I have this theory that Father was never really in charge of the Institute and was mearly a puppet with some bigger force out there pulling the strings. Now I know this might sound absurd but I have some interesting things to say. We all know the Institute came from the ruin of the Commonwealth Institute of Technology after the bombs fell. The spent years underground and became what we now know as the Institute.
From then until Father came along we have no information on who/how it was run. It’s not impossible that some outside force was leading them and providing resources to rebuild the Institute. The CIT was just as devastated as anyone else when the bombs fell so it’s not impossible some outside force, maybe the Enclave even, decided to take advantage of these scientists.
Also I find it weird that Father of all people became their leader. We all know he was the result of their brainwashing and his genetic code was used in all Gen 3 synths but besides that we don’t hear of his other achievements that merit him a leader. He carries out his own experiments (child shaun) that don’t benefit the Institute, whatever he says is final (making you the next leader), doesn’t take objections and just all around doesn’t strike me as the leadership type. It doesn’t seem like he was elected and more so given the title of leader by someone.
Also doesn’t it seem weird that he makes you out of all people the next leader of the Institute? There were obviously better candidates for the next leader but out of anyone he choose you. It’s almost like the title of leader carries no weight unless it’s true. I think that whoever is the leader of the Institute is just mearly a poster boy for whoever is working behind the scenes so as not to attract attention to themselves or be a target for the other factions.
So in summary there could have been another bigger faction out there that was controlling the Institute or the Institute is bigger than we think they are or even the Enclave could have been behind this.
Edit: Forgot to mention waking you up from the cryopod could have been another example as they purposely knew you would make a good candidate as the next leader since you were related to Father so they purposely unfroze you for that reason. Also having access to the vaults control system which was made by Vault-Tec that we know ended up becoming part of the Enclave. I probably should rewrite this now that I got these new ideas
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