Objectives: Make your way to the bridge
Regardless of your method of escape, once you're free you'll find yourself in a storage room where the Sith have somehow managed to stuff every single item in your possession into a single Locker of Holding. Retrieve, re-equip, revenge. Clear out the rest of the level, picking up any items your rescue character may have missed, then head out down to the elevator and take it to the bridge.
Command Deck
Objectives: Mayhem
This is a level dense with rooms; these rooms are often dense themselves with foes, mostly Sith troopers. The two critical areas to find here are the armory, which contains a set of space suits you're going to need, and the exit to bridge storage, which is guarded by not one, not two, but three Dark Jedi masters. Fun.
After exploring the level thoroughly and picking up the insane amount of goodies that is lying around, head to the northeastern corner of the area for the big fight. Surprisingly enough, you shouldn't have too hard a time with this battle; as long as you can continually knock the Dark Jedi around, preferably with Force wave, you should have an upper hand. Be sure to activate speed, valor, and any other defensive powers you may have before entering the room, then divide and conquer, with Bastila and your PC ganging up on one of the Dark Jedi while the other two are on the ground. If you've set up Bastila properly, she can take out any one of the Jedi in just a couple of rounds, assuming she's doing three or four attacks per round (with master flurry and one of the higher two ranks of speed); with your PC in there swinging away as well, you should be able to take out all three of the masters before they have a chance to kill any of your party members. Carth obviously isn't going to be much help here, since the Dark Jedi can reflect most of his blaster shots, so you might want to let him sit back and chuck grenades at any stunned opponents, or give him Bacca's Ceremonial Blade and let him go toe-to-toe; he'll probably have more health than Bastila, so he could be valuable as an extra target to take the heat off her.
At any rate, you'll have to get through the Dark Jedi masters in order to reach the Bridge. Once they fall, head out to the bridge storage. The door is locked, though, so you'll need a high security score (DC 34) or a security spike to get through, or you or you can head to one of the computer terminals and unlock it there; you should have found around 30 spikes on this level and the brig, so don't worry about running out.
Bridge
Objectives: Open the hangar doors so that the Ebon Hawk can escape
Go through the airlock and head out into space, the final frontier, where no one can hear you scream. Scream anyway at the proposition of another interminable sequence in a bulky envirosuit, then cease screaming, since the whole sequence lasts maybe 45 seconds.
Once you reach the second airlock, you'll find yourself on the bridge level proper. Dispatch the troopers here, then heal yourself up and let your Force Points recover before heading up the ramp to the bridge.
The Sith Troopers here will pelt you with grenades if you don't take them out quick.
Saul is guarded by two Dark Jedi and four Sith troopers scattered around the bridge. These guys are quite grenade-happy, unfortunately, so you might want to concentrate on taking down the two near the door before moving on to the Admiral and his Jedi cronies. If either Bastila or your PC has a mass-stun attack, you can use it on the Admiral, which will usually spread the effects to the other four enemies near him, leaving your other characters free to deal with the rearguard. Alternatively, you can chuck a thermal detonator towards Saul as soon as the battle begins, which will knock down all of the opponents in that direction.
Once the rearguard is finished, use Bastila and your PC to take out the Dark Jedi, then proceed on to Saul. He'll whisper his dying words to Carth. Use the computer terminal nearby to open the hangar doors, then loot Saul's body and get the hell out of Dodge.
The door to the command deck is now repaired, so no need to go through the airlock again. The command deck level will have a few new enemies, mostly Dark Jedi and Sith grenadiers. Head back to the elevator and take it down to the hangar level.