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Your first main goal is to get T3-M4 to the Fuel Depot twice - once to a dead end, then back to the Hangar, and then again to the Depot... to another "dead end" as it happens. Much later, you'll enter the hangar to find the Ebon Hawk with your main party. As usual, the numbers generally correspond with the chronological order of events and opportunities.
1 - Enter T3-M4, Party Member
Taking control of the droid once more (counting the Prologue), scour the room for items and exit through the western door; you're on your way for universal repair parts. Equip all of your best equipment, and when you encounter droids, make sure to use your Shock Arm as it completely annihilates them and has unlimited uses! Make your way up the ramp toward #2 and you'll see what I mean.
2 - Enemy Droids
If you want an easy time with these droids, use your Shock Arm.
3 - Exit
Exit to Fuel Depot (#1)
. Take this exit your first time as T3-M4.
4 - Locked Storage
Use a mine on the door to this cave storage area to find some items.
5 - Console
This control terminal is damaged the first time you get to it, and you'll need the parts found in the Fuel Depot, through exit #3. Use the parts you received from the Fuel Depot to repair, then slice into the system and open the Fuel Depot door at exit #6. Then, as T3-M4, exit back into the Fuel Depot at #6.
a) After the Harbinger and the Fuel Depot:
When you come back this way after having been on the Harbinger with your main party, and you have the Hangar 25 Control Conduit, use this console to replace the conduit and give yourself Hangar access. Then proceed through the nearby door on the east side of the room. Be prepared for a fairly large droid battle coming up, but nothing your party cannot handle.
6 - Exit
Exit to Fuel Depot (#3). The first time here, use this exit as T3-M4 after you've opened the door from the console at #5. Later, you'll come through the exit from the Fuel Depot again with your main party on your way to the Ebon Hawk. Be prepared for Mark II droids all along these corridors.
7 - Mark II Droids
From here until you reach the actual hangar, you'll encounter many Mark II mining droids.
8 - Large Droid Battle
Simply another droid battle, but with more droids this time. Don't forget to continue to the dead end and open the footlocker before going through the door here.
9 - Console
I'd recommend saving your spikes or parts and destroy the console to open the containment door, even though poisonous gas spills in the room. The cost of shutting off the contamination is too high. Continue through the gas at #10 (using a rebreather if you're worried) into the next room and you'll be safe.
10 - Poisonous Gas
This corridor is filled with poisonous gas, as you've gathered. You can shut it off using the console at #9, but I'd recommend just running through it, using a rebreather if you're concerned.
11 - Exit
Exit to The Ebon Hawk (#1). Congratulations, you've finally made it to your ship. Before entering, there are some containers strewn around the perimeter of the room if you're interested in a few more items.
As soon as you try and board the Ebon Hawk, you'll be attacked by a swarm of Sith. No worries, though, as you'll be firing the ship's gun turret in a new mini-game I like to call, Sith Wipeout. Essentially, move the turret left and right, rapidly pressing the fire button, and try and eliminate as many sith approaching the ship as possible. The more you let enter, the more you'll have to battle with inside when you've finished outside.
My first time without help, I had to battle 4 Sith troopers once I enter the Ebon Hawk, which wasn't difficult. The next time it was just one. Maybe you can eliminate the threat entirely.
Once again, another congratulations for making it off of Peragus. To continue, head to The Ebon Hawk.