The game starts in a decimated starfighter, the Ebon Hawk. You play as T3-M4 in the Prologue. Move T3 to the end of the hall. There will be a (locked) door, that leads to the Main Hold.
And a room that is open, and has a "Plasteel Cylinder" and a Communications Console inside of it. Open the Plasteel Cylinder, and obtain the Computer Spike inside of it. Then go over to the Communications Console, and select it, and it will take you to the interface. Select "Open Main Hold Door", and you will lose you computer spike, but the (locked) Main Hold Door opens.
Entering the Main Hold, there is a Locked Door, (and something, or someone. Is pounding on the door, but the door cannot be opened from the outside, so you can't help them.) Go to the left of the door, and there will be an "Old Woman's corpse", and a "Broken Droid". Obtain the Locker Key from the Old Woman's corpse, then, loot the Broken Droid that holds a Part. ( a few feet ahead of the Old Woman's corpse)
Go back to the entrance of the Main Hold, and there will be a Footlocker. Bash the Footlocker, and inside are 2 Broken Items, and 2 Computer Spikes. Go past the Footlocker, (which will now read as "empty") and head straight into a hallway, turn Right, and on the right side, there is a "Low Security Door". Open it will Security, and it will tell you that you have entered the Cargo Hold.
There is a "Large Locker", inside of the Cargo Hold, to the Right side, of you. You can now open it with the Locker Key you obtained from the Old Woman's Corpse, and receive a few handy items, including Armor (for your droid).
If you are not familiar at all with the D&D Combat System that KOTOR games use, lucky for you, there is a metal box in the Cargo Hold, entitled as "Metal Box- Combat Training". Obtain the Field Survival Pistol from the Metal Box, and Sensor Droids will appear. Since, they won't fight back, the Sensor Droids will "make for excellent target practice", as the game puts it.
After defeating the droids, There will be a "Unlocked Cylinder", containing Parts, and 3 Security Tunnelers. There is also a "High Security Cylinder" (To see how the Security Tunnelers work, I recommend using them on the "High Security Cylinder", so you can see how the Security Tunnelers help out). Inside of the "High Security Cylinder", you will find 1 Computer Spike, 1 Parts & 2 Components.
There will be a droid in the Cargo Hold named 3C-FD, who can help you at repairing the Ebon Hawk. (This is completely Optional, but if you want to have him accompany you, use a repair part, and fix him. And invite him to join your party.)
Now, exit the Cargo Hold, Go left down a Hallway, that will have 4 doors. (How you know you are in the right place, there will be a Turbolift to the right, nearby.) Open the "Low Security Door",that leads to the Medical Room, where your character currently is.
To the left of your incapacitated character, there is a storage container entitled as "Medical Storage Container", that contains 3 medpacs. Click on your character, and use the medpac to stabilize him/her. Then, head to the Exterior of the Ebon Hawk (using the Turbolift near the Medical Room).
Go to the Starboard side of the Ebon Hawk. There will be an "Engine Port" (containing 3 parts). There will also be 3 "Open Hatches that will hold 1 part each (Obtain all of these 6 parts, for they will be useful, for when you repair the Ebon Hawk's hyperdrive, to head to the Peragus Mining Station.) and an "Exposed Wing", that is the "control panel", for the Starboard side's Locking Mechanisim on the starboard dormitory.
Now, head up the sideramp to the "Portside of the Ebon Hawk. Beware of the mines (if you are caught inside of the mine's radius, it will explode, and cause damage to the character that stepped on it. Depending on the mine. Minor, Average, Deadly etc.) Now, go to the Proton Missile, (that will have a Minor Frag Mine, and a Part.)
Now, return to the interior of the Ebon Hawk, by using the Turbolift. Go straight into the Engine Room, and the door will be locked. (So, you'll need to blow it open with the Minor Frag Mine you got from the Proton Missile) after blowing it open, select the Hyperdrive, and "Rig the Hyperdrive". Now, return to the Cockpit of the Ebon Hawk, (where T3 started), and click on the Galaxy Map, and hit "Travel to Peragus."
There will be a cinematic, then after the cinematic, you'll take control of your character,and find yourself in a Kolto Tank. An Old Woman's Voice awakens you as she says, "Awaken". And now you get to Explore the Peragus Mining Facility...
