Perhaps you don't stop him and he resets the entire elderscrolls universe.
I guess it is possible. I think its unlikely though, cause something like that would probably kill the the player. It depends on who's religion is the right one though. Mer believe once Alduin eats the world they'll be freed from Nirn and able to return to where their ancestors came from. Nords see it that when the world ends...they'll die. So...its hard to say. While the Universe resetting is a possibility, I think it's unlikely.
I know the civil war will play a part in it. If I were writing the plot for Skyrim, the dragons would probably have started showing up because of the civil war itself. Not just because both things just happened to start around the same time. Its hard to say, but the Dragonborn will probably get caught up in the war, possibly knowing that they are dragonborn but its possible that they don't, and after the first battle that's when dragon's show up. The enemy of my enemy is my friend, so then the dragonborn may have to unite the fractured Skyrim much like Tiber Septim did with Tamriel.
Also, killing Aldiun is almost out of the question. Fighting him is pretty much a given, they wouldn't spend so much time on dragons to not have the last boss be a dragon, but killing him would probably unravel time. We might have to kill his avatar, and in doing so proving that Nirn doesn't need to be eaten.
Its all speculation now, so who knows.
I just want some back to the future crazyness.