Go down the stairs and you'll come to the first of the generators that you have to destroy. You take it out the same way you when you toasted the generator to free Sally. Hit the main activation switch and then, once the cooling switches are all deployed, hit them one right after the other. Stand back and the generator will explode after a short time. Once it's toast, you can go through the doorways at the end of the hallway under the stairs you just came down. At the end of the hallway is a teleporter that you can use to teleport to the beginning of the Robot Assembly Area. After that it's just a quick jaunt back to Engineering Core and all of your buddies.
Next up, the Cryo lab! If you want to bring Tercorien with you through this area and he survives he will eventually be able to make Cryo Mines and Cryo Grenades for you. You'll have to babysit him though, so it's your call. Go through the door to the Cryo Lab and deal with the attacking alien. If you have a Support Drone with you the alien will ignore you and go right for the robot. Aren't you glad we went to the Robot Assembly Area first? Head to the left and be sure to hit the switch for the Release Mechanism. Then go back the way you came, go past the door and then take the stairs on your left down. Take a left at the bottom of the stairs, open the door and go into the room you just unlocked by hitting the switch. In here is a bunch of gear, including some Earth gear, a Healing Archway and Alien Captive Recorded Log number 4. Head all the way back up to the switch you hit when you first entered the room and go past it into the next area.
In the next room are two more drones that you can have do your bidding. Approach them and interact with them (despite the lack of a prompt) and choose to realign their sensors and then choose to activate them. Voila! Robot slaves! The drones will go in the nearby labs and start killing the aliens, but for even more fun, hit the switch by the windows to the labs and watch as captive Wasteland beasties enter the fun and start ruining the aliens' day. For some reason the ghouls that get released with these switches will ignore the Ghoul Mask if you're wearing it, so be prepared to mop them up if you release them. Once everything is dead head into the southernmost lab and look around until you find the switch to get Alien Captive Recorded Log number 2, Vin from Flatbush, quite possibly the funniest thing you'll ever hear in Fallout.
Once you have everything head through the hallway to the west and follow into the next room where there will be several aliens to deal with. If you go into the first door on your left you'll find three switches. One will unfreeze beasties in the room on the other side of the window, one will either detonate the locked door or open it and the third will either detonate the switch as a proximity mine or detonate the upcoming turrets. Do whatever floats your boat, however if you open the unlocked door you'll be rewarded with more goodies. Once you're done playing with switches go through the next room mopping up and looting as necessary.
Keep following the hallways until you get to yet another room with a window that looks into a room with aliens. See that switch in the middle of the console? Activate it and you'll freeze the aliens in the room to death. Once they're dead the doors will automatically open. Head into the room and check the switches to the right and left of the door on the opposite side for Alien Captive Recorded Log 11 and 17. Go through this door, into the next room and through the door to Cryo Storage.
Once you enter Cryo Storage, go to the left and hit the switch for Alien Captive Recorded Log 25. From this room, choose to go to the left, using the Healing Archway if needed. Enter the large, two level room and kill all of the aliens. Once they're dead, head to the two staircases on your left and take the stairs on the left. Head all the way to the end of the room and hit the switch for Alien Captive Recorded Log 16. This room and its mirror image on the other side are split into two levels with aliens running around both levels. Both rooms also have two Supermutant Overlords in cold storage which can be released from switches on the upper level. Keep in mind that the Supermutants will come after you once they've killed all of the aliens so choose well if you don't feel like wasting ammo. If you do release them and kill them, loot their bodies for stimpaks and blood samples, provided you have that side quest from Broken Steel.
Once everything is dead, keep heading North and following your map marker and you'll eventually get to the next generator that you have to destroy. Take it out like you've taken out the other ones. Once the generator is destroyed activate the teleporter behind it and use it to teleport to the Cryo Lab. From here, make your way back into the Engineering Core.
