I'm playing Cairn Dock, a mission which requires stealth. I encountered several troopers and an officer in a large bay in the beginning of the level. When I happened to stumble into a fight with them, a cutscene turned up showing an officer push the alarm. And the following cutscene are some empty scenes that froze the game up.

I restarted my computer a few times to check out what would happen when stealth failed. As soon as the officer sounded the alarm, the game stopped with scenes with no one in them. It was weird. It wasn't likely that the scenes are just giving you screenshots of empty corners of the level. But i don't know what is wrong.

I jumped up a slope at the left corner of the bay, mind-tricked and sneaked past several troopers, and dropped into the control room of the electrified pool. The room was empty. After I managed to turn off the electricity and force-jumped across the pool, the rest of the level had no enemy at all! Now I'm on a bridge which looks over everything in the level. I entered the ship-like thing (I think it's Doomgiver), and checked my objectives. My objs are all crossed off with mission complete sighns. But the level refuses to end!

Odd weird strange!

Sounds like something is not quite right with one of the pk3's as when you get caught it should goto a sequence with Kyle in a cell with Imperials and a Interegator Droid coming in, then camera going down hallway

If you have winzip you can open the pk3 with it and press 'shift' + 't' to test it's ok IIRC asset0 has the main map bsp's in it though testing all the pk3's would be a good idea (I'm sure other utils like pakscape should also be able to do this)