Mystery Meat

Mystery Meat is a side quest in Fallout 4.

Detailed walkthrough
Upon arrival at Longneck Lukowski's Cannery, Theodore and Trader Rylee will be arguing about her ability to sell his product and they will mention people getting sick after eating his canned meat. Asking Theodore about it after she leaves will give the Sole Survivor the option to offer to help him out by clearing the mole rats from the building. He will pay 50 caps up front for the service.

Despite Theodore mentioning that one shouldn't go into the basement, there's nothing in the cannery proper itself to do, except get the Barter bobblehead and the Tales of a Junktown Jerky Vendor magazine inside the metal catwalk hut at the top northwest corner of the main cannery room, so head to the elevator in the southeast corner and take it down. When it reaches the bottom the elevator will be locked out by Theodore. One can then read the terminal to get a little background and discover that Theodore had been using mole rats in his meat to increase his supply and is still looking for an alternative meat that will allow him to produce even more canned meat. The room straight ahead is trapped and has some minor loot and critters; there's a good chance the radroaches will trip the trap and die on their own.

A bit further along is a room with some feral ghouls and a hole in the wall; continue through and kill. The tunnel is fairly linear but at the first place where one is required to dip into the irradiated water, there's an area that can be reached behind the stairs with a few extra bits of minor loot and an advanced-level safe.

Up some winding stone steps is a wooden walkway that forks. The left-hand side leads to a dead end with a machine gun turret and novice locked ammo box and the right-hand side will lead back, past a generator with a fusion core (there are a couple of frag mines on your path here and just past the broken generator in the next room). This leads up on the gantry that overlooks the area where one first encountered the ghouls.

After a while the Sole Survivor will get back to the factory and find out that the meat Theodore has been selling contains some ghoul too. Upon returning to the cannery floor, Theodore will threaten the Sole Survivor from the control room and turn hostile along with the 3 cannery robots. Theodore has companion-level health but no armor. Killing him will end the mission. Alternatively, if one gets within close range to him during the gunfight, he will plead for his life, offering to run the business and split the profits with the Sole Survivor. One can either agree or kill him to complete the mission.

It is also possible to pacify Theodore to get the dialogue option to come up when he is approached. However, there is no way to make him stop his shady business practices without killing him.

The endings and rewards are similar. If one is with him you get some caps and some XP; if he is killed, one receives the same XP but no caps, save for what he might have on his corpse.

Alternative shortcut
Before taking the elevator to the basement, press the red button to send the elevator down. Once it's at the bottom, press the button to bring the elevator to the top and immediately jump down. The player character will take some fall damage but this will trigger the "Confront Theodore Collins" message to pop up which is needed to finish the mission, whilst also returning the player character to the main room so the entire sewer area can be skipped.

Walk to the metal catwalk hut where Theodore will be waiting in the area where the bobblehead is located. If one talks to him he'll only try to sell potted meat and the top option will be left blank. Alternatively, he can be killed to end the quest that way.

Bugs

 * Talking to Trader Rylee before Theodore will cause a dialogue bug that removes the option to ask him about people getting sick; you can still start the quest by going inside of the cannery and going down the elevator in the southeast corner. Leaving the dialogue and talking to him again may fix the problem.
 * Sometimes Theodore will speak to the player while at full health, but his dialogue will cut out, making it impossible to spare him. Killing him completes the quest. However, if the player character pacifies him and then speaks to him, there is a chance they can spare him.
 * Theodore may start to engage in his speech after the climb through the sewers but will immediately cut himself short, with the dialogue unable to continue. Moving him while he is in this state and walking back to where he started to talk will sometimes fix this.
 * Theodore can be killed by ghouls while you are exploring the basement. This results in the quest being completed successfully.
 * Theodore can be killed by ghouls before completing the "Inspect the cannery" objective is completed. This will result in failing the objective, and failing the quest.
 * When Theodore turns hostile, the cannery robots will turn hostile but will not attack the player character. They will instead head towards the basement.
 * Alternatively, the robots may just flee and/or stand still.
 * Cannery robots are actually incapable of attacking and will simply flee from the Sole Survivor.
 * This was fixed in a patch.
 * After agreeing to partner with Theodore, he may be found dead when returning to the cannery later, apparently killed by the cannery robots. This seems to occur if the robots take damage during the fight prior to speaking with Theodore and coming to a truce.
 * After killing the cannery robots, hurting Theodore and walking up to him, he will just stand still and continue being marked hostile.

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