Just finished it. I sided with The Institute.
The Brotherhood are back to being assholes. Instead of building on their depiction in Fallout 3 (which I was fine with; it had an explanation that made sense), they junked the whole deal and decided to put a real prick in charge. Disappointing, but after being hammered for so long with "hur dur they fucked up BoS" I imagine Bethesda thought they didn't have much choice.
The Railroad were naive. Just naive. They thought that Synths were human beings (they're not), and they thought Synths were slaves (they're not). Synths are robots. Machines. They need to be closely monitored and controlled. They're not people, even if they look like it.
The Minutemen were... eh, they're there. They're not that interesting. I could have built up resentment over the fact that every time I handed in a quest Preston had another one waiting for me, though. I didn't even get a chance to do any Minutemen end game quests for some reason.
Out of all the available factions to choose from, I had to go with The Institute. They're not bogeymen. They're not evil. They're just scientists and engineers underground, living in a safe environment and conducting their research. Siding with them, you see their Wasteland interactions from the other side. If anything, the Institute being so secretive is what has set the Commonwealth against them. They don't abduct people by force; they ask politely, and most agree to go. They corral escaped synths because without close monitoring and control, synths can go haywire and malfunction. You know, like that guy who got shot at the noodle stand. Pretty much everything the Commonwealth had to fear from the Institute was given a satisfactory and understandable explanation. The Institute were not the bad guys. Nobody in the game are "the bad guys" save Kellogg, and he's just a mercenary with no personal involvement in your plight at all. Hell, the only reason you fight with the Railroad and the BoS is because one won't stop stealing your shit and the other wants to take all your shit. The Institute leaves the Minutemen alone, because the Minutemen are just regular people trying to help other people.
I think the plot suffers a bit for this, having no real villain. At the end of the day the game ended for me at my son's death bed, saying goodbye, and promising to lead the Institute to a brighter future for all mankind.
Oh yeah, your son puts youin charge when he's gone. By the end of the main quest there's nothing in the Commonwealth that'll stop you from making things better.
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