Which faction do you think are "the bad guys"
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I'd say Brotherhood or Institute. Brotherhood is bad because they're basically huge d**ks that give you cool stuff to play with so long as you kill literally anything that isn't normal (which is technically racist towards ghouls and synths). I also say Institute because out of the 4 main faction endings, the Institute explodes in 3/4 of the endings. To me, that implies villainy (of course the bad guy is supposed to die).