With two generators down, all that's left is to tackle the Hangar so follow your map marker to it and go through the door. Go into the next room and watch is an alien ship is brought up and suspended in mid-air, seemingly by magic. Go down the stairs into the lower level and feel free to use your Drone Control Device to control some drones. There's an alien and two turrets in the side hallway to the East, so deal with them before moving on. Cross the lower level of the hangar to the stairs on the other side. If your original drone is toast, you can grab a Guardian Drone here and use it to help you take out the aliens at the top of the stairs as well as the one on the balcony to the west. Once everything is dead go up the stairs and head to the energy field using the nearby switch to turn it off.
Go up the stairs and into the control room overlooking the hangar. Note the five pylon switches and the switch to open the energy field on the door to the West. Once you hit that switch an alarm will go off and aliens will start pouring into the hangar. Use the pylon switches to activate the pylons and kill the aliens. Some will get through to you however if you use the nearby drones as well as the Healing Archways, eventually you'll kill them all and be none the worse for wear. Once everything is dead you can go through the now deactivated energy field, take out the last generator and then head back to the Engineering Core.
Once you're back in the Engineering Core, find Sally and talk to her. You may have some aliens to deal with, presumably from your jaunt in the Hangar, so if you do, take them out like all of the others you've already killed. Sally will tell you that it's time to don your spacesuit and head to the top of the ship, but we've got some more Alien Captive Recorded Logs to get first.
First, use your map and head to the teleporter to the Maintenance Area. Once you enter the area, follow the linear path until you see what looks like an open elevator with Sally in it. Talk to her and she'll talk about how you're both exploring. Once you mention that you should be going the doors will close and the room will start moving. Looks like you're in an express elevator to Trash Land. How proud you must be. Sally will keep fiddling with the control panel to take you different places. Feel free to look out of the window, however occasionally an alien will shoot at you, so be careful. Eventually the elevator will stop, the window will open and you'll have to kill three aliens. Once they're dead Sally will climb out of the window and the car will shimmy and shake and you'll be treated to a cut scene where you get dumped out of the car onto your ass and into a world of hurt.
Once you wake up you'll see Sally on a high ledge. Talk to her and agree to split up. She'll try and help you navigate through the garbage, but basically you're on your own and you should meet up in the Engineering Core. There's only one way out of here, so take the door to the Waste Disposal Area. Go through the next area to another door, through that door and then shimmy your way through some tight places until you hear Sally talking to you. Keep moving on through using your map to point yourself in the right direction if you get turned around. Eventually you'll get to another door which leads to a long, garbage filled hallway and a Healing Archway. The hallway leads to a room with a Support Drone in it, so deal with it and then head through the next door.
In the next room you'll come out on the lower level with some aliens above you who can very easily get the drop on you if you're not careful. Either back into the room so that you can shoot them first or just be ready to fire back. Once they're dead head along the arched walkway and through the next door. An alien will be on the other side of the room (the side you just came from) so kill it and head through the next door. There's a Guardian Drone at the top of the stairs so be prepared to take it out. Once it's been dealt with go up the stairs. Sally will turn off the energy field so head through the opening and try not to get squished. Use the switch to turn the compactor off and then once Sally turns off the next energy field, go through it.
You're going to go through several more rooms with compactors and energy fields however some aliens will also get thrown into the mix so take care of business and keep on moving on. Eventually you'll come to a large, circular door and Sally will mention how things just got quiet which is never a good sign. Go through this door and you'll have some aliens to deal with so just snipe them from the doorway. When the battle is over, come through the doorway and turn to your right, hit the switch and get Alien Captive Recorded Log number 19. There's a Healing Archway you can use to heal your boo-boo's once you're done killing so use it and head through the doorway opposite where you came in.
Sally will tell you that you're almost out of there, which is a small comfort considering she's the reason you're there in the first place. Go through the next room and up both staircases and deal with the alien at the top of the stairs. Approach the energy field and Sally will disable it. Talk to her and then follow her to the teleporter that will bring you back to the Engineering Core.
Next up is the Cargo Hold which will nab us the last of the Alien Captive Recorded Logs we'll need before taking the space walk. Again, use your map to get to the door and head on through it. When you enter the Cargo Hold you'll notice a door to your left to get to the Research Lab however it has to be opened elsewhere so just ignore it and move forward through this room, nabbing gear from the containers as needed.
