All companions will follow your orders no matter how vile they may be.
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File credits
Thanks to alanos for the Boone Faction Tweak and Veronica Faction Tweak mods, was able to figure out how to make all companions docile by looking at their esps.
Thanks to ladynibenay for their Recruit Arcade Gannon as a friend of Caesar mod, was able to make him recruitable even if you were already legion because of that mod.
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Somehow you have managed to brainwash all of your companions. Did you use your high medicine skill to lobotomize them in their sleep? Or perhaps your science skill allowed you to craft some sort of slave collar. Maybe you used political connections with Caesar to have a frumentarii do the brainwashing for you. Mr. House might have given you a behavioral modification device. Regardless of how you did it though, congratulations!
Boone will no longer shoot the legion on sight, Arcade doesn't care if you are evil or work with the legion, Cass will help an evil character slaughter the NCR now, and Veronica will even help blow up the Brotherhood of Steel if so ordered. Rex no longer even cares about hats anymore, though long standing grudges against rats still hold true. Raul, Lily, and ED-E already answered orders without question. Companions will also follow suicide orders if you so desire, the passive combat stance has been fixed. A hostile enemey can unload an entire magazine of ammo into a companion set to passive now and they will just take it. Doesn't modify the companions themselves, so any cosmetic mod should be compatible.