SPOILER WARNING: This article contains major spoilers for "Elseworlds, Part 3," the final installment of this year's Arrowverse crossover.
Just because he looks like Superman doesn't mean he's the Man of Steel. In "Elseworlds, Part 3," the final installment of this year's three-show Arrowverse crossover, Doctor John Deegan used the Book of Destiny to rewrite history again. This time, however, he changed himself in a major way: he turned himself into Superman.
After Superman came to Earth-1 to fight Amazo in "Part 1," Deegan became fascinated by the Last Son of Krypton, so much so that he rewrote reality to become exactly like him. Deegan's version of Superman, though, wore a black-and-gray costume. This allowed audience members to tell the two apart when Clark Kent's Superman showed up to help save the day.
In Deegan's reality, he was a superhero. Everyone revered him and his might, despite the fact he used it to push others around and destroy things in his anger. His base was located at STAR Labs, where he had assembled a team of agents, almost like an evil D.E.O. However, because Superman and Supergirl weren't from his reality, his knowledge of them was incomplete; he couldn't really alter or change them totally because he didn't understand them.
Deegan only changed back to his true form when Oliver arrived just in time to save the day. After negotiating with the Monitor, Oliver used a special arrow -- presumably one gifted to him as part of the deal -- to neutralize the Book of Destiny's power. Oliver's aim was true, and the resulting explosion not only transformed Deegan back to his real self, but melted his face.
Per the stinger at the end of the episode, Deegan ended up as a patient at Arhkam Asylum with Psycho Pirate as a neighbor. Through their borrowed wall, Psycho Pirate reassured Deegan that "everything is as it should be. The stage is set. Worlds will live. Worlds will die. And the universe will never be the same" -- the infamous tagline from Crisis on Infinite Earths. This suggests Deegan could return for the Arrowverse event of the same name, though he likely wouldn't come back as black-suited Superman if that was the case.
The Flash returns from its winter hiatus on Tuesday, January 15, with Supergirl coming back on Sunday, January 20 and Arrow on Monday, January 21.