The Cargo Hold is a giant, two story room with an upper catwalk and a lower area. Stick to the upper catwalk and take out the now familiar assortment of aliens and drones. You want to work your way to the southwest corner of the map where the door to the Research Lab is. Take the nearby stairs down so that you can get to the door. Before we go through the door let's take a moment to get the MPLX Novasurge, a unique plasma pistol. Check the tables near the door until you find a terminal you can hack. Hack it and then use it to unlock the safes. Once the safes are unlocked stay on the lower level and head to the SW corner of the room, near a column-like structure that's dumping garbage into a giant pit. Look in the debris piles near the pit for the safe you just unlocked and the weapon is in it. Once you have it, head back to the door to the Research Lab and then go through it.
In the Research Lab you'll find lots of interesting artifacts but before you do any exploring take out all of the aliens and the three turrets up in the ceiling. In the back of the room you'll see a lunar capsule floating in mid-air. Position yourself in front of the stairs leading up to it and turn to your left. The switch you see will nab you Alien Captive Recorded Log 13. You can look around some more but once you're done, leave by the door that's on the same wall and to the right of the one you came in from.
Go down the hallway and you'll come to a Drone Pod you can activate. Once you have your robotic friend, turn left and enter the next room which appears to be the robotic horses room. I don't know why aliens would need robotic ponies and frankly, I don't want to. Kill everything and then check the center of the room for a switch that you can activate for Alien Captive Recorded Log 21. Against the wall you came in from is a door switch that you can either rig to explode or use to open the door which leads to a Healing Archway. Once you're done in here, open the orange, circular door and go through it and into the next pony room. Go through this room and into the next one where some unfortunate test subjects met their end at the hands, er, hooves of the pony in the center of the room. Use the teleporter in the corner to make it back to the Cargo Hold. Use the switch to open the door in front of you and then make your way back to the Engineering Core.
The last place to visit is the Engine Room. There aren't any Alien Captive Recorded Logs in this section of the ship though, so if you don't need stuff or don't want to kill things, skip this section and go take your space walk. If you want to visit it though, well come on then. Go through the door to the Engine Room and down the stairs into the next room where you can get a taste of what you'll be dealing with. When you're done sightseeing open the door and head through it. Head on through the next set of hallways and rooms dealing with all of the aliens, Support Drones and Guardian Drones. When you get to the large room, take everything out and then you can use the nearby switch to overload the turret circuitry or act as a proximity explosion.
Go through the doorway to the South and through the hallway into the next room where you can hit a switch and open a nearby room. Two aliens will come out so kill them and then go through the door you just opened. Be prepared to deal with two Support Drones and an alien coming from the hallway to your left once you go through the doorway. Keep following the hallway but be ready to take out a turret after the hallway curves to the right. Go beyond the turret and you'll come into a room with a set of stairs leading downwards, complete with two drones coming up the stairs to greet you. If you want to continue to your right and leave the room you'll eventually come to a Healing Archway, another drone and a room with some gear. Once you're done, head back to the stairs and take them down.
At the bottom of the stairs there's another switch you can use for various destructive purposes. When you're done tinkering open the door and deal with the drones and aliens. Head through the next two rooms until you come to a Healing Archway and yet another switch you can use to make things go boom. Random aliens will accost you so just kill them and be done with it. Go up the stairs beyond the archway and take out the room full of hurt that the aliens have prepared for you. There's a whole bunch of Alien Epoxy and crystals on the table in the back of this room so grab what you need and then go through the door and head back to the Engineering Core.
Ok, time for a spacewalk. If you have missed any of the Alien Captive Recorded Logs so far, now is the time to get them as once you take your jaunt in space, there ain't no coming back to this part of the ship. Check the list in the "Alien Archivist" section of this guide for all of the logs you should have so far. When you're ready for a walk outside, don your space suit and head out the door to the Decompression Chamber. Hit the switch in the Decompression Chamber and an alarm will sound while the chamber decompresses. Once the process is over the door on the far wall will open and you can go through it.