Major_Tom said:
Oh. The "malignant growth" sounded like a supervillain speech, and the PC shot down a Vertibird so I assumed... nevermind.
No you can fight the brotherhood in the game, and I've had the end spoiled for me, while not the level of zealotry the BoS displays in new Vegas or earlier fallouts, FO4s brotherhood definitely aren't the shiny good guys from FO3 and can be morally justifiably fought against if you side with the other factions in the game. You get the chance to fuck their shit up if you want to, they just aren't as morally grey as the west coast chapters, who are basically colossal douchebags on the verge of being exterminated by the NCR.
Oh, also, in case it wasn't obvious, there are end game spoilers being spammed on social media and 4chan right now. Best not to go there if you don't want the entire story spoiled. Some are fake but some are also very real.