Gentlemen, am I the only one that doesn't really question their presence, but rather the fact that they suddenly seem to be evil? As far as I know, they were allies of the Empire (heck, they are considered holy by the empire). There is also this thing with "Their defeat was merely a delay"... what defeat? Did I miss some kinda epic, yet cliché war between the goody-goody humans and the Evil Dragons?
Yeah, this is what is making me scratch my head. As far as I am aware, Tiber Septim (I think it was him) gladly took in the dragons for safekeeping in Cyrodiil, after fleeing Morrowind. But, he made a condition that they were to come to the aid of the emperor, should an emperor call for their aid (like in Redguard).
The only group of dragons I can only see as wanting to attack Tamriel are the kitty Akaviri ones. While I'm not going to fully believe the dragons are from Akavir, or could be an Akaviri invasion, it was the dragonborn, Reman, who defeated the Tsceaci invasion. And the kitty leader of Akavir, Tosh Raka(?), who did say he had plans to invade Tamriel once the snakes were defeated.