Mothership Zeta bugs

All platforms

 * If you save the Cryo lab's generator for last, you will not be able to use the teleporter. This will get you locked in the lab where you must freeze the aliens and Elliot's team, with no way back to Sally! Killing Elliot may fix the problem but he must be with you when you kill him. Also, turning your system off and on again may fix the problem. Save before trying.
 * If a container is opened on its side with one's back to an unmovable object, the player will be pushed into the object or wall and become stuck even when the container is closed, and only noclip console command (PC only) or reloading a save (PS3/Xbox 360) will fix this.
 * If you ask Sally "Are there any cool secrets on the ship" (her Child at Heart option) then interrupt her as she climbs into the vent (near the closed door she opens to show you her stash) she will reset and run back to the engine core, leaving the room locked permanently.
 * The World map in the Pip-Boy 3000 incorrectly displays that you may be in any random indoor area, such as Megaton, The Citadel, Shalebridge or Tenpenny Tower, due to the world map's handling of location tags. "Orbiting Earth" cannot explain this, as the view of Earth from the ship never changes.
 * When you kill a guardian drone, while searching in the bottom left hand corner (where the weapons image usually is) the drone cannon has a square with a line through it and says PipOS Error 26 [File not found]. The cannon in the looting screen is at full health but when taken the health is less.
 * When you get the General Chase's overcoat in the garbage disposal area, it will appear as a suit of Winterized combat armor (this will always happen with the female one), or the armor will become the texture of any random thing around you.
 * In the Cryo lab when you get to the point where you have to freeze the aliens to continue, in the room there will be three wastelanders (or Elliot Tercorien's squad if he came with you) the dead, frozen bodies will be on the tables, with a leg or arm sticking up in the air. Although that is supposed to happen because they're frozen, if you use the "grab" command on any of the corpses, the limbs will become limp, and they will fall as if they were a regular corpse.
 * There have been times when looking down at the Earth just after the Space walk, Earth's image will just become black.
 * When using the drone cannon in V.A.T.S., the shots are fired straight even though the projectiles have weight, making them fall to the ground usually before coming near the target.
 * There is also a glitch if you have the Mister Sandman perk that grants you infinite XP when doing it on Sally.
 * If you still have allied drones following you from Robot assembly when you enter the Space walk, they may reappear after the Space walk on the other side of the door. They will constantly attempt to open the door, trying to get back to your side, causing a message that says "Room Must Be Pressurized" to pop up every few seconds (or more frequently). It will continue until you make it to the button to compress the chamber and the room becomes pressurized.
 * When you leave the Bridge back to the Capital Wasteland, your Pip-Boy and weapon in first person view may appear to be orange. Saving and loading may fix this.

PC

 * When the PC gets abducted and the first cut scene is finishing, the aliens may freeze and the PC may get stuck, unable to move or progress and the game hangs up, making the player unable to complete the add-on.
 * There may be a way to fix this. If you happen to be running a mod called "Purge Cell Buffers", then that may be what was causing this bug. Try disabling PCB for the duration of Mothership Zeta and you should be able to get past this cutscene.
 * If still stuck try bringing up the console using the "`" key and typing.
 * After using the, you might still find Somah nowhere to be seen. If this happens, you can input the following commands: " (with xx being the load order of the Zeta.esm file in the mod manager), , . Somah should materialize in front of you, allowing you to continue the quest.
 * Still in the holding cells, when you have to free Sally, she might be missing. Unlike Somah, the / commands don't seem to work. However you can input in the console: (with xx being the load order of the Zeta.esm file in the mod manager), and then: . She will appear before the player, then proceed to open the door. (Tested only after disabling the force fields in the cells.)
 * Once reaching the Cryo Chambers Paulson may be missing from his tube. If so he can be safely added in by bringing up the console and typing: (with xx being the load order of the Zeta.esm file in the mod manager),, . Paulson will appear in his tube, allowing you to continue with the quest normally.
 * Two invisible turrets (perhaps more) in the Living quarters section. Though they do not attack, when you come within range your 'Hidden' status will change to 'Detected'. They can be destroyed through conventional fire or explosives if one pinpoints their location.
 * When receiving the objective to disable the Death ray, if you go into the Weapons lab and grab the Destabilizer and test it on the brahmin you strangely complete the quest and it tells you to go to the bridge. Sometimes not even this is required, and the quest will just randomly be marked as complete.
