jason to order Xavier to kill all the mutants.
The X-Jet is followed by two fighter planes. In an effort to ditch them, Storm creates a series of tornados. She destroys the planes, not before one successfully launches two missiles. With her amplified telekinesis, Jean takes out one missile, but is too late to stop the other from damaging the X-Jet. Rogue is thrown out of the X-Jet, but is saved by Kurt. Magneto repairs the X-Jet and stops it from crashing.
They set up camp with Magneto and Mystique. They piece together Stryker’s purpose of infiltrating the mansion for Cerebro and the capture of Xavier to operate a duplicate Cerebro. Magneto needs the X-Men’s help to find Stryker’s base, thinking Logan would have the answers. They turn to an eavesdropping Kurt instead. Jean enters Kurt’s mind and finds the base underground. Later, Logan confronts Jean about his feelings for her. He kisses her but Jean pulls away, stating that she loves Scott.
The following morning they set out for Alkali Lake. Rogue still harbours hatred for what Magento did to her. John is the only one who interacted with Magneto. They discuss strategy on how to infiltrate Stryker’s base. Magneto sends Mystique down there, disguised as Logan. She gets into the impenetrable control room disguised as Stryker and locks it from inside. Magneto and the X-Men enter. Mystique has located the duplicate Cerebro. Magneto and Mystique are headed towards Cerebro to stop Stryker’s plans. Jean tags along to monitor them, as well as find Cyclops. Storm and Kurt go to rescue the captive students. Wolverine disappeared from the group to track down Stryker on his own.
Jean, Magneto and Mystique encounter Cyclops on their way. Jean deals with a mind-controlled Cyclops while Magneto and Mystique head towards Cerebro. While defending herself from Cyclops’ blasts, Jean’s telekinetic blast damages the dam. She manages to snap Cyclops out of the mind-control.
Scott: “Jean! No no no, it’s okay. It’s me.”
Scott: “I’m so sorry.”
Jean: “I thought I’d lost you.” (Scott embraces Jean and kisses her on her temples.)
Scott: “I’m sorry. I did see you but I couldn’t stop myself. I tried. I’m sorr—”
Jean: “Don’t be sorry.”
Scott: “I love you.”
Meanwhile, Stryker’s plans for Xavier proceed. Wolverine stumbles upon the laboratory where he was experimented on. He recalls some moments of his horrific past. Stryker finds him there, and Wolverine battles Yuriko, who had undergone the very same procedure. Wolverine finally kills Yuriko by injecting adamantium into her. John grows impatient and goes off by himself while Bobby and Rogue remain on the plane.
Magneto takes out the guards with ease and enters Cerebro. Xavier had already started his attack on mutants. Rearranging some of Cerebro’s panels, Magneto has Mystique disguise as Stryker to re-order Jason to order Xavier to kill humans this time around. Thinking that his plans have come to fruition, Stryker makes a quick getaway as the dam is becoming unstable. Wolverine is there to stop him, still demanding answers. He chains Stryker to the chopper and returns to save the X-Men. Magneto and Mystique take off in the chopper instead, taking John with them.
Storm has Kurt teleport the both of them inside to rescue Xavier. Storm lowers the temperature inside Cerebro until Jason relinquishes his hold on Xavier’s mind. Suddenly, the spillway floods. Storm and Kurt get Xavier out of Cerebro in time. Wolverine arrives to redirect the X-Men from the spillway and out via another exit. But the chopper is gone.
With Rogue at the controls, she pilots the X-Jet to where the X-Men are. But her crash landing has damaged the X-Jet, and they can’t take off again. Jean tells Cyclops to go help Storm. Suddenly the dam explodes. Realising the dilemma they are in, Jean decides to take matters into her own hands. She leaves the X-Jet, and controls it from the outside. She gets the X-Jet and everyone in it to safety, but sacrifices herself in turn. Cyclops is devastated seeing his fiancée commit suicide to save them.
They head to Washington D.C. as the incident has “gone beyond Alkali Lake”. Everyone except the President in the Oval Office is frozen as the X-Men make their appearance. Xavier intends to inform the President on Stryker’s unscrupulous acts, and the has the power to help prevent the war between humans and mutants.
Back in the mansion, no amount of words could comfort an anguished Scott. Even when Logan conceded and admitted that Jean did “make a choice” and it was Scott. The end sequence panned over Alkali Lake, and the flickering image of a Phoenix can vaguely be made out.
Alternate Ending Outtake
The scene opens exactly like the end scene in the Oval office. Except that Jean appears to be alive and enters the office, much to the astonishment of the X-Men.
Jean: (Whispers mainly in Cyclops’ ear.) “Sorry I’m late.” (She stands by Cyclops.) “Couldn’t find any parking for the X-Jet. Did I miss anything?”
Iceman: “You just missed--”
Cyclops: “Nevermind. You can have my box.”
Jean: (Addresses the President.) “Hi, how are you? Nice to meet you. Jean Grey.”
Xavier: (Laughs.) “She surprised you; she’s not really here.”
Wolverine: (To Jean.) “I saved you a spot over here.”
Jean: “Oh. Oh, okay.” (Drapes her arm around Cyclops and smirks at Wolverine.) “Well I’d like to be with my fiancé.”