You fight your way through.

You shoot through several rooms full of Sith before you get to the bridge. No one on your side is left alive.

"Bastilla must have left in an escape pod already!" says Trask.

"Crap," you think. "This trip just got a lot more worthless."

You two run for the escape pods, but Trask gets waylaid in a fight with a Dark Jedi. You leave him behind and run for it. You and a guy named Carth take the last escape pod and crash land on the planet. You are knocked ****.

Much later you wake up and Carth explains the situation: You are trapped on Taris, a Sith controlled planet. You have to find Bastilla and escape before Darth Malak finds you.