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If I travel with Danse, complete any quest/ wander around for a while, dismiss him, then fast travel to any Brotherhood occupied location (i.e. Boston Airport, The Prydwen), everyone within the vicinity proceeds to gun me into Swiss cheese. I have not once hurt a single member of the BOS while traveling with him previously, and back before I'd experienced bugs, dismissing him to another settlement after traveling together for extended periods of time did not cause the hostility. I haven't gotten very far in Railroad quests, I'm permanently hostile with the Institute, I stopped doing Brotherhood quests after Blind Betrayal, and the faction I plan on ending the main story with is the Minutemen.

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    Have you tried waiting a bit after dismissing him, or taking another companion with you? After blind betrayal Danse and BoS are hostile (and so are you if he is your companion). Maybe it takes a while until the game "recognises" Danse is not your companion.
    – Bounce
    Apr 27, 2016 at 13:04
  • @Bounce Yes, I have. I even completed a couple of missions traveling alone afterwards as well, but even then, they're hostile. Apr 27, 2016 at 15:18
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    That's strange. Have you tried waiting 30 days in an area away from both Danse and other BoS members?
    – DCShannon
    Apr 27, 2016 at 17:57
  • @DCShannon 30 in-game days, yes? No, I have not. Does waiting that long make any sort of difference? Apr 27, 2016 at 23:23
  • @MavisEverdeen That resets any cells not currently loaded. In other words, it recreates all the areas you're not at. If the BoS members are mad at you, but shouldn't be, then once you wait and return they should be reset and okay. This can fix most things in the game.
    – DCShannon
    Apr 27, 2016 at 23:50

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This is intentional and what happens after "Blind Betrayal". The BOS isn't hostile to you, they're hostile to Danse -- so when you travel with him that hostility transfers to you. You'll find that if you travel with another companion, the BOS will cease being hostile to you (assuming you're not actually enemies with them.)

This makes sense from a lore perspective. In the "Blind Betrayal quest, we discover that:

Danse is a synth. The Brotherhood of Steel hates all non-Humans, including Synths. Likely, however, this hostility is more because it's a personal betrayal from Maxson's perspective, especially since none of the other non-Human companions trigger similar behavior (this sentence is my speculation.)

This is why the BoS becomes hostile.

If you refer to the wiki page for this quest that I linked above, you can find this little blurb down in the notes. (There's a similar blurb on Danse's wiki page.)

If the Sole Survivor spares Danse, traveling with him will cause the Brotherhood of Steel to be hostile to the Sole Survivor. When Danse is dismissed, the Brotherhood will return to neutral status afterwards.

There are some side effects of this, of course. Even if you are friendly with the BoS, anyone associated with Danse in a temporary sense will inherit his BoS hostility status. When you don't travel with Danse, he's passively part of the minutemen faction; if the BoS attacks him, any minutemen in the area will also become hostile to the BoS.

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