Curiously, at the end Dr. Manhattan goes off to roam the cosmos, contemplating creating life himself, to become a creator god himself. Variations of this ascent to the heavens trope have been common with these sort of beings in comics at least since Lee/Kirby's initial Him (aka Warlock) story in the FF in 1967. I wouldn't be surprised if their are earlier versions, but that's the first I'm aware of. In relation to the Watchmen, based as it is on so much of Ditko's work for Charlton and his Objectivist views, Kirby conceived of the Cocoon/Him storyline as a critique of Objectivism but Lee whittled those aspects away in his script (add another straw to Kirby's load of frustrations with Marvel Comics).
Also, of course, when Him was reborn as Warlock by Roy Thomas, he became an even more godlike, specificially Christian, figure. The original series as a whole wasn't so great, but Jim Starlin spun some gold with Warlock's post-resurrection stories. As for what Dr. Manhattan adventures as a "god" in the depths of space, that'll be forever left to our imagination, at least as far as Alan Moore seems concerned.