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I want some advice, I started a new playthrough, and the furthest I got before this one was going into caesar's camp or something dressed as one of his legion, but when I returned to the friendly faction, I left the armour on by mistake and they turned on me, and I lost my save.
I haven't got a companion yet, but I'm about to fix ED-E. What happens if I try something similar, and try to dress up like a normally enemy faction and go to their base with a companion (ED-E or other)? I'm trying to do a speech/int run , how should I manage my companions so they only shoot when I start to get into combat, or I am sneaking around or walking around in costume?
As far as I remember, your companions will only attack if the npcs are hostile with the exception of boon. Boon will always shoot legion on sight. You can have some decision over their actions though by talking to them.
As for the armor it does matter when and where you have it on. Again my memory may be foggy but factions can be peaceful or aggro depending on what you are wearing. You can even go into a camp with hostiles if you have their faction armor on.
Take all of this with a grain of salt though, it's been a long time and I did play with and without mods.