The film opens in Poland, 1944, and recreates the same introductory scene featured in X-men (2000). Erik Lehnsherr, just a boy, follows the procession of other captive Jews being rounded up by the Nazis. Erik and his parents are separated; with Erik on one side of a fence and his parents on the other. Angrily he reaches for them, and using his magnetic superpowers, bends the fence into a crumpled mess. A Nazi raises his rifle and butts Erik in the face, knocking him out cold. Erik comes to and is led to the office of Dr. Schmidt (Kevin Bacon) who had watched the events from earlier from his window. Schmidt goads Erik into showing him his magnetic powers. He places a Nazi-marked coin on his desk, and asks Erik to move it using his mutant ability. Erik is unsuccessful and pleads for understanding from Schmidt. Schmidt frowns and calls in two armed guards who are holding Erik's mother captive. Schmidt tells Erik that he has until the count of three to move the coin. Erik struggles, and makes no change on the coin's position. Schmidt loads his Ruger and on the count of three shoots Erik's mother. Erik loses control, and tears apart every bit of metal in the office, including the two soldiers' helmets, and their heads within them. Schmidt laughs, happily, and gives Erik the Nazi coin.
New York, 1944. A ten-year old Charles Xavier hears a commotion in his palatial family home. He heads downstairs into the kitchen where he finds his mother rummaging through the fridge. Happily his mother offers Charles a hot cocoa. Charles demands to know who she is because his mother has never stepped foot in that house and never made cocoa for him. Defeated, a young Raven (AKA Mystique),reveals herself to Xavier. Rather than showing disgust Xavier welcomes Raven into his home, citing his happiness upon finding someone else like him.
Geneva, 1962. An older Erik (Michael Fassbender) sits in a hotel room, and studies a map and diagram tacked to the wall, upon which is pinned a drawing of Schmidt. He spins the Nazi coin in his fingers methodically and propels it across the room, straight into Schmidt's forehead. Erik heads to the bank, and speaks to the manager. Erik produces a gold brick embossed with a Nazi seal. The bank manager feigns reluctance to accept the brick, as possession of a Nazi brick is against the law. Erik asks the manager for the location of Schmidt. The Bank Manager feigns confusion. Erik tells him that the brick is all that is left of his family's possessions: jewels, watches, and gold tooth fillings. The bank manager reaches for the alarm, but not before Erik stops him. Erik crosses the room, pushes him back in his chair, and proceeds to rip the banker's gold fillings from his teeth. The banker finally admits Schmidt's location: Argentina. Erik thanks the cowering banker and promises to return, and kill him, if the information is incorrect.
Las Vegas, 1962. CIA agent Moira MacTaggert and her partner sit in an undercover sedan across the street from the Hellfire Club. They watch as dozens of high-ranking military officials and politicians flood into the building, followed by a stream of scantily clad girls and prostitutes. Moira, desperate to get in, strips down to her skivvies and sneaks in. She tails Colonel Hendry (Glenn Morshower) and his escort Emma Frost (January Jones) as they make their way to a private booth. Moira parts the booth's curtain and finds the booth empty. She locates a hidden switch which swivels the booth 180 degrees into Sebastian Shaw's hidden office. She peaks through a hole in the wall. Inside she sees Shaw (Kevin Bacon), Emma Frost, Azazel (Jason Flemyng), and Riptide (Alex Gonzalez). Shaw attempts to convince Colonel Hendry to place Russian-targeted missiles in Turkey. Hendry refuses, and is violently forced into a wall by Riptide and accosted by a glittering, diamond-skinned Frost. Hendry eventually relents and agrees to do Shaw's bidding. Azazel grabs Hendry's hand and the two disappear in a puff of red smoke. Moira, shocked by the impossible things she's seen returns to her car and calls the CIA director (Matt Craven) who is sitting in a massive war-room surrounded by various politicians and heads of state. He jokingly dismisses Moira's claims, citing that Hendry could not have been in Las Vegas because he is sitting in the very same room at that moment. He also makes fun of her claims of seeing "disappearing men" and "sparkly dames", and hangs up on her. Colonel Hendry votes to place missiles in Turkey. Moira, in disbelief, tells her partner that she needs to find the brightest mind in mutation.
