Originally Posted by Chevron 7 locke
They might have been on their way to dantooine when Malak ambushed them. Or they might have been on a mission to taris itself.
I believe the Council had already did their trick with Revan's mind by the time he awoke. He was just supposed to have awakened on the Academy, so I believe that the Endar Spire might have been indeed ambushed.