Once you've collected all of the logs, head to the West (right out of your cell) and you'll come to a Healing Archway. If you activate it, you can attempt to modify it and make it more effective, but at the cost of burning it out earlier. Do what you need to, or leave it alone and then walk through it. Doesn't that feel better? Hey, your radiation levels have decreased too. Thanks alien oppressors! Look around the room you enter upon coming through the arch and you'll find Alien Captive Recorded Logs 1, 3 and 12. Once you have everything, go through the door on your left and you'll see Sally locked in her cell. Your quest log will update with a note to rescue Sally, so make with the rescuing.
Head to the far end of the hall and you'll see a control switch as well as three core coolant switches. Hit the main switch and then go around and hit all three of the core coolant switches. Eventually the core will overheat and explode, taking out all of the cell energy fields in the process. Go and talk to Sally and she'll offer to show you around. You'll need her to open the locked door back in the room you just came from, so tell her to lead the way and hightail it out of there, back the way you came, following your map marker if you get lost.
Talk to Sally after she opens the door for you and your quest log will be updated with a task to find your gear. Not a bad idea if you ask me. Head straight and look to the room on your right for an alien to come out. Take care of him, enter the room and then open all of the containers to get your gear back as well as some extra stuff. Once you're equipped again (don't forget to reassign your weapon hot-keys) hit the switch to unlock the door in the outer room. Go through it and then through the door to the Steamworks.
Once you enter the Steamworks you'll see a party of aliens on the prowl for you. Sally will tell you that you're too big to fit through the steam vents and sneak past them so you'll have the option to either take them all on yourself or the option to give her a grenade so that she can blast them from behind after you distract them. If you choose the latter option, give her whatever grenade you have on your person. Give Sally a minute and then when she tells you to go and get their attention, head on over to the aliens and Sally will send them all back to alien hell. Search their bodies for Alien Biogel which heals you 30 points of damage but reduces your intelligence by 1 and Alien Epoxy which will allow you to repair any item for 25 points of damage even if you don't have the necessary items to use for repair. Sweet! Go Sally!
Move forward down the corridor and wait for Sally to take her sweet time to get the locked door open. If you hang back you should be able to avoid the attention of the other alien party looking for you. Go through the opened door and check the containers for more stuff. Head through the other door and deal with any aliens you come across as it's pretty likely that you'll be discovered. Loot the corpses for even more cool new toys. Follow the hallway around until it links up with the hallway you entered the last room from. There's an alien to your right that you can either avoid or kill. Go through the door forward and to the left and deal with the aliens on the other side.
Now, at this point you can either go through the pair of doors ahead of you and deal with the various aliens and support droids or you can go up the stairs to your left and let Sally make a distraction. Do whatever you want to, but remember that distractions are for cowards and cheaters. However you decide to get through the room, get through it and go through the door on the other side.
Once you get there, hold off on blasting the Alien Workers as doing so causes you to lose Karma, something it would have been nice to know before I disintegrated one. Oh well, I sin so that you don't have to. Keep moving forward and Sally will tell you that you're own for a while. Be brave little soldier! Deal with any aliens that accost you as you continue through the ship towards the marker on your map. After heading up some stairs through some rooms and back down some more stairs you'll eventually hook back up with Sally.
Enter the next room and deal with the various alien threats including a turret up high and to the left. Once everything is done, follow the path to the door and go through it. Go up the stairs and to the left and deal with two more aliens. After they're dead, a door to a closet will open and Sally will come out. Check the closet for more gear including rare Alien Power Cells on the back shelves. Once you have all you need come back out and talk to Sally. She'll tell you that she plans on "staying there until it's safe" which is little girl for 'step to it and try not to get killed, mullet head.'
Follow the catwalks, dealing with turrets as needed until you get to the door to the Engineering Core. Sally will rejoin you so once everyone is accounted for, head on through the door. Follow Sally up some stairs and then up some more stairs where she'll ask you to follow her again, as if she hasn't been paying attention all this time. She'll lead you to a busted teleporter and then ask you to follow her. Again. Do so and she'll lead you through a large room into a room filled with stasis pods. Sally will tell you to wake up the astronaut so that you can get his space suit and use it for a space walk to escape the ship. Agree to talk the astronaut and the quest will end, you'll get 300 experience points, the "Not of This Earth" achievement and 20 points.
Among the Stars - 20 pts
This quest will start up automatically when the previous one ends. Somah will join you from out of nowhere so don't be surprised when she does and accidentally shoot her. Before we go waking folks up, activate the control switches next to all four pods and you'll get Alien Captive Recorded Logs 5, 6, 7 and 8. When you have all of the recordings, use the switch to activate the stasis pods and then talk to Sally. Sally will tell you that the astronaut is dead so you'll have to do all of the space walking. She'll also tell you that the ship is crawling with aliens but if you turn off the generators located throughout the ship it will suck a bunch of air out of the ship and help kill some aliens. Once you're done talking to her she'll head off to start unlocking doors for you.
At this point you can talk to the newly rescued humans. Paulsen is a cowboy and while initially wary of you will agree to come along with you for your run through the hangar and help out if you ask him. If he dies at any point, feel free to loot his corpse for his unique revolver as he won't be needing it at that point. Private Tercorien is a medic and can take the Alien Biogel you have and turn it into Adapted Biogel which now heals you for 180 points of damage. He'll also lend a gun for help in the Cryo Labs if you ask. You can also try talking to Toshiro Kago but he doesn't speak English and you don't speak Japanese so don't expect much. Talk to Somah again and she will repair your gear for some caps as well as lend a hand in the Robot Assembly Area. Your compatriots can't take too many hits before getting killed, so if you think you're going to need their services later, leave them where they are. Grab the spacesuit from Colonel Hartigan's body, pick where you're going next and get moving.
I chose the Robot Assembly area first for reasons that will become clear later, so I suggest you do the same. Use your map to find the door to the Robot Assembly area and go through it. Head forward and go down the stairs and an alarm will sound followed by some drones coming after you. The Tesla Cannon makes short work of them if you still have it. Be sure to grab the Drone Cannon off of the Drone Guardian. Nice! The Drone Cannon shoots a globe of energy which can't hit higher targets so don't use it against turrets. Keep moving through the room, taking out Drone Guardians and use the nearby Healing Arch if you need to. You can modify this one for extra healing if you so wish.
Go through the hallway into the next room and activate the switch. You'll have the option of leaving the communicator alone, rigging it to explode with a proximity charge or overloading the turret circuitry. Do whatever you want and press on forward. You'll come to a dead end, so use the switch on the control panel at the end of the room and choose to overload the assembly line. Doing so will cause an explosion (hope you weren't standing near the panel) and open up a way for you to get through the wall.
Before you walk all the way down the assembly line, prepare yourself for a fight. The Drone Cannon doesn't work too well against more mobile foes like the aliens that will be running around, so be sure to arm yourself for the slow drones and the more mobile aliens. When everyone is dead, search all of the alien bodies until you find the Drone Control Device. This handy little tool will allow you to open up the nearby drone pods and put the drones contained within under your control. If you go up the stairs there's some more gear, including Alien Biogel and Alien Epoxy. In the room under the stairs there's a Healing Archway. Gear up and heal up and then keep pressing forward.