Argentina. Erik crosses rolling hills and finds himself at an old cantina, wherein sit three fair skinned, blonde men. He orders a beer, drinks it, and remarks that it is German. The two men behind him happily praise the superiority of German beer. Erik peers at a framed photo of three men hanging on a wall, perched on the back of a boat docked in Miami. Two of the men in the photo are sitting at the table behind him, and the third is Sebastian Shaw (AKA Schmidt). Erik asks the two men at the table what they did in Germany. One remarks that his father was a pig farmer, while the other's was the finest tailor in Dusseldorf. Erik shares that his family was killed by pig-farmers and tailors, and shows the men the serial number tattooed on his arm. One of the men immediately pulls a knife whilst the bartender produces a rifle. Erik easily dispatches the three men: one with the gun and the other two using the same knife.
Miami. Shaw sits on his opulent mega-yacht with his crew of mutants. Colonel Hendry arrives to receive his money for placing missiles in Turkey. Feeling threatened, Hendry reveals a grenade to Shaw, and threatens to pull the pin if Shaw does not show him the respect he deserves. Shaw plucks the grenade from Hendry's hand and pulls the pin himself. Shaw demonstrates his own mutant power: the grenade explodes, but Shaw somehow consumes the energy of the blast into his own body. Seconds later he appears completely unharmed, and explains that his power allows him to absorb kinetic energy and dispel however he pleases. He reaches over and simply touches Hendry. Hendry glows white, and presumably explodes.
Xavier and Raven are in Oxford, where Xavier is holding scientific lectures on mutation. He chugs beer at a pub while Raven (Jennifer Lawrence), posing as Xavier's sister watches jealously. Xavier hits on various women, whilst using his genetic knowledge as pick-up lines. Raven tires of Xavier's drunken flirtation and begs that they leave. As they are about to, Moira appears, and asks to have a word with Xavier. Xavier reads her mind and agrees to meet with her superiors. The next day Xavier, Raven, and MacTaggert sit in a small conference room populated by various CIA big-wigs, who all dismiss Xavier's powers as a magic trick. Xavier ups the ante and asks how he must know that the USA has missiles, aimed at Russia, in Turkey. Angry, MacTaggert's bosses accuse her of bringing a spy into the CIA. Tired of fighting Raven immediately changes her form to that of MacTaggert's boss. All in the room are stunned, including the mysterious Man in Black (Oliver Platt). The Man in Black invites Xavier to his secret compound in Virginia. While there Xavier and Co. meet a young Hank McCoy (Nicholas Hoult): a child prodigy who graduated Harvard at fifteen and now designs supersonic jets for the military. Xavier reads Hank's mind and is happy to find that he is a mutant. This upsets Hank who, to this point, has not told his superiors of his mutation. He takes off his shoes and socks, revealing large feet with opposable toes, with which he is capable of incredible acrobatics. He develops a small crush on Raven, who returns the feeling.
Miami. Erik sneaks onto Sebastian Shaw's yacht. Shaw sits on the deck with Emma Frost, Riptide, and Azazel. Shaw wears a peculiar-looking Russian made helmet which Shaw had made to repel telepathic intrusion. Erik draws a gun on Shaw but is immediately overpowered by Frost in her diamond form. He is tossed overboard. Seconds later bright lights appear on the starboard side of the ship. CIA boats are moving in on Shaw. Xavier is at the helm reading minds from afar. Emma Frost, herself a telepath, blocks Xavier's power, creating white-noise. Riptide, using his wind-power, easily tosses a trio of Zodiacs heading for the yacht. Erik appears in the water, unharmed, and grabs hold of the ship's anchor which he uses to tear the ship's upper floors apart. Shaw, Frost, Riptide and Azazel flee below deck where a detachable submarine sits. The sub detaches from the boat and sets off. Erik magnetically attaches himself to the sub, and trails it, but is soon dragged underwater. Xavier, sensing Erik's presence jumps in after him, convinces him that his current course of action will cause him to drown, and helps Erik let go of the sub.