 * During the This Galaxy Ain't Big Enough... quest, after activating the Engineering core teleporter to bring Sally and any of the other surviving non-player characters up, and after being given the objective to "Disable the Death Ray" and/or "Make Your Way to the Bridge", these objectives may auto complete, moving you to the objective "Defeat the Alien Captain" without any interaction by the player. There does not appear to be a specific trigger for this happening and it may happen at any time without any notification given to the player that these objectives have been completed. This results in being unable to complete "Disable the Death Ray" quest and prevents you from entering the Living quarters area. Saving the game with the problematic objectives still incomplete on a frequent basis, and reloading your game if they auto complete without the players interaction does work, but is very tedious. Once these two objectives have been properly completed by the player, there does not appear to be any ill effects to any of the other objectives in this quest. Hopefully this problem will be addressed in a future patch.
 * After the Space walk in the "This Galaxy Isn't Big Enough…" quest: If the teleporter back to the Engine room cannot be activated, use the following console command: where "xx" is an add-on specific ID. This command will advance the quest to the next stage and activate the teleporter.
 * When you go the Bridge to defeat the alien captain in the final mission, after Sally comes through the teleporter and opens the first door, all non-player characters (including Sally) may immediately return back through the teleporter and all stand at the door downstairs which is inaccessible, which means you cannot continue any further through the mission as you need Sally to open all the doors. To fix this, try talking to all of the non-player characters while Sally is away opening the first door. Then when the door is open, push Sally to the end of the doorway and she'll make her way to the second door instead of turning around and running away.
 * Sometimes all the company may become stuck or run into the wall at the right of the second door if Sally opened the first one.
 * In some cases, Sally won't open even the first door when you turn the teleporter on. All non-player characters including her will immediately teleport back to the engine core and run to inaccessible door. If that happens just hit tilda key to open the console, click on the door to show the door code, write and hit enter. Do the same for the next door.
 * If the above options don't work, use the command to get through the door and finish the DLC.
 * The game may randomly crash whenever you equip the Drone cannon.
 * If you have RL-3 as a companion, when you leave Zeta he will be near the crash site. If you go into the building at Greener Pastures disposal site nearby, he will clone himself. If you tell him to wait, one of the two will become hostile and attack the other.
 * After the quest Among the Stars Sally will open the first door, but for the second door she will go on the opposite side of the door where vent is absent and just stand there after a while assuming the door is opened.
 * When you destroy the plasma shields you can take the plasma stuff that is there for a little but if you do it will freeze and crash the game.
 * If somehow Private Beckett and Sergeant Daniels make it alive in through the Cryo lab and Cryo storage and follow you back to the Engineering core, they will attack Somah.
 * Some mods have tried to let you back to previous cells of the Zeta space ship once the quest is finished, but none have been reported to fully get you back without suffering crashes, bugs, and/or other problems.
 * When you defeat the alien captain and move into the space ship fight sequence, the Death ray may never become available. Reloading may fix this.
 * Sometimes, turning off a force field will only make it disappear, however it's not possible to walk through it. This is fixed by reloading your game (it's possible to save and then reload).
 * The door leading to the Bridge might become inaccessible if you enter the Waste disposal area when you are supposed to go to the Bridge instead. This is easily fixed by using to walk through the door, or clicking on the door in the console and disabling it.

Xbox 360

 * After the main quest, some respawning aliens can become allied with you.
 * After destroying the attacking alien ship the Earth may be missing sections.
 * A large black diamond of sorts takes the place of certain parts of the ship. A version of this "glitch" occurs on the PC. If you noclip and look and the earth at different angles in front or under the Bridge, graphical pieces appear and disappear, even if Earth cannot be seen through the front window of the Bridge. It may be that the earth is not supposed to be seen at all and the glitch is actually seeing Earth. This would make sense considering access to the weapon on the bridge. The story may be that the ship was re-positioned, in reality this means that the graphical representation of Earth may have been disabled only at viewing angle from the Bridge. The glitch may be seeing through or past an unloaded black texture.
 * Said sections seem to re-appear after some time.
 * Clearing the cache and/or re-downloading Mothership Zeta seems to have solved this, as well as the other missing texture problems, i.e. invisible walls in the Engineering core and missing foreheads.
