Two days prior to this I asked over on Reddit for help regarding why the hell the Faceless were attacking me when trying to ally. Also consulted the wiki, but my search found that I should, at worst, be merely neutral with them.
To whit, I have:
-Healed the Core City faceless, and he survived (he even met me in the Institute)
-Got my mind read by the Rail Crossing faceless (managed to talk him down to spare Chopper)
-Talked with the Foundry faceless, told them where the Cube was (at the time), and let them live
-And at the time I talked with the Commander, my kill count was 18 but my Effective Thought Control was at 140 (actual was around 80 or 90)
The last part had someone tell me I should throw my savegame here because, according to them, even with a kill count the Thought Control check should've set them to neutral at worst.
The save is at the Deep Caverns checkpoint, immediately after the elevator sequence and before meeting Rahm-Umbra
-Here's where I would've put my google drive link to the save file, but the start new topic says I can't-
Addendum: If anyone wonders how I know exactly how many Faceless I killed, I got so mad at the circumstances that I spent an hour trying to blindly parse hex code so I could edit it safely. This save is *before* I went and did any of that, as at the time I had a quicksave slot before talking to the Faceless Commander.