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Just kill them and you can repopulate Covenant
So a no to siding with Institute and a yes to finishing the game?
If you went into the sewers across the lake and killed the Covenant guards there that would have made them hostile as well.
My own quest was royally screwed up because I accidentally found the Compound before starting the quest, and the guards were instant aggro (I stepped too far in, need to halt and wait for dialog) and before I could think "hey, this is hte kind of situation quests start with, NPCs and hidden areas" I'd killed Manny. I'd talked to Dan before, I think, but not enough to start his part, so I was hosed. Later on (post-finish) after a fruitless hunt for Dan I went back in the compound and snuck past everyone to see if I could get things to trip by talking to the doc.
All I got was "I will not beg for my life". Great. Looked around a bit and tried a few things, finally popped a gas tank next to the doc just to see if that furthered things (I'd opened Amelia's cage, found out via pickpocket that she's literally *holding* a synth component and possibly not integrated with one, and only got "I'm not a synth" out of her). Nothing was happening, so I figured I'd just take over... spawned some base ghouls to get the guards going, didn't work as planned and they found me and aggro'd so I cleaned out the compound. Back to Covenant and everyone there was aggro (but NOT the defenses!) so I lured them in ones and twos out the front door and basically hosted a slaughter party. Shame.
Back in, searched the bench, got a Covenant. Amelia's probably still sitting in the compound in an open cell protesting that she's not a synth, Stockton doesn't mention anything about it, whatevers.
For the console command crowd, the quest was on level 900, that's unlisted as a marker. Haven't tried setting it to 700 or 720 yet, but I may because all the covenant items are still listed as owned. Left the place empty, so far. Deezer's all alone and 27% happy...
I tried 'unlock' but the second I set foot in Covenant everyone attacks me...
I have found a way around my problem now but it's not ideal. If I turn off collisions and hover - so as not to touch the ground - no one seems to want to kill me.
Personally, I've "clicked" the workbench many times without issue.
Then like mfree and me said if he killed the compound people in the sewer pipe that could be his issue as well.
Those are the only two things that will make them hostile without ever entering Covenant.
I haven't sided with any faction yet (I never felt I liked any of them), I have visited the Institute though.
I haven't killed any people in the sewer pipe or done anything in the sewer pipe. The people inside Covenant only attack when I turn off collisions to get through the locked door. My problem is the door is locked for no reason - I've done the test and they have let me in before so I should be able to enter.