The next part of the game will be to explore and escape from Peragus. Open the Door with the Kolto Tanks in it, and there will be a door on your left. Open it, and get the 2 Medpacs from the "Medical Storage Container", there is a locked door, that requires Security to slice open, if you have security, open it and get your 2 Medpacs and 25 chemicals. If not, go to the Terminal, and go to the category: "System Functions." Then, there is an option to "Unlock Medical Storage Door", select that, and "Open Morgue Door".
Access the Mining Logs next, and after seeing all 3, choose the "Patient Treatment" action, and (Treat Injury) "Track the last treatment request". Then, "Log Out", and go to the room across from you (Morgue). And there will be 2 corpses.
One is an Old Woman, and the other is a Corpse that contains a Plasma Torch. Loot the corpse, and the Old Woman wakes up. Then follows a brief conversation about where you are currently. And then the conversation steers into the fact that you were once a Jedi. After the Conversation, turn left and there will be a "Damaged Door". Use the Plasma Torch to bash open the door.
In the next room, is a vibroblade (To obtain this, loot the corpse near the "Broken Droid".) Then, turn left, and there will be a door. On the other side, is 2 "Damaged Mining Droids", that will attack you. Because the Vibroblade does more damage than the Plasma Torch (Plasma Torch: 1-1 +1 fire. Vibroblade: 1-10), equip the Vibroblade to combat the droids.
After defeating the "Mark I Damaged Mining Droids", loot the mining laser, from the one closest to the next door. Same thing for the next room. 2 "Mark I Damaged Mining Droids" attack you. There is another door with nothing in it (except a Corpse, and a "Broken Droid").
In the next room is the Security Office, which has only a few corpses, and a "Large Locker" (contents: 2 Ion Grenades. *NOTE: Ion Grenades are the MOST EFFECTIVE grenade when battling against shielded opponents and Droids.)
Go to the Security Desk. And Access the 6 Security Logs, and then "Log Out". After opening the next door, in the middle of the next room, Kreia will caution you about "A lot of energy in the room beyond. But it stems from nothing that lives." This is where you get your "Perception" power.
My advice for wiping out the 3 "Mark I Damaged Mining Droids" in the next room, is to target the one in the middle and throw and Ion grenade destroying all 3 of them in a matter of seconds. (Or if it appeals to you, bashing or blasting them works too.)
Then, there will be a conversation where you can start to feel the force again, and Kreia says she'll lead you down the "familiar paths", that you took before, and mentions you'll need it if you two are to escape from the Mining Facility.
You can now level up, and choose a force power. Then in the next HUGE room, will be 8 "Mark I Damaged Mining Droids" lurking around, and a Force Fielded door. You can fight all 8, or go to the Blister Console, and shut them all down.
Then, you meet an odd man named Atton Rand. After a conversation about the Mandalorian Wars, The Jedi Civil War, and the Exchange posting a massive bounty on any live Jedi, Atton realizes you're the Jedi that the miners were talking about, and offers to help you escape Peragus.
So, you let Atton out of his lovely Force Cage, and the 2 of you head towards the Blister Console, and Atton slices the console, and tries to end the lockdown, and gets pissed off because he can't get it, and all the 2 of you have are communications.
So, you need to check the Logs in there, and then try to communicate to any miners in the Dormitories, and there is no answer. So, you must now try the Hangar Com, and T3 answers it, and you once again take control of T3, and this time, you need to find a way to end the Peragus Administration Lockdown.
Open the 2 Low Security Doors. (One has 2 " Mark I Damaged Mining Droids", that you destroy, then there is another 2 droids you get to combat.
After that, there is a door, that leads to the Peragus Fuel Depot. And there is a Broken Droid and a Corpse, inside of the first room. Then inside of the second room, is 2 more Mark I Damaged Mining Droids".
After defeating the 2 "Mark I Damaged Mining Droids", loot the corpse of a miner, and receive: 3 (Deadly) Sonic Mines, 1 Droid Ion Striker, and the Datapad: Peragus Fuel Depot Survey. Return to the Peragus Hangar Bay, and there will be a first encounter with 2 shielded "Mark I Damaged Mining Droids".
After defeating them head back up the way you came. Go to the "Cargo Hold Room", and blow the damn thing open with a mine. 3C-FD will be in there, but he is way beyond repair. It looks like whatever got T3, got 3C too. But 3C got the more severe part of it.
There will be a Droid Flame Thrower as well as a few more handy items in the "Cargo Hold Room". And the other "Low Security Door" leads to the Hangar Bay.