- "The day of reckoning, it is here. All your buildings... All your buildings and temples... ... will fall. The dawn of a new era will emerge."
- ―Professor X
The Battle of Cairo was a major battle in the revised timeline. It was fought between the X-Men and Apocalypse and his Horsemen of Apocalypse. With Apocalypse putting the world in danger, a new team of X-Men had to be formed, the first since 1962.
Apocalypse takes the kidnapped Charles Xavier to Egypt, once the domain he ruled over thousands of years ago. Amplifying Charles's telepathic abilities he uses Charles to send a threat across all minds on Earth, that he has returned and will be cleansing the Earth, but that mutants should not fear. Charles manages to send a hidden telepathic message to Jean Grey saying that she needs to get help and rescue him. Using his massive telekinetic abilities Apocalypse turns the city of Egypt into Apocalypse's Pyramid which will be the center of his new Earth and where he will transfer his consciousness into Xavier giving him the ability to control all minds on the planet. Magneto begins using his enhanced abilities to disrupt the magnetic fields across the globe causing major devastation.
Jean Grey, Scott Summers, Kurt Wagner, Beast, Quicksilver, Mystique and Moira MacTaggert are on their way to Egypt to stop Apocalypse, having all just escaped Alkali Lake. Realizing that she cannot hide in the shadows any more Mystique takes control of the team, giving them orders for battle. She and Quicksilver, go to Magneto in hopes they can convince him to stop his actions. Beast, Cyclops, Jean, and Nightcrawler go to rescue Charles from the pyramid, while Moira guards their escape route, the stolen X-Jet.
Apocalypse sends his Horsemen to defend him while he begins the process of transferring his mind into Charles. Kurt uses his teleporting powers to try and find Charles but is caught by Angel and the two duel. Psylocke and Storm engage the rest, Storm uses her powers of wind to send a car flying towards the X-Men, but Beast manages to catch it and throw it back at her, but she is saved at the last moment by Psylocke who uses her psychic energy beam to cut the car in half. Storms calls upon massive lightning strikes to separate the X-Men and Jean hides in a nearby building communicating with Kurt, telling him to hurry and find Professor X as his mind is almost been lost.
Beast and Psylocke fight, using similar acrobatic and agile fighting styles, while Cyclops and Storm's powers collide in a duel on land and air. Quicksilver and Mystique are trying to negotiate with Magneto, but he is too lost from the death of his wife and daughter. Nightcrawler's teleportation manages to overpower Angel's flight, and he temporarily knocks him unconscious and locks him in a cage of debris. Kurt teleports back into the temple and finds Charles, luckily before the transference was complete, he transports him back to the X-Jet and soon grabs the other X-Men as well. Moira begins to take the ship out of Egypt.
Angel regains consciousness, he and Psylocke attack the jet, Jean puts the Jet on a crash course as Angel begins to break into the hull of the jet. Kurt manages to teleport the entire X-Men team safely to a nearby building but is also left unconscious. Psylocke manages to escape the craft, using her psychic powers but Angel is caught in the crash headfirst and is killed. Apocalypse awakens in the pyramid furious, realizing that the transference was not completed. Mystique and Quicksilver, leave Magneto, with Mystique telling him that she's going to fight for her family.
Apocalypse finds where the X-Men are hiding but is attacked by Quicksilver, using his super speed Quicksilver seemingly has the advantage, but soon Apocalypse gains the upper hand using his adaptive powers and breaks Peter's leg. Psylocke walks forwards and Apocalypse tells her to execute Quicksilver, but it is actually a shapeshifting Mystique, who slices Apocalypse's neck instead. However, with his regenerative powers, it has no effect and he begins to choke the life out of her, taunting Charles, to come and save them. Magneto and Storm watch from the sidelines, both conflicted and unsure of their choices.
Charles realizes that he's still connected to Apocalypse telepathically and begins to fight him in the psychic realm. Magneto soon realizes that Xavier and the X-Men are his family and joins them, hurling waves of magnetic debris at Apocalypse and soon Storm also joins against him, after trying to kill her hero Mystique also dishonoring Angel who was killed during the battle. Apocalypse is able to simultaneously fight off Magneto's metal waves, Storm's lightning, Cyclops's energy blasts and Charles's telepathic attack. Beast also jumps in to try and help but Apocalypse is still too powerful.
Moira, holding Charles proclaims that Apocalypse is just too powerful for the team to stop. Charles, who is getting beaten by Apocalypse in the telepathic world, begs Jean for help, the once shy and scared Jean unleashes her true power. She obliterates the mental version of Apocalypse and her advanced telekinetic and pyrokinetic powers prove to be too much for Apocalypse to handle and his body is disintegrated.
Psylocke watches from a distance, choosing not to attack the X-Men on her own and leaves Egypt secretly.
With Apocalypse defeated and the world saved, the X-Men returned home and Magneto and Jean rebuilt the X-Mansion together. A now bald Charles returned Moira's memories of their time together with the first X-Men team in the sixties. Now aware that threats like Apocalypse are out there, the X-Men are reborn consisting of Mystique, Beast, Cyclops, Jean Grey, Storm, and Quicksilver, now Mystique acting as the team's field leader. The new X-Men, train together in the Danger Room to fight some Sentinels. Charles and Erik have a discussion, Erik asks him if he ever awakens in the night with the fear that one day someone might come after him and his children, Charles tells him that he feels a great swell of pity for anyone who comes to his school looking for trouble.
Over the following years after defeating Apocalypse the X-Men would end up becoming celebrity figures with comics about their adventures being made although the comics often exaggerated and sometimes lied about the X-Men's adventures something that angered Logan one of its members.