Over its decade-long run, Marvel's Ultimate Universe radically reimagined the characters and concepts that defined the main Marvel Universe for a generation. While The Ultimates reenvisioned the Avengers for a new century and Ultimate Spider-Man created a thoroughly modern Peter Parker, Ultimate X-Men featured a new take on Marvel's mutants that was filtered them through the lens of realism and modernity reflecting the then-recent X-Men movies.
Initially, the team dealt with threats like Magneto, the Brotherhood, and Sentinels, but the series soon began introducing original takes on newer villains. Chief among these was Apocalypse, whose mainstream counterpart had become a fixture of X-Men epics. However, the Ultimate Universe foreshadowed his coming and turned him into a truly frightening powerhouse enemy who was especially scary in a world where anything could happen.
Apocalypse was first established in the "Tempest" arc from Brian K. Vaughn and Brandon Peterson. This arc reenvisioned Nathaniel Essex as a serial killer who targeted mutants. The mental insanity surrounding Sinister made the enigmatic Apocalypse that much scarier, as his power was seemingly tied to the deaths of these mutants. Moreover, it wasn't exactly certain if Apocalypse himself was real or simply a hallucination formed by Essex's fractured mind. After he's captured by S.H.I.E.L.D., Sinister imagines his dark lord one more time. Instructing the failed Essex to kill himself, Apocalypse appears in his cell in a form resembling a less armored version of his mainstream counterpart.
Further developments involving the villain were planted with the arrival of Cable in Robert Kirkman and Ben Oliver's Ultimate X-Men #75. The time-traveling mutant comes to the present, intent on trying to kill Professor Xavier. Unfortunately for the X-Men, he seemingly succeeds before returning from whence he came. Meanwhile, Sinister somehow returns after his suicide and begins slaughtering underground Morlocks to complete the ritual. Engaging the X-Men in a grievous battle, a mortally injured Sinister finally achieves his desired mutant kill count. Flying into the New York sun, Sinister finally transforms into Apocalypse.
In the Ultimate Universe, Apocalypse resembled a bulkier version of his Marvel Universe self, though with a red armor replacing the usual blue color scheme. Despite being a transformed Sinister, Apocalypse is a completely separate entity, with vastly different and more devastating powers. His main abilities involved stealing the powers of other mutants and adding them to his own arsenal, which made him extremely powerful when he faced the X-Men and the various mutants of the Morlocks. More than making good on his alluded threat, Apocalypse makes quick work of his several attackers. S.H.I.E.L.D. and the Fantastic Four even attempt to take him down, with the result being a stronger, even more heavily armored Apocalypse.
Cable and Xavier returned from Cable's future wearing armor resembling Stryfe and Onslaught. This turned the tide momentarily, with Xavier managing to get inside Apocalypse's head and end his manipulation of nearby mutants. Unfortunately, Apocalypse blocked Xavier's telepathy and prepared to kill the X-Men's leader. Spurned into action by the situation, Jean Grey was overtaken by the Phoenix persona. The relatively grounded Ultimate Universe played with the idea that the Phoenix, like in the movie X-Men: The Last Stand, was a misanthropic aspect of Jean's personality. This was contradicted, however, by Phoenix's actions and statements facing Apocalypse. Claiming to be something far beyond mutant, she overpowered even Apocalypse, leaving on a battered Essex once she unleashed her true power.
Phoenix remarked that Apocalypse's claims to be an ancient mutant were lies. This matches the eventual revelation that mutants in the Ultimate Universe were the result of 20th-century experimentation and not a longstanding natural evolution of humanity. Given her statement that he was Sinister's true form, it's possible that Apocalypse literally was just a transformation of Essex. Either way, his immense power made him the greatest physical threat to the Ultimate X-Men team, and he was the last villain that they would face together before the catastrophic events of Ultimatum. The showdown between Phoenix and Apocalypse was echoed in X-Men: Apocalypse, further showcasing how this version of the villain was truly the ultimate Apocalypse.