The CIA, now working in conjunction with Xavier, Erik, and MacTaggert run a field operation in Russia. A Russian general (Rade Serbedzija) is due to meet with Sebastian Shaw at his vacation home. Shaw's personal car arrives, but instead of Shaw Emma Frost steps out. She explains that Shaw is busy elsewhere and was unable to make it. The CIA handler says that the mission is a no-go, as their target is Shaw - not Frost. Erik ignores the order and storms the mansion singlehandedly, taking down guard after guard. Xavier, worried for Erik, follows. The two reach the master bedroom where they find the Russian general in a trance, believed to be making love with Emma Frost who sits across the room, rolling her eyes. Frost quickly changes to her diamond form, explaining that it's properties make her impervious to Xavier's telepathy. Erik forces her against the bed's metal frame and contorts the metal into a cage. He chokes her violently, until she finally gives up, and returns to her human form. Xavier reads her mind and learns Shaw's location. Emma tells them that Shaw will kill her for what she's told them.
Back at the Secret CIA installation Hank has retrofitted one of the facility's spherical satellite antennas so that it can amplify Xavier's telepathic abilities. Inside of the antenna a primitive version of the first three films' "cerebro" sits. Xavier climbs into the apparatus and receives visions of various mutants across the world. Using this data Xavier and Erik set out to find various mutants. They find Angel Salvadore (Zoe Kravitz), an exotic dancer with the unique abilities of sprouting insect wings from her back, and spitting acid. Sean Cassidy (Caleb Landry Jones) who is capable of producing supersonic screams. Alex Summers (Lucas Till) who is able to produce plasma rings from his body. Darwin (Edi Gathegi) who can adapt his body to survive in any environment. Lastly the pair comes to a bar where Logan (Hugh Jackman) swigs booze and puffs on a cigar. Erik and Xavier approach him, and half introduce themselves before Logan tells them to "go fuck yourself!" They leave without him. The new recruits playfully show off their powers to one another at the secret CIA installation. Cassidy dons the moniker "Banshee" and demonstrates his ability by shattering a pane glass window. Angel demonstrates her ability to fly and spits acid at a statue standing in the courtyard. Alex reluctantly demonstrates his plasma ability and fires plasma bursts through the courtyard, slicing the statue in half. He is given the nick-name "Havok". Darwin submerges his head in a fish-tank and immediately sprouts gills. Xavier and Erik go to meet the recruits and are disappointed by the team's antics and lack of professionalism. Raven asks for forgiveness and dons them both with their nick-names. Xavier will be "Professor X" and Erik will be "Magneto."
The recruits continue to stir in the secret installation, when explosive thumps from outside distract them. It's Shaw, Riptide, and Azazel. Riptide first creates a tornado, which destroys Cerebro. Azazel teleports in and out of the courtyard, where he grabs numerous CIA agents, teleports them high into the air, and drops them to their deaths, including the Man in Black. Shaw enters through the front door, and demands to know where the mutants are being kept. Dozens of CIA guards appear and fire on Shaw. Shaw absorbs every shot into his body, including a few RPG explosions, and forcibly expels it, destroying the room and all it's inhabitants. With all the humans dead, Shaw introduces himself to the recruits. He gives a compelling speech of how humanity cannot accept mutants and manages to convince Angel to come with him. Darwin, frustrated, exchanges a brief glance with Havok, and tells Shaw that he will come too. He grabs hold of Angel, forms an armored shell over his back, and tells Havok to shoot. Havok aims a well placed blast directly at Shaw, but Shaw simply consumes the energy, with no injury. Riptide and Azazel take Angel away from him while Shaw replaces Havok's energy upon Darwin. Darwin consumes the energy, grows silvery and scaly, and bursts into a ball of white light. Shaw, Riptide and Azazel leave with Angel.
