In 3600 BC, the aged but powerful mutant En Sabah Nur rules ancient Egypt. Following a ceremony in which his consciousness is transferred into another man's body in order to gain his healing factor, he and his four followers, the Horsemen of Apocalypse, are betrayed by conspirators. In the process, his followers are killed and he is entombed alive.

In 1983, Scott Summers manifests his mutant powers to shoot concussive kinetic energy blasts from his eyes, so his older brother Alex takes him to Professor Charles Xavier's educational institute, hoping that Xavier and Hank McCoy will teach him to control his mutation. Scott meets and befriends Jean Grey upon arriving. In Egypt, En Sabah Nur is awakened by Moira MacTaggert while following a group of worshippers. He meets a mutant who can control weather, Ororo Munroe, and learns about humanity. Determined that humanity has lost its way, he plans to remake the world. Ororo becomes his follower after he enhances her power.

Meanwhile, in Communist Poland, Erik Lehnsherr lives happily with his wife Magda and daughter Nina. During the worldwide disturbances caused by En Sabah Nur, Lehnsherr uses his powers to save a coworker during an earthquake, alerting the Milicja Obywatelska. They hold his daughter hostage in the forest to lure him into turning himself in. As tensions rise, Nina heartbrokenly demonstrates her animal communication mutant powers, and the police accidentally kill her and her mother in the ensuing confusion. In despair, Lehnsherr kills the police. In East Berlin, shape-shifting mutant Raven, revered as a mutant hero following the attack on Washington, D.C., rescues Kurt Wagner from a cage fight and requests black marketeer Caliban to transport Kurt to America. He reveals Lehnsherr's situation to her, leading Raven to take Kurt herself in hopes of requesting Xavier to find and rescue Lehnsherr. En Sabah Nur recruits Caliban's assistant Psylocke and another cage fighter Angel, and enhances both of their powers.

En Sabah Nur finds Lehnsherr and takes him back to Auschwitz, showing him the true extent of his powers; Lehnsherr destroys the camp and joins En Sabah Nur. When Xavier contacts Lehnsherr, En Sabah Nur remotely accesses Cerebro and forces Xavier to make countries launch their nuclear arsenals into space to prevent interference. He and his Four Horsemen arrive at the mansion and kidnap Xavier. Alex attempts to stop them but causes an explosion that destroys the mansion. Peter Maximoff, having learned he is Lehnsherr's biological son, arrives and uses his super-speed to evacuate everyone except Alex, who got killed in the explosion prior to his arrival. Colonel William Stryker's forces, believing Xavier to be responsible, capture McCoy, Raven, Peter, and MacTaggert, and take them for interrogation. Scott, Jean, and Kurt secretly follow them and liberate their comrades using Stryker's experiment Weapon X, whose memories Jean partially restores.

Lehnsherr uses his powers to alter the Earth's magnetic field, causing destruction across the planet. En Sabah Nur plans to transfer his consciousness into Xavier's body to gain his psychic powers. Xavier sends a telepathic distress call to Jean and the others, who travel to Cairo to battle En Sabah Nur and his Four Horsemen. They rescue Xavier and flee in a plane. …

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X-Men: Apocalypse was announced by Bryan Singer in December 2013 via Twitter, before X-Men: Days of Future Past (2014) was released to theaters. In the same month, Simon Kinberg, Dan Harris, and Michael Dougherty were revealed by Singer to be attached to work on the film's story. According to Singer, the film would focus on the origin of the mutants and feature the younger versions of Cyclops, Jean Grey and Storm. Singer also said that he was considering Gambit and a younger version of Nightcrawler to appear. According to Kinberg, it would take place in 1983, and completes a trilogy that began with X-Men: First Class (2011). In September 2014, 20th Century Fox officially announced that Singer would direct the film. Singer has called the film "kind of a conclusion of six X-Men films, yet a potential rebirth of younger, newer characters" and the "true birth of the X-Men".
Singer said that Apocalypse is the main focus of the film. Kinberg said that the younger versions of Scott Summers, Storm and Jean Grey appearing in the film are "as much a part of the film as the main cast". He described Summers as "not yet the squeaky-clean leader", Storm as a "troubled character who is going down the wrong path in life", and Grey as "complex, interesting and not fully mature." Kinberg also said that the film delivers on the dramatic story and emotion of the last two films and that it acts like the culmination of the main characters portrayed by Lawrence, McAvoy, Fassbender, and Hoult. Kinberg said First Class, Days of Future Past, and Apocalypse formed a trilogy about Mystique, explaining,

She starts in First Class entirely on Charles' side, ends up following Erik, and we then find her in Days of Future Past and she's on her own because Erik is gone. She's on her own side in that movie but is drawn toward Charles by the end of the film and shoots Erik. Then in Apocalypse she comes back to Charles. There's a full circle narrative over the span of this little trilogy that is about Mystique from beginning with Charles in the mansion and ending with Charles in the mansion, but not as the same timid little girl we met in First Class.

