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NOTE: This spoiler was sent in by The Petri Dish Kid who says... "It's awesome! Definitely better than the first movie in my opinion and on par with the second. The movie is good except that it cuts from here to there really quickly so my sequencing may be a little off. The last 1/2 hr or so is definitely the highlight of the film."
The movie starts off 20 years ago with Charles Xavier (Patrick Stewart), who is not in a wheelchair, and Erik Lensherr (Ian McKellan), arriving at the Grey residence. They are there to meet a prospective student, Jean Grey. The CGI done on Stewart and McKellan is awesome as they do look very much younger.
Jean's parents are a bit apprehensive about their daughter attending Xavier's school and her father sees her mutation as a kind of disease but Xavier asks to meet Jean alone. They talk and he tells her she is special and just like them. She seems doubtful about it and levitates the cars parked outside her home with her mind. Stan Lee and Chris Claremont make cameos as a guy who's watering the flowers but the water flows upwards out of the hose instead and a guy who's lawnmower levitates, respectively.
Cut to 10 years later and we see a young Warren Worthington III attempting to cut something out of his back with a variety of knives. His father knocks on the door and ask him what's wrong. Warren hastily stows away the knives before his father forces his way in and sees blood, feathers and a reflection of his son's back in the mirror. You can see the wings that are about to sprout out.
Now we cut to the danger room sequence and you see Wolverine (Hugh Jackman), Storm (Halle Berry), Bobby Drake/Iceman (Shawn Ashmore), Kitty Pryde/Shadowcat (Ellen Page), Rogue (Anna Paquin) and Peter Rasputin/Colossus (Daniel Cudmore). Lasers are flying everywhere, zapping everything and the X-Men are ducking around. Colossus and Rogue hide behind a car and he touches her and she turns to metal just in time for a huge boulder to bounce off them and hit Wolverine in the face. His face is scratched badly but it heals and he is pissed. A missile is heading straight for Iceman and Kitty and he freezes it. But he is caught off-guard when another missiles launches for him and Kitty grabs him and the missile passes through. Rogue sees this and she is clearly jealous.
Wolverine and Storm take cover behind a car they talk a bit about the situation and she grabs him and spins off just as the...wait for it...SENTINEL!!! attacks. Storm calls for a retreat but Wolverine wants to face the sentinel, he gets Colossus who "metals up" and they do the Fastball Special where Colossus swings Wolverine towards the sentinel. We see the sentinel head drop on the ground and Wolverine walks out from behind it and goes, "Class dismissed."
Next we see Bobby and Rogue in an argument about her not being able to touch him.
From here on my memory of the sequence of events might be out of place so just bear with me.
The next shot shows Beast reading a magazine and like in the cartoons, he is sitting upside down on the ceiling when an aide comes in and tells him that the meeting is ready. We then go to the president and his aides who are watching a footage of Mystique, who was captured. They are questioning her about the whereabouts of Magneto and she refuses to answer. The president hands Beast a file about Worthington Labs developing a cure for the Mutant X Gene. It seems that this was what Mystique was after when she was captured.
Sometime around here we see Cyclops (James Marsden) who is still very distraught over Jean's death and he keeps hearing her voice calling his name. He packs his back and decides to go to Alkali Lake. On the way out Wolverine stops him and trys to talk some sense into him but Cyclops won't listen.
Beast pays Xavier a visit and talks about the cure. Storm is against it but the Xavier tells her that they're already announcing it. Flash to Alcatraz Island which is one of the bases for Worthington Lab that is developing the cure for the mutant gene. This is also where they are keeping the boy Jimmy AKA Leech who is the source of the cure. Warren Worthington II announces the cure on TV. Rogue sees this and she confronts the others but Storm tells her that there's nothing to cure because nothing is wrong with them.