Xavier, Erik and MacTaggert arrive in the morning to find the CIA facility mostly destroyed and what's left of the recruits sitting amongst the rubble, all saddened by Angel's betrayal and Darwin's death. Many don't want to go home. Xavier comes up with an idea. They all return to Xavier's childhood home. There they immediately begin training to improve their powers. Hank invents a paragliding harness, when worn by Banshee, allows him to use his supersonic screams to achieve flight. "Havoc" dons an invention which channels his plasmatic power and focuses it in a single direction. Xavier seeks to improve Erik's magnetic ability by reading his mind. In his mind Xavier discovers a singular happy memory, of his mother, which brings tears to Erik's eyes. Erik is now compelled by positive energy is able to control metal even greater than when he was compelled by anger. Xavier commends him on his power and tells him that he might've been able to lift Shaw's sub had he been using the proper motivation. Raven, now codenamed Mystique, finds that she requires so much attention to maintain her human form that it weakens her reflexes and athleticism. Erik asks her why she hides when her mutant form is far more desirable. Eventually Mystique develops feelings for Erik, who does not return the sentiment, arguing that she is too young for him. She jokingly changes to an older version of herself (Rebecca Romijn) before changing back. Hank, repulsed by his mutated feet synthesizes a chemical from Raven/Mystique's blood which will rid him and Raven of their physical imperfections. He tries to convince her to inject herself, but she refuses, arguing that her mutant form is her true form. He injects himself. Initially his feet change form from animalistic opposable digits to typical human feet. The cure is short-lived. His feet grow large and furry, along with his arms, body, and face.
Shaw, now in Russia, meets with the same Russian general. He convinces the general to place missiles in Cuba. Back at CIA headquarters, Emma Frost sits in an interrogation room while two CIA officials argue that she won't tell them anything about Shaw's location. Annoyed, and feeling betrayed, Emma scratches a ring into the sound-proof glass and speaks to the men face-to-face, and explains that Shaw is headed to Cuba. John F Kennedy gives his famous Bay-of-pigs speech over the TV, and warns humanity that if the Soviets park their ships near Florida, this will be the start of World War 3. It is surmised that Shaw's plan, all along, has been to destroy humanity through nuclear war, and rebuild society with him as it's mutant leader.
Inside of Shaw's sub he has donned his protective helmet to shield himself from telepathic intrusion. He tells Riptide to max out the radiation coming from the submarine's nuclear engine. He intends to absorb the submarine's massive radiation, using his power, and then expel it like a nuclear bomb that will destroy humanity.
The "X-men" go in search of Hank, whose lab is destroyed. They discover a note saying that he's gone back to the CIA to pick something up and that there's a present sitting in a box waiting for them. They open the box which contains yellow-and-black flight suits. They don the suits and make their way to the CIA airport where Hank's "X-Jet" sits in a hangar. Hank arrives, revealing his blue fur, thick appendages, and animalistic attitude. Erik jokingly teases Hank's appearance, for which Hank nearly chokes him to death. They all board the X-Jet and fly out to Cuba. In the bay both American and Russian fleets sit across from one another - their big guns and rockets trained on each other. On a radar screen an American ship captain draws an invisible line of no return. If a Russian ship passes this line, the Americans will fire on them. A single Russian ship goes silent as it approaches the line. It doesn't return radio transmissions from either fleet. On board Azazel is shown to have killed all those on the main bridge. The Americans prepare to fire, when the X-Jet screams above them. Xavier, on board, enters the mind of one of the dying men on the silent Russian ship, and sees Azazel. The Americans watch as the silent ship approaches the line, while the Russians desperately attempt to stop the ship. Xavier quickly enters the mind of a ship mate on another Soviet ship. He forces the man to cross the bridge, and fire a missile at the silent ship. The ship explodes, just a few feet short of the invisible line. Confused, both the Americans and Russians hold their fire. On board the X-Jet, the team searches for any sign of Shaw, lamenting that the jet does not have Sonar. Banshee realizes that his supersonic screams could potentially act as sonar. He dives into the water below, and sends a sonar pulse through the water, and finds Shaw's sub. He relates this information to Xavier telepathically. Erik lowers himself beneath the X-jet. He searches the water, and using his magnetic power he grabs hold of the submarine and lifts it out of the water, hundreds of feet in the air. Awestruck the Russians and Americans turn away from one another, and aim their weapons at Xavier and Shaw's teams. The sub hovers for a few seconds as Erik leads it to the beach. Riptide appears on top of the sub and create two huge, funneling waterspouts which cause the X-Jet to spin out of control. Both the sub and jet crash onto a nearby beach. A massive fight erupts between the X-men and Shaw's team. A three-person battle ensues between Azazel, Havok, and Beast. Angel and Banshee engage in an airborne dogfight. Erik, MacTaggert and Xavier lay in the remains of the X-Jet. Riptide appears, and is quickly flattened by a huge chunk of the sub which Erik sends falling on top of him. Erik runs inside of the sub, where he searches for Shaw with the aide of Xavier's telepathy. He makes his way into the ship's engine room where he discovers Shaw, newly saturated with radioactive power. The engine room's doors shut, cutting off Xavier's telepathic power.
