In the Ultimate universe, Proteus was a composite of elements from 616's Proteus and Legion. His name was David Xavier, the neglected son of Charles Xavier and Moira MacTaggert. Xavier abandoned his family to run off with Magneto and found their mutant utopia. David's powers emerged the day after his father left, and their devastating effect on his body led Moira to keep David in a medically-induced coma for nearly seven years. David telepathically sensed when Professor Xavier brought his favored students the X-Men to Europe for a good will tour, and forced himself awake despite the drugs. David escaped from Muir Island and lashed out at his father through a series of bodies as Proteus. He possessed the S.T.R.I.K.E. agent Elizabeth Braddock to get close to Xavier, but her telepathic mind was strong enough to hinder Proteus and his powers. Colossus killed Proteus in Betsy's body before he could escape to another form.
In What If..? (2nd series) #110, the X-Men's first encounter with Proteus went differently because Colossus never joined the team. Piotr Rasputin blamed Charles Xavier for the death of his sister Illyana, and so he rejected the American's dreams for him and joined the Soviet Super-Soldiers instead. As a result, "Brian" MacTaggert moved on from his father's body in Edenburgh and possessed Jean Grey as the Phoenix. The fear of this cosmic entity possessed by a reality-bending mutant got the Kremlin's attention, and they sent Colossus and the Super-Soldiers to Scotland to intervene. Colossus was opposed to working with Xavier, but they reached an accord and Professor X coaxed Proteus out of Phoenix's body and into his own. Colossus then killed Proteus using his metal form while Proteus was in the more-vulnerable body of Charles Xavier.