Well, I didn't do any quest for the Brotherhood before Reunions so I guess I am out of luck here.
Still though, I agree with the user below that this "best" ending is mostly for personal profit of having everything available. I dislike the Brotherhood vehemently and want them gone from the Commonwealth and I want the Institute to stop performing outrageous science experiments.
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I'll tell you what i told him, hell if you want three factions go for it :P It's a nice save to have, and only have one faction gone