Other than showing up to fight against Onslaught during the final battle of the Onslaught Saga, good old Apocalypse hasn’t been seen since Age of Apocalypse. However, the time was approaching for the oldest living mutant to return, and this time, it was a much bigger conflict than the X-Men could have predicted.
In reality, this story began with a young mutant named Tanya Trask, the daughter of now deceased X-Villain Bolivar Trask, famed creator of the feared Sentinels. With the aid of Rachel Summers (working under the guise of Mother Aksani), she travels through time and discovers a prophecy relating to the Twelve, a group of mutants destined to lead the race in a war with humans. This prophecy is found again by Cable (Rachel helping a bit once again), the time-traveller witnessing the rise of Apocalypse. This knowledge was implanted within Cable in the hopes that he might stop Apocalypse’s plans, but it was too late, the mutant conqueror already beginning his final scheme...
Apocalypse started his campaign by sending a Skrull disguised as Wolverine to attack the X-Men, sowing distrust among the team and causing them to disband temporarily. They discover the deception soon after however, leading them to a Skrull base to get answers. Upon arrived, they are attacked by the Horsemen Death, who after he is defeated is revealed to be the real Wolverine. In the midst of all this, Xavier discovers that the Twelve include himself, Magneto and his estranged daughter Polaris, Jean Grey, Cyclops, Cable, Iceman, X-Force leader Cannonball, Bishop, Sunfire, Storm, Mikhail Rasputin, the Living Monolith and Apocalypse. Slowly, but surely, Apocalypse captures each of the Twelve, leading to a confrontation in Egypt with the remaining X-Men. His followers defeat them, but he keeps them alive as he begins to channel the energies of the Twelve into a thirteenth, revealed to be X-Man. Apocalypse, whose frail body is dying and unable to receive the full power the Twelve would provide, plans to supplant his consciousness into Nate’s body, and continue his reign of destruction.
However, he didn’t count Magneto’s power being greatly weakened at the time of his capture, and the power of the Twelve ran out sooner than Apocalypse had planned. One by one, the mutants broke free, overwhelming Apocalypse’s forces. Apocalypse tries to get to Nate anyway, but Cyclops intercepted him, Apocalypse taking over Cyclops’s body instead, the X-Men leader sacrificing himself to save his other-dimensional son.
With at least part of his goal accomplished, Apocalypse travelled through time in an effort to finish the transformation process. The X-Men give chase, in both the past and the future, stopping his plans, leading to his final defeat. The would-be conqueror’s spirit leaves Cyclops’s body and disappears, Apocalypse rarely seen since.
This storyline is somewhat forgotten by X-Fans, which is more than a little sad since it was a fairly big event, and one of the last major stories where the iconic 90s roster were together in one place. Out of all the X-Men, Wolverine and Cyclops were the most affected. With the former, Apocalypse had regrafted Wolverine’s skeleton with adamantium, bringing back his metal claws that had been absent since Fatal Attractions during his transformation into the Horsemen Death. For the latter, Cyclops was deeply shaken by Apocalypse’s possession of his body, something that never truly left the X-Men leader. Ironically, these two would lead the X-Men for the better part of the next fifteen years despite all this, taking them mutant team into the future as the New Millenium edged ever closer.