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In addition to the fact that they may not be as perfect replications of humanity as theorized.
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That they do have emotions, such as anger, affection, and love. Kirk was able to show how these androids may not be as "unfeeling" as the scientist implied. Kirk demonstrates the failure in this logic though in a very similar fashion to how the Lone Survivor can persuade John Henry Eden that he isn't an Artificial Intelligence. They wouldn't have any use for war because those negative emotions could be removed. The Institute discusses how Synths are superior to humanity, or rather an evolution of humanity, that can persevere in the Commonwealth (and the Wasteland in general) due tot heir resistances to disease, radiation, hunger, etc. Thus, shedding their mortal form in favor of an android body. His theory was that immortality and peace could be achieved by replicating humans exactly as they are. You see, the facilities to create androids still existed and functioned perfectly fine. However, the part that I think Bethesda took from this episode is what the scientist wanted to do with the androids. These androids destroyed the people that created them because they were flawed in comparison. The episode "What are little girls made of?" of Start Trek shows a scientist that discovers this ancient "race" of androids. My best guess though is that they were inspired by Start Trek: TOS when it came to the purpose of Synths.
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Technically we don't actually know their plan because Bethesda, as always, never really went into detail on it. I think they have good intentions (which we all know how good intentions go). I think their intentions are a lot less evil than people think. That's not really what the Institute is doing. I was genuinely exited until I found out new faction has no ending it's a sidetrack nothing more, still It's my faction choice and I'm gonna nuke the institute one way or another So Player, the choice is yous which evil you see as lesser? that's actually a good narrative choice, but in this setup makes me want to forget main questline even exists, but wait we have new Raider faction hundreds of players cried about, Bethesda listened and delivered. On the other hand we have neo-socialistic Railroad children (Railroad being major faction is a serious overstatement imo) and the Minutemen., both are terribly written the last suffers from additionally bland questline and Preston, while first is just infantile I went with institute on my first playthrough and got terribly disappointed, especially with their "let's kill all humans and substitute them with our controllable machines" for that even BoS and Enclave are better while being effectively flavours of Nazis of the Fallout age
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