 * Upon entering the Weapons lab, it is possible that weapons will not fire correctly, and will not fire any sort of projectiles when triggered. They might fire on their own when exiting the pause menu or Pip-Boy, or when loading a save game. The drone cannon might fire like a machine gun, making survival even more difficult. Loading a previous save carried the bug to that point in the game. Using V.A.T.S. may cause a lengthy slo-mo animation of the player character in attack stance doing nothing whatsoever, while the enemy attacks. The only way to fix the bug is restarting the game.
 * Sometimes after completing the Space walk, a guardian drone can be found on the teleporter you arrived in.
 * Sometimes after completing the Space Walk, the teleporter which teleports Sally, Elliot, Paulson and Somah will be on before the button is pressed. Due to this, once the button is pressed no allies are teleported through. This locks you out of the Space walk, the teleporter, and the following room. Restarting your console will fix this.
 * If your teleporters have all frozen (normally starts at the Death Ray hub teleporter) and reloading and restarting won't fix this. You need to delete your latest saved games, from the area the glitch started, one by one until they work again. It may also work to leave the Biological research area, save your game, return to the 360 dashboard, and start the game up again. Return to the teleporters and repeat as necessary. It may also work to save your game next to the teleporter you wish to enter then restart your console. You may then be able to enter the teleporter.
 * If you target enemies as they are waking up from hibernation (standing inside the cryo-pod but targetable) in V.A.T.S you may become trapped in V.A.T.S and have to reload your save.
 * After defeating the first aliens in the cell at the beginning, Somah will keep fighting the player to the death. Saving and reloading fixes this.
 * After completing Mothership Zeta the player character may be bathed in a red or orange light. This may be a result of a teleporter lighting effect continuing after you have teleported. Restarting the Xbox seems to fix the problem. Another solution is to set yourself on fire with a Heavy incinerator to reset the glow effect. Unequipping your armor may also fix the problem.
 * After destroying the Cryo lab generator, it becomes impossible to leave the area through either the transporter or the doors (status of "Requires Key"). Sign out of Xbox live and restart your load the teleporter will work.
 * When destroying the generators, if the player enters the Engine room and kills all the enemies there before destroying the last generator, the game will not register the deaths of the aliens. The red cursors will appear, footsteps could be heard, and the player will also be attacked even though the alien corpses are clearly visible. The only way to fix this is by going around and shooting all the corpses of the already dead aliens.
 * If you attack Toshiro Kago and he becomes hostile, Elliot may run away and disappear from the game.
 * If you have not yet completed Who Dares Wins upon entering Mothership Zeta, the game may alert you that you've discovered the presidential metro location. The "Who Dares Wins" quest now has "enter the presidential metro" marked as completed.
 * After you finish your space walk, Elliot's forehead is see-through. Somah also presents the same bug.
 * When you fight through the Waste Disposal area and get to the end, the teleporter matrix may not work. This stops you from completing the DLC unless you reload a save before you enter the area, and then don't enter it.
 * Toshiro Kago may simply pick up a combat knife somewhere to use instead of his Samurai sword (which means you can't shoot his katana out of his hand to get it without killing him).
 * When in the Experimental weapons area, after you head to the far end where radscorpions and raiders spawn in a room below for you to test your weapons on, albino radscorpions will spawn constantly (around 20 were noted) and will stand around trying to find a way to attack you. The Xenotech Expert perk may also be awarded even if you didn't attack any of the targets.
 * Sometimes when the player picks up the Drone cannon Ex-B (correctly labeled on the floor) it will turn into a regular drone cannon.
 * In this case the Ex-B can often be found on the "corpses" of the destroyed bots, the Ex-B stays attached and falsely named regular drone cannons drop to the floor.
 * After you blow up the controls on the wall in the Robot assembly room, you can actually walk through the glass right beside the wall and be in the assembly line. Nothing except the glass around it is solid.
 * If you die or change the difficulty immediately after using the first healing arch there is a possibility that further healing arches will not be usable, either to heal or modify (although the options do appear, choosing to activate an arch does nothing).
 * When entering the Garbage disposal area, teleporters may lock. You have no choice but to load up a previous save and avoid that area. This may also happen in the Living quarters.
 * Exiting the game and restarting can fix this bug.
 * If the player completed "This Galaxy Ain't Big Enough..." quest and heads back to the Capital Wasteland and goes back on Mothership Zeta, Paulson will still be there, but the non-player characters will tell you that he left the ship.