Inside the engine room Shaw demonstrates his power. He merely touches Erik with a finger and sends him flying across the room. The glass entryway shatters, allowing Xavier to re-communicate with Erik. As Shaw is about to deliver a killing blow Xavier stops time for Shaw, allowing Erik to remove Shaw's helmet. Xavier pleads with Erik to not kill Shaw. Erik takes Shaw's helmet and places it on his own, blocking Xavier's telepathy. Erik draws the Nazi-branded coin from his pocket, given to him by Shaw when he was a child. He slowly raises the coin to Shaw's eyeliner. He repeats the phrasing used by Shaw on their first meeting, counting 1… 2… 3… before he slowly pushes the coin through Shaw's forehead, which kills him. Erik exits the submarine wreckage, with Shaw floating like a doll a few feet ahead of him. He unceremoniously drops Shaw's corpse to the ground. He explains to all those left on the beach, both good and bad, that the men on the ships in the distance are at war with mutants and suggests that they all unite to destroy them.
The American and Russian ships aim their guns at the beach and prepare to fire. Moira flees to the radio on board the X-Jet and pleads that the men on board turn their guns away. Her request is ignored, and all at once every single ship in the bay fires at the beach. Erik raises his hand and catches each missile in midair, spins them all around and guides them back to their point of origin. Xavier angrily attack Erik, who losing focus causes a few missiles to explode in mid-trajectory. Erik grabs the remaining missiles and continues their course to the ships. Xavier attempts to break Erik's focus again, and causes a few more missiles to deviate and explode. Finally MacTaggert, guns drawn, bolts toward Erik, firing. He easily deflects the bullets; one ricochets and hits Xavier in the spine. Xavier howls in agony, and slumps on the ground. Erik's focus is lost, and the last missiles explode before reaching the ships. Erik angrily lashes out at MacTaggert and screams at her for shooting Xavier. Xavier, weak, tugs at Erik's leg and tells him that it was his fault. Holding back tears Erik asks the other mutants to join him. Mystique tearfully approaches Erik and then kneels to see Xavier. Xavier, in pain, tells her to do what she wants, and to go with Erik. Erik, Mystique, Angel, Riptide, and Azazel join hands, and disappear in a puff of smoke. Xavier doubles over in pain, shouting that he can't feel his legs.
Back at the Xavier mansion, Xavier and MacTaggert meander through the gardens. Xavier sits in a wheelchair. She tells him that he is a professor now, since he finally has students, and that she will keep his, and the school's location secret. Xavier responds that he knows she will. The two kiss, and blankness passes over her face. We transition to CIA headquarters, where MacTaggert blankly stares at her bosses, who all eagerly seek to learn Xavier's location. She smiles, dimly, and tells them that she can barely remember anything. There are a few snippets of trees, sunlight, and water, but nothing definitive… and a kiss. Her bosses roll their eyes. Downstairs a massive explosion rocks the building. Emma Frost sits alone in her holding cell. The metal door twists and contorts and is sucked from it's hinges. In steps Erik, decked out in Shaw's helmet, now painted red and purple, and a long red suit and cape. He calls himself Magneto and he has come to rescue her. Magneto's brotherhood stands in the doorway, ready for the new recruit.
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