In 3600 BC, the formidable mutant En Sabah Nur (Oscar Isaac), known as the first of his kind, rules over ancient Egypt. As his health declines with age, he faces the looming specter of death. Nur possesses formidable destructive powers, such as Telekinesis, Cyberpathy, teleportation, and the unique ability to amplify the powers of other mutants.
During a pivotal ceremony, Nur attempts to transfer his consciousness into a younger mutant's body, seeking to gain his healing factor for immortality. However, betrayal strikes as conspirators cut his sunlight access, halting the process prematurely. This results in the tragic demise of his followers and his own entombment within a collapsing pyramid. Just before his death, one loyal follower secures Nur's new body in a protective casket, shielding it from the falling debris.
Fast forward to 1983, a devoted cult discovering the location of his tomb inadvertently completes the transfer when sunlight shines upon it, awakening Nur. Awakening with a strong belief that humanity has lost its way without him, his return sends shockwaves felt across the globe. Nur, now with a resolute intention to devastate the world and create a new one in his image, begins to recruit his followers. Among them is Ororo Munroe, aka Storm (Alexandra Shipp), a Cairo pickpocket capable of controlling the weather, whose powers he enhances.
Meanwhile, in East Berlin, Raven, also known as Mystique (Jennifer Lawrence), is on a mission to investigate an underground fight club. Here, she stumbles upon Angel ([Ben Hardy]), a mutant champion with magnificent feathered wings, and the teleporting Kurt Wagner, also known as Nightcrawler ([Kodi Smit-McPhee]). In a bid to rescue Kurt, Raven enlists the help of Caliban ([Tomas Lemarquis]), a black marketeer, to transport him to America.
Encouraged by Nur's burgeoning force, Raven’s journey escalates when she meets Psylocke ([Olivia Munn]), who leads Nur to Angel. Nur enhances both Psylocke and Angel's powers, transforming Angel's wings into formidable metal appendages. Meanwhile, Alex Summers, known as Havok ([Lucas Till]), discovers that his younger brother, Scott Summers, or Cyclops ([Tye Sheridan]), has begun manifesting his own powers to unleash destructive optic beams. In a moment of concern, Alex brings Scott to Professor Charles Xavier ([James McAvoy]), the world's most powerful telepath, at his institute in Westchester County, hoping that he and Hank McCoy, aka Beast ([Nicholas Hoult]), can guide Scott in controlling his abilities.
Scott and Jean Grey ([Sophie Turner]), a fellow student with developing powers, form a romantic connection, while Raven successfully takes Kurt to the institute. As Apocalypse's rise sends tremors around the globe, Xavier and Alex turn to Moira MacTaggert ([Rose Byrne]) for insight into Nur's past. With no memory of her previous encounters with Xavier due to a mental purge, she shares her findings on Nur's history, revealing he once had a team of four protectors he called the Horsemen of Apocalypse.
Meanwhile, Jean grapples with nightmarish visions of impending destruction. In Poland, Erik Lehnsherr, also known as Magneto ([Michael Fassbender]), attempts to live a peaceful life with his family. After a horrific incident involving militia forces leads to the loss of his loved ones, Erik retaliates with devastating force. Nur, upon learning about Erik through the internet, approaches him at Auschwitz, where his powers first emerged, leading Erik to join his cause after obliterating the camp.
Raven frantically informs Xavier about Erik's resurgence, prompting him to delve into Cerebro to locate him. However, Nur infiltrates Xavier's mind while he is using Cerebro, seizing control and forcing global superpowers to launch their nuclear arsenals into space to avoid any interference. As Nur and his followers invade Xavier’s mansion, chaos ensues, resulting in Alex inadvertently triggering an explosion that decimates the building and leaves Peter Maximoff, also known as Quicksilver ([Evan Peters]), scrambling to save the students just in time.
Following this disaster, Colonel William Stryker ([Josh Helman]) captures Hank, Raven, Peter, and Moira to interrogate them in a military facility. A covert operation by Scott, Jean, and Kurt leads them to rescue their comrades with the help of Weapon X (Wolverine/Logan, portrayed by Hugh Jackman), whose memories Jean partially restores.
Meanwhile, Nur orchestrates widespread destruction globally, all while secretly intending to transfer his consciousness into Xavier's body. As a last effort, Xavier discreetly sends a telepathic call for help to Jean and their team, prompting them to confront Apocalypse and his Horsemen in Cairo to rescue Xavier before it’s too late. In the climactic battle, Apocalypse faces defeat as Jean unleashes her full powers, vaporizing him amidst the chaos. Psylocke narrowly escapes the mayhem.
As the dust settles, Xavier works to restore Moira's memories, and he rekindles their relationship. Meanwhile, Erik and Jean aid in rebuilding the school, though Erik declines Xavier's offer to stay and teach. In a poignant twist, Peter decides to hold off on revealing his lineage to Erik. Together, as the new X-Men, Hank and Raven begin training recruits, including Scott, Jean, Ororo, Kurt, and Peter.
In a chilling post-credits scene, mysterious men in suits invade the Weapon X facility, hunting for Stryker's research and revealing an X-ray and blood sample marked "Weapon X," hinting at further dangers lurking ahead.
