Someone lets you out.

You recover from the Sith's violation of your body and try the door only to find it locked.

Just when you think you'll be trapped in the closet until the ship is destroyed you hear the lock click and the door slides open to reveal Trask.

"Bastilla is gone!" He yelled, dragging you out of the supply room and down the corridor. "We need to get out of here! The escape pods are this way!."

You both board an escape pod and it launches you away from the crumbling Endar Spire, which begins to break apart and finally explodes in a brilliant fireball just as you manage to escape.