 * Save games may become unloadable (crashing on the loading slides) after saving on the ship. Pre-abduction saves appear to be unaffected.
 * Fix (does not work all the time): restart the main quest in Mothership Zeta, save, then load the original unloadable file.
 * Sometimes while fighting an alien, it will just disappear and may reappear right behind you or somewhere else nearby.
 * Sometimes after completing the Space walk and trying to activate the lift for your allies to join, they may never appear, which makes it impossible to have the door unlocked to continue. This may be fixed by uninstalling and then reinstalling the patch. (Confirmed.)
 * Another way to solve this problem is to simply turn off your Xbox and then turn it back on.
 * While in the Cryo chambers with Elliot's fallen unit, if you run in to the back room and unfreeze the two living members before Elliot enters the room and begins dialogue the doors can lock permanently preventing any kind of exit.
 * While in the Experimentation lab, when you destroy the generator in order to bring down the force field blocking the exit, the animation for the force field will disappear but the door will still be blocked. Firing a weapon at the doorway causes a ricochet (energy impact in the case of energy weapons), just as if the force field were up. Loading a previous save does not seem to fix this.
 * Saving and loading the save again should fix this.
 * If you have the Gauss rifle you may use it to knock down any of your non-player character allies in the Bridge (assuming they are alive) and when they are knocked down keep pressing "A" and you can reverse pickpocket and subsequently pickpocket all their unique items.
 * Not necessarily a bug. Any knocked down character can be looted and reverse pickpocketed although you may have to wait for them to be knocked down again after planting the items on them.
 * When after completing the "Among the Stars" quest you meet up with Sally and Somah, the hologram of the alien will not appear, therefore the door will not unlock and all you can do is stand there and stare at the Earth through the window in the ship. It seems if Elliot stays alive this problem will not occur.
 * If you had the Winterized T-51b power armor in your inventory before you got on the ship and the aliens took it, when you get it back and if started but never completed the quest "You Gotta Shoot 'em in the Head", you will complete it upon receiving your armor back and you will get the achievement.
 * When in the Cryo lab if you freeze yourself and save your game while your character is still frozen, and then load that save your character will remain lying down on the ground and won't get back up making that save unusable. Using a previous save is your the only option.
 * In the Cryo lab if you teleport out before the generator explodes, it won't register on the game as achieved. You must stay in the room for the explosion. Also the teleporter back to the room will not function, you must reload a save to get it to work.
 * In the Cryo lab, if you freeze Elliot, you will be able to pickpocket him when he is on the floor without negative Karma.
 * When shooting any chair, blood will come out.
 * After finishing the add-on and entering the Engineering core, the game may constantly crash while loading back to the Bridge.
 * After the Space walk, Somah may not teleport to the Observation deck with the others. If you teleport back to the Engineering core, she will still talk about the Death ray and give you the quest to destroy it. Then if you teleport back, she follows.
 * The console will freeze when you go through the portal to the Bridge from the Engineering core. (Cache issue.)
 * The console will freeze when going to the Bridge from the Capital Wasteland while over-encumbered. (Cache issue.)
 * After falling from the elevator in the Maintenance level, jumping up the scrap pile to the character's rear may result in being trapped and requiring a reload.
 * After completing the Space walk if you happen to have Chinese stealth armor in your inventory its condition will be broken.
 * After a certain point in Mothership Zeta, you will not be able to use the health generators.
 * After using the teleporter to access the ship's bridge, upon walking forward your character falls through the ship. After reloading the save you are unable to walk forward and your shots will stay in mid-air. If the rounds are explosive, they will NOT explode.
 * The holotape that accompanies General Chase's overcoat may fail to play i.e. choosing to "Play Audio" fails to produce any sound and may cause the game to crash soon after.
 * Trying to acquire the 2nd drone cannon Ex-B may cause the game to crash when trying to pick it up.
 * Each time Somah and Elliot Tercorien needed to use a teleporter (to escape the Cryo storage area for Tercorien and to get down from the 2nd floor to the first floor in the Robot assembly section for Somah), they would freeze on or near the teleporter and would not follow. The dialogue box would not open up to ask them to continue to follow. In each case it was necessary to return to a prior save and start over. Eventually the bug will stop occurring and the non-player characters would assist as intended.
 * While working on destroying the mothership power generators in the 3 sections needed for the quest "Among the Stars", the Paulson character died while in the hangar, so bug is untested on him.
