I think this is unfair to Bethesda’s version. Yes, the Brotherhood in Fallout 3 is benign, but that’s because it is being run by Elder Lyon who is an unusually kind and open-minded guy (and from comments by his subordinates we learn that not everyone respects that). In Fallout 4, after Lyon’s death, we find the Brotherhood back to its usual bigotries against non-humans. They are “good guys” in that you can ally with them against the Institute, but at some point you have to decide whether helping synths (which they hate) is more important than having them on your side.
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