Access Aft Data Core
The aft data core access corridor is overrun with Trandoshans, of course, but you do run into a spot of luck here; the defensive turrets in the hallways are still active and working to repel the invaders, leaving a bit of a safe zone in which a number of troopers have holed up, one of whom will try to get mouthy with you. We decided to discipline him the old-fashioned way--with a bullet to the head--and then repeated the treatment for all of his squad, just to teach them a lesson.
If you let the Trandoshans access the turret control console at the end of the hall, they'll subvert their targeting routines Deus Ex-style and start them firing at you. You obviously don't want this to happen, so shoot any baddies you spot going for a console before they can cause any mischief.
After moving on a bit, you'll come to a large open room. If you head inside, you'll notice a bunch of Trandoshans assaulting a trooper. There are too many for you to safely assault head-on, so backtrack a bit into the previous corridor and use the cover it affords to set up some sniper shots; your sniper attachment will place you well out of range of the shotgun blasts, and the Trans won't run towards you so long as they have a ranged weapon available, letting you easily pick them off one by one. One of these guys will drop a box of Thermals, as well, so feel free to use those on them if you're looking for some explosive fun.
At the end of this large room, you'll come to another corridor. Save your game before heading through the doorway, if possible, because doing so will trigger an event. If you spot the Trandoshan running down the hallway, shoot him as quickly as possible; if he reaches the turn, another two or three baddies will spawn in, which is bad news in these kind of close quarters. A sniper shot to the back of the head will probably take the dude down without a problem; if he's dead, then you won't have to deal with the baddies. However, four Trans will appear in the second section of the hallway no matter what you do. There's a box of flash grenades near the bacta dispenser at the beginning of these corridors, so feel free to use them on this little group of guys to stun them while you get up close and personal with your APC array gun.
Around the second corner here, you'll have to take down a pair of ceiling-mounted turrets. Wait until the Trans nearby are dead, then engage in your standard strafe-out-of-cover maneuver, and they'll go down fairly quickly. Soon afterward, you'll come to a pair of deactivated turrets, which will form the basis for the next little challenging triggered event.
There's a turret control console in the aft data core room, so head in there and start slicing it. As soon as you complete the slice, a huge number of Trans will start spawning in and coming at you; the absolute safest place to be here is directly underneath the turrets themselves. Feel free to lend a hand in the killing with your APC gun; ammo is probably going to be running short for the rest of your weapons, but you'll have plenty of it for the shotgun, thanks to all of the instances of that weapon that'll be dropping on the ground. The Trans apparently can't re-hack the console to flip the turrets back to their side, so don't worry about that. Note that, although the flash grenades are apparently only for biological targets, they will blind the turrets as well, leaving you temporarily defenseless if you use one. So don't.
Rescue the Squad
Rendezvous With Delta Squad
Find the Exit To the Landing Gear
So, you've gotten cut off from two of your squaddies, who may be dead. You have the flight records you came for, though, so now's your opportunity to find out what happened to your incommunicado commandos. You're going to have some pretty tough fights before you can reach them, however, starting with a little melee in the guts of the ship.
All we can really say about this level is to proceed extremely slowly. There are a number of Trandoshans and scavenger droids that will be coming after you, but they won't appear until you run past certain trigger spots on the ground, so a good plan of action is to run forward a bit until you either hear shots or the battle music, then backtrack behind cover to scope out the situation. There are plenty of explosive barrels scattered around, so feel free to use grenades to set them off for extra explosivey goodness. The droids are, as usual, going to be the biggest annoyance here, but if you can land a thermal or EC grenade underneath them, they should go down without a hitch. If they're really distant from you, then a sniper round will do the trick as well, but you may not have enough ammo for it to go around using it all willy-nilly.
When you hit the first ramp leading up, blow the explosives at the top to clear out any Trans waiting for you, then start walking up the ramp backwards; there's another Tran waiting on a platform overlooking the ramp to shoot you, so you'll want to get the drop on him. There's also a turret in a small alcove at the top of the ramp. After you get its position, throw an EC grenade or two underneath it to disable it before placing your charge on the debris nearby.
Luckily, the turret's position also holds a bacta dispenser, which you can use as an insurance policy while you're fighting your way to the next ramp. Feel free to use any remaining blaster ammo you have on the enemies here, including the turret that's barely visible at the top of the far ramp, as you'll be finding another box of it just before the ramp itself. When you've got that, fight your way up the ramp and to the end zone. You'll be able to grab a glimpse of a very fiercesome-looking Trandoshan as you top the last ramp, but you won't be able to kill him--yet.