 * After getting to the Observation deck with Sally, Paulson, Elliot and Somah ALL of the characters just stand there and do nothing, halting the progress through the Mothership.
 * Maintenance level teleporter is lit up but doesn't work.
 * Solution: restart your Xbox 360 and load up the game and Maintenance level teleporter should work again.
 * After getting the Xenotech Expert perk and moving on to the Experimentation lab, your character will simply disappear in 3rd person mode.
 * This can be fixed by restarting the Xbox.
 * After completing Mothership Zeta, if you try to enter Tenpenny Tower, the game will freeze.
 * If you have a follower before beginning Mothership Zeta, tell them to wait at your house (Megaton or Tenpenny Tower). Then, when you complete "This Galaxy Ain't Big Enough…" and upon return to the Wasteland, your follower will come running at you and begin following. Because of this, the game thinks you have no follower and it will be possible to hire another follower. (if you have taken in Dogmeat as a follower and he is either following you, waiting somewhere, or at Vault 101, you will have to kill him in order for this glitch to work).
 * After completing Mothership Zeta, if you have not already triggered the events at Andale, when you arrive there, the residents will all be standing around the shed, and upon approaching them they will confront you about why you were poking around in the shed, regardless of the fact that you had just arrived.
 * After completing the Space walk, the teleporter to Engineering room activates but is unusable. This leaves you trapped and unable to continue.
 * At the teleporter leading from Biological research to the Death ray hub, when all of your teammates are standing idly by, waiting for you to enter ahead of them, if you attack Elliot with sufficient damage to the legs (possibly so that his now "fleeing" status would realize that it cannot outrun you, and thus choose the next best option) he will escape from you into the teleporter which leads to the Death ray hub. However, once you pass through the device, he does not appear on the other side, as per the flow of the story.
 * It is possible that after downloading Mothership Zeta that the previous installation such as The Pitt and Operation: Anchorage will become inactive with weapons and armor from them missing. Not fixed by restarting game or by loading previous save. (Might be fixable by deleting all the FO3 DLCs and reinstalling them after clearing the cache and re-patching.)
 * It is possible that after the installation of Mothership Zeta that your character will no longer have the ability to gain experience and that previous saves will become corrupt with the same glitch.
 * After completing Mothership Zeta, the game will freeze/crash when attempting to enter the Museum of History and subsequently Underworld.
 * Upon the entrance to the Observation deck, an error message may come up telling the player that a non-existent door cannot be opened until the chamber is de-pressurized. After hitting the "OK" button at the bottom of the message, the message will continue to pop up until a certain point in the Observation deck is reached (this point is very nearby and reached simply by walking forward). Once the player reaches this area, the message will stop appearing.
 * Once you complete the Space walk and enter the room after the decompression room, the transporter you are supposed to activate to allow Sally and the rest of the people to gain access to your level of the ship is already active but your party doesn't come to you. Thus you are stuck in that room and can't move since it requires Sally to open the door to progress.
 * Upon completing Mothership Zeta then teleporting back to the Capital Wasteland, the player is able to fast travel to Rivet City and trade with its occupants, but when you leave the entire game freezes. Reload last save to fix this.
 * Upon completing Mothership Zeta then teleporting back to the Capital Wasteland, the player is unable to fast travel anywhere without the game freezing.
 * If the character has completed Tranquility Lane and activated the Chinese invasion, multiple Chinese soldiers may appear in the Cryo lab, but only if Elliot is with you.
 * After you equip one of the Alien atomizers there is a very small chance that you won't be able to drop it or change weapon (the Pip-Boy will still show as if you had two guns equipped at the same time.) If you will equip another weapon it'll show that you have no ammunition for it. Changing back to the Atomizer will render it invisible in your hand. In order to get rid of the glitching Atomizer you must put everything you have in the container and then simply pick everything but the Atomizer up. The patch seems to fix this bug.
 * There is a glitch where when you complete the unmarked quest Election Day that when you try and go to the Bridge the game freezes.
 * After defeating the enemy ship, it is possible for Elliot Tercorien to become frozen in one place, any attempt to converse with him simply creates a black box where text should appear. After a few minutes, he should unfreeze and act as normal.
 * Sometimes after freezing he will occasionally move and then re-freeze in his new position, the player will still be unable to converse with him.
