I figure they perhaps left to find some higher plane of existence, and the Altmer were like 'oh damn that looks fun' and tried it for their own (by banning Talos worship, etc.) and now they have returned after finding some kind of disappointment. Whether it being that the God they tried to find is gone/dead/non-existent, I dunno. Perhaps they find out that they CANNOT ascend to heaven. And instead they must make NIRN into their own heaven. Perhaps an apocalypse or two to clear the way.
In terms of GAME, I don't think they would be introduced like Alduin, who pounces and attacks you, or Oblivion, where you slowly climb up the hill to Kvatch and see the massive gate.
I think the return of the Dwemer would be similar to that of maybehttp://www.youtube.com/watch?v=3cIFNDy2zDM in Halo, or something of the like. I know they appear in Morrowind as kind of weird Bosmer, but I just can't let go of the image of larger-then-Man, hulking masses with big brains, so they're all-round badassery. I haven't played morrowind, by the way.
I pictured the Dwemer coming down from some throne, with this aura of raw power, grabbing the player character (whoever he/she will be next game), giving the usual "I'm awesome, you're not. We're back, step aside. Here's an example of what we can do" and they, I dunno, he snaps his fingers and the sky shatters, and the Gods are cut off from Nirn. So the game consists of stopping the evil Dwemer and returning Nirn to the Divines. Thus meaning that you become the greatest hero of all time. Never mind TAMRIEL, the whole damn world would want to kiss your feet.
So... what do you think?