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 him about it after she leaves will give you the option to offer to help him out by clearing the mole rats from the building. He'll give 50 caps up front.

Despite him mentioning that you 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. You 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, killing them as you go. The tunnel is fairly linear, but at the first place where you're 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.

After going up some winding stone steps you will be on 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 you 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). You will now be up on gantry that overlooks the area where you first encountered the ghouls.

After a while you'll get back to the factory and find out that the meat Theodore's been selling has some ghoul in it as well; upon returning to the cannery floor, he'll threaten you 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 you get within close range to him during the gunfight, he will plead with you. He offers to run the business and split the profits with you. You can either agree or kill him to complete the mission.

You can also pacify him to get the dialogue option to come up when you approach him. However, there isn't any way to make him stop his shady business practices without killing him.

The endings seem to be about the same. If you are with him you get some caps and some xp, if you kill him you get the xp (same xp) but no caps save for what he might have on him.

Alternative shortcut
Before taking the elevator to the basement, press the red button to send the elevator down. Then once it's at the bottom, press the button to bring the elevator to the top and immediately jump down. You'll take some fall damage, but this will trigger the "Confront Theodore Collins" message to pop up which you need to finish the mission, whilst also returning you to the main room so you can skip the entire sewer area.

Walk to the metal catwalk hut where Theodore will be waiting in the area where you get the bobblehead. If you talk to him he'll only try to sell you potted meat and the top option will be left blank, or he can be killed to end the quest that way if desired.

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 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.
 * 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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