Kinberg was paid $8 million for writing the script, the same amount he received for X-Men: Days of Future Past. The plot was partially inspired by the 1988 X-Men story arc "The Fall of the Mutants".
In October 2014, casting for X-Men: Apocalypse began. In November, Singer confirmed that Oscar Isaac would portray Apocalypse. In January 2015, Singer announced that Alexandra Shipp, Sophie Turner and Tye Sheridan would portray young Storm, Jean and Cyclops, respectively. Grace Fulton, who would go to play Mary Bromfield in the DC Extended Universe Shazam films, originally auditioned to play Jean Grey, but lost out to Turner. Ashley Benson was also considered for Jean Grey. The same month, Kinberg confirmed that Rose Byrne would reprise her First Class role as Moira MacTaggert in the film. In February, Kodi Smit-McPhee was cast as Nightcrawler and Ben Hardy was cast in an unspecified role. In March, Singer announced that Lana Condor was cast as Jubilation Lee. In April, Singer confirmed that Hardy would portray Angel, Olivia Munn would portray Psylocke, and Lucas Till would return as Havok. In May, Singer announced that the mutant Caliban would appear in the film. In July, Hoult revealed on Conan that Josh Helman would return as William Stryker. In April 2016, Hugh Jackman confirmed that he would make a cameo appearance as Logan / Wolverine.

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In July 2015, Singer, Lee, Hugh Jackman, and cast members McAvoy, Fassbender, Lawrence, Isaac, Hoult, Munn, Peters, Smit-McPhee, Turner, Sheridan, Shipp, Condor, Till, and Hardy gave a presentation at the 2015 San Diego Comic-Con, together with the release of the film's first teaser poster, featuring En Sabah Nur and a wreckage of the X-Mansion. Footage from the film was screened.

In October 2015, Mars Chocolate partnered with 20th Century Fox for the marketing of the film, using M&M chocolates in their promotional materials. The deal included retail displays and special packaging markings, TV and cinema commercials, and social media posts featuring M&M's characters mixed with elements of the X-Men. The first image of M&M candies wearing Storm and Magneto costumes was released on the day of the announcement.

In December 2015, Kia Motors collaborated with 20th Century Fox to create a custom Kia Sportage to promote the film. Designed after Mystique, the car was revealed at the 2016 Australian Open. It is Kia's second "X-Car" project after the Kia Sorento customized for the home media release of Days of Future Past and the 2015 Australian Open. A trailer released in the same month received criticism from Rajan Zed, a United States–based Hindu cleric, who stated that the part where Apocalypse claims himself to have been called "Krishna" was an offense to the Hindu religion, and demanded that Singer remove all references to Krishna from the trailer, and the film itself. The references to Krishna were removed from the film's final cut. On January 4, 2016, Kia Motors released the first promo video of the car, featuring Spanish tennis player Rafael Nadal.

Concerning the character Apocalypse, the director Bryan Singer has said,

The way I describe him the most, the best is he to me is the God of the Old Testament and all that comes with that. If there isn't the order and the worship then I'll open up the Earth and swallow you whole, and that was the God of the Old Testament. I started from there and when Oscar and I met we began discussing, since he isn't really God, he's the first mutant perhaps, but he's not God necessarily, he's imbued with certain unique powers. Some of them may or may not be from this Earth, we don't know.

In April 2016, Coldwell Banker partnered with 20th Century Fox to list the X-Mansion for $75 million. The fictional listing included a video tour of the mansion and stories of the home from the perspective of characters such as Charles Xavier and Scott Summers. The fake property was listed by agent Kala V. Rhomedren, an anagram for Raven Darkhölme. That same month, Fox released a faux TV show called "In the Footsteps of ..." narrated by George Takei which is inspired by the classic TV series In Search of ... that focuses on En Sabah Nur's origins. In May 2016, Fox released a faux TV commercial for the Xavier School for Gifted Youngsters with Lana Condor as Jubilee. They also released a video voiced mail message a week later and a faux TV show called Fables of the Flush & Fabulous with Robin Leach which is inspired by Leach's show Lifestyles of the Rich and Famous.
Billboards in Los Angeles and New York City promoting the film garnered controversy for showing an image of Apocalypse choking Mystique, with critic…

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