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. Read the terminal to get a little background, then push on. 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 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 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; at that point he'll be hostile and you'll have to kill him, finishing the mission. Alternatively, if his health becomes low enough 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. You're either with him or against 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).

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. Kill him and you will get a good end to the mission.

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 in full health leaving him to stop where he is talking and can't complete the quest. Killing him completes the quest.

Theodore can be killed by ghouls while you are exploring the basement. This results in the quest being completed successfully.

When Theodore turns hostile, the cannery robots will turn hostile but will not attack the player character. They will instead head towards the basement.