Magneto attends a mutant meeting of sorts where they are debating the cure. Magneto takes to the stage flanked by Pyro and talks about the humans forcing the cure on them. After his little speech he is confronted by some mutants, Arclight, Callisto and Quill. Callisto can sense the powers of other mutants and he asks her to find one for him. We see a convoy transporting some mutant prisoners, Mystique amongst them.
Cyclops gets to Alkali Lake and he still hears the voices. He looks into the water and the voices get too much for him so he rips off his ruby quartz glasses and shoots his beam into the water. Suddenly a huge whirlpool is created a the force from it throws him to the ground. There is a bright light and as it clears we see Jean Grey. The 2 embrace and she asks Cyclops to take out his glasses, he is reluctant but she tells him she can control his powers. He does and she holds back the beam and they kiss but then her face turns dark and menacing and we hear a shout and the screen fades back to Xavier's school. A shockwave of sorts ripples through and everyone feels it and Cyclops is killed by Jean (damn!). Storm and Wolverine run to Xavier and he instructs them to go to Alkali Lake.
As the convoy is driving on the road, Magneto stands in their way. He flattens the first two cars and tosses them out of the way, tosses the back two and rips the container holding the prisoners. He goes in and frees Mystique, Multiple Man and the Juggernaut (Vinnie Jones, who is so hilarious in this movie). A security guard that was knocked out wakes and aims a gun at Magneto, Mystique takes the bullet but it turns out to be the cure. She is cured and Magneto leaves her, telling her, "You're no longer one of us."
We see a group of people lining up for the cure and Dr Kavita Rao is talking to Warren Worthington II about his son getting the cure. Warren Worthington III/Angel (Ben Foster) comes in and he is strapped standing up. As Dr Rao is about to inject him with the cure he stops her and pleads with his father who is unrelenting. He struggles and frees himself, speading his wings in the process. He tells his father it's not what he wants and breaks out the window and flies away.
Wolverine and Storm get to Alkali Lake and it's all foggy. Storm clears it up and they see stones floating around. Wolverine spots Cyclop's glasses floating when Storm yells for him. She's found Jean unconscious and they take her back to the mansion. Xavier explains that Jean survived X2's drowning because her powers enabled her to be cocooned in her telekinetic energy. He also talks about her being a very powerful mutant with split personality. One is the Jean Grey we know and the other is the Phoenix. He explains that he's put a series of mindblocks in her head to prevent the Dark Phoenix from emerging but Wolverine argues that that's not ethical.
Phoenix awakes and Wolverine is with her. They talk and start kissing passionately before Wolverine realizes that something is different about her. He questions her about Cyclops and she freaks out and tells him to kill her before she kills anyone else. He tells her that they can fix it but she switches to Phoenix mode and flings Wolverine away before escaping. Xavier is teaching a class about something to do with transferring one's consciousness into another body as he shows them a video of his good friend Dr Moira MacTaggert with a catatonic patient (IMPORTANT LATER!). He is interrupted by Storm and Wolverine and the 3 of them go back to Jean's old home. Callisto sense Jean's powers too and Magneto and his cronies go there as well. Magneto and Xavier go in to confront Jean while Quill, Callisto, Arclight and the Juggernaut stand guard.
Xavier tries to reason with Jean but she wouldn't listen, her face turns dark and scary and all hell breaks loose. Wolverine can't wait anymore and he charges in but is confronted by the Juggernaut. Storm faces off with Quill, Arclight and Callisto. Jean uses her powers to lift Xavier up from his wheelcar and to throw Magneto through the wall. It's a very powerful scene as Wolverine and Storm are getting their asses kicked. Xavier tries to reason with Jean but her powers are getting stronger and he is slowly getting vapourized. Magneto yells at her to stop but she doesn't and she blasts Xavier into ashes. Magneto is well and truly shocked but nevertheless he takes Jean with him. Storm and Wolverine finds Xavier's empty wheelchair and they break down and cry.