 * If you had followers in your control when you were beamed up into the ship, you may receive a message in the middle of the Mothership Zeta quests stating that they have died, even if it is a follower as tough as the Broken Steel-enhanced Fawkes, whose health is extremely high. To fix this, you must revert to before you were beamed up into the ship, and make sure that all your followers are fired and get back to their respective "home zones" safely. Then you may begin the quest.
 * In the Hangar after you cross the area where the ship is and attempt to open one of the force field doors, it can look open, but physically you can not pass or shoot.
 * Sometimes when Sally will spawn out of her holding cell, you can simply run up to her and talk, skipping the First Module. However if this happens, and you skip the Module, Somah might stay near the Module and won't follow the player for the rest of the add-on.
 * Sometimes there may be invisible walls and you will simply be unable to move anywhere. Usually occurs randomly in the game.
 * Upon returning to Zeta, the teleporters to and from the Engineering core as well as the teleporter back to Earth may malfunction and no longer work, stranding you in space. This may be fixed by restarting the console or loading a previous save that is not an autosave.

PS3
The Number 1 thing to do to stop glitches in this (and all parts) of Fallout 3'' is simple: TURN OFF AUTOSAVES. Immediately doing this, the game stabilizes and makes a lot more content playable the first time. Just remember to save yourself more often.
 * The repellant stick from Moira's chain of quests may still stay in your inventory after all of your items have been removed.
 * During the Quest "This Galaxy Ain't Big Enough…", when you turn on the teleportation pad nobody will come. Deleting the game data (not the save data) fixes this.
 * After staging the fight with Somah and killing the aliens, she may remain hostile to you.
 * After finishing Mothership Zeta, the player may not be able to return to the ship once they set foot on the Wasteland due to crashes during the loading screen.
 * When first beamed up to the ship, the game may freeze at the probe scene. The game won't progress, but you can pause, and an alien in the background is moving. This can be fixed by deleting the game data cache and/or reloading a save from the Wasteland or restarting the console and re-entering Mothership Zeta. However when an older save is loaded your arms may glow the color of the abduction ray when in first person. Can only be fixed by restarting the console, or exiting to the main menu and reloading a save.
 * After the aforementioned bug has occurred and you have reloaded the autosave, the hand holding the grip of a hunting rifle (the left hand) will be glowing a brilliant light blue, the same color that envelops the player when they are being abducted.
 * When older save is loaded you start off looking between the players legs. This is fixed simply by moving. This can happen if you are carrying or using weapons and armor from any other DLC. So before starting the Mothership Zeta make sure you are not carrying weapons and armor from the other DLCs.
 * When returning to the Wasteland, your followers may be at the beacon waiting for you even if they were asked to wait at your house. As there are often sentry bots and albino radscorpions around, make sure they are well armed and armored before you leave for MZ.
 * During the "This Galaxy isn't Big Enough…" mission, on the Observation deck en-route to the Bridge: Sally will just stand on the glass floor which overlooks the Earth, and won't open the door. This makes it impossible to advance any further. Some users have reported fixing this issue by loading an earlier save. May take several times. Leaving and re-entering the area may also work.
 * During "The Quest for the Stars", Somah may go up to the top level and stay there. This causes the game not to continue later on during "This Galaxy Ain't Big Enough…". Reloading an earlier save seems to fix this, as Somah will come through the teleporter in "This Galaxy Ain't Big Enough…" anyway.
 * When standing on the Bridge trying to shoot the other alien ship the character may randomly explode after a couple of seconds.
 * Sometimes, usually when you advance to level twenty, the skill point assignment and perk screens will not appear. Entering the next area seems to fix the problem, although this may cause you to skip a level. It is advisable that you save before entering the next area.
 * After killing the first aliens in the Holding cells Somah will not come with you. Instead she will stay in the cell and repeat her speech from before the plan. Verifies: 4 Reloading a previous save file seems to fix this.
 * Any teleporter may stop working, trapping the PC in certain parts of the ship or rejecting them access to other.
 * When first entering the Steamworks area, Sally will offer to assist in killing the aliens ahead. If you offer her a grenade, then go back to the Holding Cells, then return to the Steamworks area, Sally will be frozen against the vent, telling you to be quiet. Your grenade will be gone, and you must kill the aliens yourself. Everything will return to normal afterwards.
 * After completing Mothership Zeta, you'll sometimes freeze when you first enter the bridge. Hold your PS button down and it should work again.