As far as I know, if you finish the main questline and side againt the BOS(meaning, you destroy the Institute but not with the BOS), the BOS take (or should take) a dislike to the MM artillery, and radiant quests start: "Defend Artillery", which leads to MM and BOS becoming enemies. But I think that is bugged, as I have never seen that radiant quest. I think after main quest line, the game should not stop you becoming permanent enemy with the BOS. I will see if I can find a saved game for me to test (to see if I can force BOS to become enemy). --------------------------------------------- The only way I found was to kill elder maxon, yes, I had joined the BOS earlier in that game. After that, talk to Preston, and he says its time to deal with the BOS. So all I can suggest if you do not want to go deeper into Institute questline, is to join BOS early in main quest line, and follow thier questline up until at least getting access to the airship. You can then kill Maxon if you want them to become permanent enemy.