The immortal psychic mutant En Sabah Nur rules ancient Egypt until he is betrayed by his worshippers, who entomb him alive. En Sabah Nur's lieutenants, the Four Horsemen, die protecting and preserving him.
Awakening in 1983, and believing that without his presence humanity has lost its way, En Sabah Nur decides to destroy the world and remake it in his image. En Sabah Nur recruits new Horsemen, beginning with Cairo pickpocket Ororo Munroe.
In Berlin, mutant Raven Darkhölme, investigates an underground fight club and discovers mutant champion Angel, who possesses a pair of large feathered wings on his back, and the Nightcrawler, who can teleport. Raven rescues Nightcrawler and employs the services of underground black marketeer Caliban to safely transport him to the United States. En Sabah Nur locates Caliban, with Caliban's enforcer Psylocke siding with him and leading him to Angel. Both become Horsemen, with Psylocke's powers enhanced and Angel's wings transformed into metal.
Meanwhile, Alex Summers takes his teenage younger brother Scott, whose own mutation for shooting optic beams from his eyes is manifesting, to Professor Charles Xavier's educational institute in Westchester County, New York, where Xavier andHank McCoy will teach him how to control his abilities. Scott meets Xavier's protégé Jean Grey, and the two develop an attraction over the fact that they both cannot fully control their mutant powers. Raven brings Nightcrawler to the institute, and informs Xavier about the threat of En Sabah Nur, leading Xavier and Alex to consult with Moira MacTaggert, who has been researching the legend of Nur, to learn more about him.
In Poland, Erik Lehnsherr lives with his new wife and daughter, Nina, but when authorities attempt to capture him for the incident at the White House, his family is accidentally killed in the crossfire. En Sabah Nur approaches the heartbroken Erik and takes him to Auschwitz, where he upgrades his powers. Erik destroys the camp and joins Sabah Nur, completing his new Four Horsemen.
En Sabah Nur hacks into Xavier's mind while Xavier is using the mutant-locating computer Cerebro, and co-opts Xavier's powers to force all global superpowers to launch Earth's entire nuclear arsenal into space to prevent interference. En Sabah Nur and his Horsemen arrive in the mansion and kidnap Xavier. Attempting to stop them, Alex accidentally causes an explosion that destroys the mansion. Peter Maximoff – having learned that he is Erik's son, and hoping that Xavier can help to find him – arrives in time to use his super-speed to evacuate the mansion, but Alex dies in the blast during his heroic sacrifice. William Stryker's forces subsequently arrest Hank, Raven, Peter, and Moira, believing them to be involved in En Sabah Nur's attack, and take them to the Weapon X facility for interrogation. Scott, Jean and Nightcrawler covertly follow and liberate their comrades with help from Stryker's brainwashed experiment Logan, whose mind Jean frees... but on the cost ofamnesia. At En Sabah Nur's behest, Erik uses his powers to control Earth's magnetic poles, causing widespread destruction across the planet and mass casualties. Following a telepathic distress call secretly sent by Xavier, the others arrive in Cairo and battle the Horsemen, managing to rescue the professor before his mind was transferred into En Sabah's body. Angel is killed by Apocalypse for failure. Erik and Storm are convinced to turn on En Sabah after spotting his true colours through his brutal attack on Angel and Mystique, and keep him occupied while Xavier fights him in the astral plane. Finally, Xavier encourages Jean to unleash the full might of her powers against him. Letting go, Jean uses her unchecked power to cast Apocalypse into the astral plane, presumably, for all eternity. In the ensuing chaos, Psylocke escapes.
In the aftermath, Erik helps reconstruct the school, but turns down Xavier's offer to stay and help teach. Scott, Jean, Hank, Ororo, Nightcrawler, Peter and Raven become the new "X-Men" and begin training for the battles ahead by having a Danger Room training session against Sentinels.
In a post-credits scene, the abandoned Weapon X facility is infiltrated by a paramilitary team that begins retrieving data on Stryker's mutant research, including an X-Ray and a blood sample marked "Weapon X" on behalf of the Essex Corporation.
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