I prefer the brotherhood to the NCR, but have been helping them because I don't mind them . I have been given a quest to destroy the brotherhood but I would rather destroy the NCR. I have talked to everyone I can think of I'm the B. O. S. but no one is giving me a chat option that isn't idle chat. How do I side with the brotherhood against the NCR?
There isn't really a way to side against the NCR with the Brotherhood -- Instead, you have the following options:
Broker a truce between the NCR and B.O.S.
Destroy the B.O.S.
Ignore the NCR quest to destroy the B.O.S. and side with a different main faction (Yes Man or Legion, since House is taken care of at this point), while continuing the B.O.S questline
To broker a truce, you must not have ousted Elder McNamara during the quest Still in the Dark. When the NCR gives you the quest to destroy the B.O.S., and you've finished Still in the Dark, go talk to Elder McNamara and tell him that the NCR wants to destroy them. That will prompt McNamara to propose a truce. If you've finished Still in the Dark and Elder McNamara won't talk to you, try waiting outside the bunker for 2-3 days, then re-entering and talking to him again (known bug).
If you ousted McNamara, the only way to make a truce between the B.O.S. and the NCR is through the following console command, which makes the game think that the Elder offered a truce:
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