Remember the intro to The Sands of Time? The prince was narrating and in the end *spoilers*
it turned out that he was telling a story to Farah. In Warrior Within's intro, he seems to be in Babylon and running away from the Dahaka. The game camera zooms into the prince's eye and it appears to reveal a ship. I'm starting to think that the entire game is some sort of flashback and that the Dahaka is still alive.