Wow, the Brotherhood sure are annoyed with you if your Minutemen take out the Institute.
'bring your brothers and sisters next time' whine, whine, whine.
As I played the 3-faction ending, saving both the Railroad and Brotherhood,
PAM will happily send you out to kill 'rogue' Brotherhood (which is remarkably easy to accomplish),
and yet the Brotherhood don't notice and remain your allies.
Too busy whining I guess...
Does anyone else find the Brotherhood a whole load of no-fun if they are not used for the final showdown?