A funeral is held for Xavier. The X-Men are debating whether to close the school when Angel comes in seeking refuge and Storm tells them that the school will remain open. We see Kitty in her bedroom crying and Iceman comes to comfort her. He freezes a fountain and they go ice-skating. Rogue sees this and gets jealous again. She is preparing to leave the next day and Wolverine tells her to do what she wants for herself. Iceman can't find Rogue and he goes to where the mutant cure is given out. He is confronted by Pyro (Aaron Stanford) who eggs him on in a fight but Iceman walks away. Pissed off, Pyro blasts the mutant cure centre.
Wolverine goes off to find Jean because he is also hearing her voice. Magneto has gathered an army of mutants and they're hiding out in the forests. Wolverine rages through the forest before Magneto controls him and sends him flying out. We see the army swapping their metallic weapons for plastic guys fitted with the cure darts. Mystique now human has given them intel on Magneto's whereabouts. The army closes in but all the "mutants" turn out to be replicas of Multiple Man.
Magneto now sets his sights on Alcatraz and the destruction of the source of the cure, Leech. The best part of the movie now begins as Magneto storms the Golden Gate bridge, ripping a part of it off in order to connect the mainland with Alcatraz. The X-Men are getting prepared to face Magneto even though there's only 6 of them against his whole army. Magneto sends his "pawns" towards the army guarding Alcatraz and they shoot the mutants with the cure. Magneto's powers are useless against the plastic guns so he has Arclight send out shockwaves to destroy the guns. He then levitates cars from the bridges and Pyro lights them up and rains them down on the soldiers. It is now that the X-Men arrive! Awesome arrival by each one of the X-Men and they form a line in front of the army. More Brotherhood mutants charge and the fight is on. Juggernaut is sent to kill Leech and Kitty goes after him. She jumps him and pulls him down into the ground and that's when Juggernaut goes, "Do you know who I am? I'm the Juggernaut, bitch!" Kitty gets to Leech but her powers won't work and Juggernaut knocks his way in. He charges at them and they jump out of the way as he knocks himself unconscious on the wall. His powers don't work either. Storm faces off with Callisto and she throws Callisto down on a metal fence and electrocutes her.
Quill, Arclight and Pyschloke take Warren Worthington III and Dr Rao. Quill kills Rao and Arclight and Pyschloke throw Worthington off the building but not before Angel swoops down and saves his father wearing a pretty cool outfit (not the X-Men uniform though) looking smug. Wolverine sees some cure darts on the ground and he has a plan, he looks at Beast knowingly. Wolverine tells Iceman to go get Pyro, who's been itching to face off with him. The fight is awesome and Pyro gains the upper hand, blasting a huge fireball at and around Iceman. Iceman goes full ice mode and he grabs Pyro's wrists, freezes his arm and knocks him out. Wolverine and Colossus do the Fastball special again and Magneto controls Wolverine and throws him on the ground saying, "Do you ever learn?" Wolverine replies, "As a matter of fact I do," and Beast jumps out from behind Magneto and stabs him with the cure darts. Magneto falls to the ground, shocked. He is cured.
This is when Phoenix unleases her fury and the buildings around her start to vapourize and ash. Everyone is retreating and Quill, Arclight and Pyschlocke are ashed just as they are getting away. Wolverine tells Storm to go first as he is the only one who can stop the Phoenix. He walks up the steps to her as his uniform starts to ash and his skin peels off but re-heals itself again and again. He confronts her and tells her he loves her before stabbing her. She dies and he cries over her.
We see Kitty standing in front of the memorial to Jean, Cyclops and Xavier as Storm comforts her. Rogue returns and she is cured. She can touch Iceman now. We then see Angel flying over the Golden Gate bridge as a kid looks up.
The camera moves to a bunch of people playing chess and Magneto is by himself. His chess pieces are metallic and he moves his hand over one of them and it moves ever slightly. A blink and you'll miss it scene.
After the credits...we see Dr Moira MacTaggart and the catatonic patient. He wakes and says, "Hello Moira," and she says, "Charles?". As Xavier had explained earlier on, he has now put his consciousness into the catatonic patient.
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