Saving The Ship
Fix The Detention Center Lockdown System
After your elevator runs into some unfortunate booby-traps, you and your squad will be forced to fight your way through the detention center (again) in order to repair three circuits. When all of them are patched up, you'll be able to activate the area's lockdown system, which should enable you to prevent any of the Trandos here from leaving.
There's a pretty basic floorplan here, consisting of multiple corridors at right angles to one another, with guard stations at each intersection. The guard stations can often be used as sniping spots, and you can also find the corridors leading up to the overwatch portals in the corridors; these will usually have some kind of ammo within, and there'll often be a bacta dispenser in the corridor as well.
After heading through the first corridor to the first intersection, you'll find the first circuit. Set someone in snipe position at the guard station while someone else hacks the circuit, and protect them both from fire until the hacking is done. At the next intersection, you won't find a circuit, but you spot something much more ominous: if you zoom in your sniper rifle all the way down the hall, you'll spot a wicked-looking turret that's been set up. The best way to proceed here is to keep all of your soldiers behind you while you slowly creep down the hallway, sniping Trandos in the head from long range; you can definitely get the guy standing behind the turret from a distance, even if you can't clearly see his head. When he falls, though, another Trando will come up shortly thereafter and attempt to man the turret again, so be prepared for it.
As mentioned, the second circuit is in the middle of this long hallway, so repair it before heading down to the turret position. Said turret isn't going to be tremendously useful to you, due to its huge area of effect and inability to turn completely down the next hallway, but feel free to task a soldier to it during the next wave of enemies. Regardless, though, you'll have to proceed down two more hallways to find the last circuit; fix it, then return to the turret and locate the newfound charge spot in the hallway near it; you can blast this to exit the level and head down to the garbage level.
The Wrath of the Republic
Exit the Garbage Airlock
Advance to Hangar A
Wow, a whole lotta clone's have been dispatched by the Trandoshans, it would seem. Time to make them pay for their crimes against the Republic!
As you exit the garbage dump, send your troopers up the ramp ahead of you; there are going to be a lot of scavs here, and it's obviously better to have them aiming for your friends than for you. You'll want to set one of your soldiers into sniping position by the crate while another starts slicing the console to the rear of the corridor; when hacked, this will instruct the turrets to fire on all hostile targets, including the scavs and the Trandos, so walk up the hallway a bit to cause some of those enemies to spawn in. When the coast seems clear, walk into the opposite trash dump to pick up some thermal detonators (if you need any), and move on.
Around the corner from the end of the turrets is another set of Trandos, with one of them attempting to hack a console. You can't get too close to this guy due to a mine in the path, but you need to stop him from hacking the turrets, so pop him with a sniper round or just chuck a grenade at his feet before disabling the mine and hacking the turret your own self. This will let you pass through to Hangar A, where yet more Trandos are waiting for you.
Eliminate All Trandoshans
Getti ng the Trandos out of the turrets is going to be the most difficult part of destroying their ship.
It's regretful that the Trandoshan community is undoubtably going to sue LucasArts for inciting violence against them, because this mission is kind of fun. In order to complete the level, you're going to need to destroy the Trando dropship that's positioned in Hangar A. You'll note that there are two entrances to the hangar, with one of them on the upper level of the ramp and one farther down. To begin with, enter the upper level, kill the Trandos there, then set up a sniper behind the box before you start chucking thermals and using your blaster to kill the Trandos on the lower level. They'll quickly respawn, but you might make a little dent in them before you head to the lower portion of the hangar to blow the ship. Leave your sniper up here before you head down the ramp; he'll quickly be able to take out the grenadier that appears on the far right walkway of the hangar. This grenadier will be very annoying if he hangs around while you try to move around on the lower level.
On your way down the ramp, you'll have to kill another Trando with a new weapon; in this instance, he'll be packing a Concussion Rifle, which creates a devastating shockwave when it hits. There'll be plenty of ammo for it in the hangar, so feel free to use it on any Trandos you see, but be aware that you can be hurt by your own fire if the projectile lands too close to you. It's most useful in taking out the turret gunners here.