This has been a theory since Fallout 4 began and honestly I always dismissed it for the simple fact that the Sole Survivor has no recall code. It's hard to believe Father wouldn't use it if you rebel against the Institute. And yet he lets you walk around and contribute to the downfall of the Institute (unless you side with it obviously).
However after seeing Westworld which has remarkable similarities to Fallout 4 in many ways, I'm starting to think the theory might not be completely crazy.
There are questions not clearly answered like why does the Sole Survivor not remember anything before the day the bombs dropped or why is he so proficient at VATS and weapons even without a Pip-Boy? (apart from "game mechanics bro" explanation) Could it be that he's a prototype Gen-4 synth?
Anyway, no proof either way but here's the (crackpot) version of might have really happened:
– both parents died, one shot by Kellogg, the other due to a cryo-malfunction at some point in those 60 years
– Father became Director but grew increasingly disillusioned with the Institute
– Father also secretly came to believe that synths are people, he's only against synth freedom publicly because he wants to remain in power for now (one conversation with Desdemona in the vanilla game actually reveals that the Directorate could remove a Director who doesn't toe the line, hence why she doesn't believe that even you as a pro-synth Director could change anything, Father also seemed to be very fond of his younger synth version which makes little sense if he believed synths were just robots)
– Father evidently doesn't like the Railroad either way, but this might have more to do with their tactics than goals (not all that different from how Ford in Westworld believed Arnold didn't know how to set the hosts free, that only he could set them free, which actually turned out to be true)
– Since he cannot neither set the synths free nor work with the Railroad, he comes up with an alternate synth uprising plan involving a Gen-4 synth modeled after his refrozen parent. This synth would have all recoverable memories from the dead parent (hence some gaps like not being able to remember childhood when DiMA asks) and share his/her personality, would have greatly improved combat abilities hence being able to kill off entire bases of raiders, gunners and even kill coursers, deathclaws and behemoths. Most importantly though, NO recall code, no turning back once released
– he tricks his inner circle to go along with the plan as part of some "experiment" (and for his own morbid curiosity having missed out on what's it like to have a real parent) and he tricks the rest of the Institute into believing this is in fact his real parent
– the first victim of this plot is Kellogg (even in the vanilla game Father admits he wanted Kellogg to die out of revenge)
– as in the vanilla, synth Shaun is used to lure the (Gen-4) Sole Survivor BUT why was Kellogg given the assignment to kill off Dr. Virgil if he wasn't ever going to make it? the truth is, Father never intended for Kellogg to kill Virgil, he intended for you to kill Kellogg and find Virgil in order to reach the Institute
– if you do side the Institute Father tells you "don't worry about taking my place, make your own place", so even if you fail to destroy the Institute and set the synths free, there's still a chance you might rebel later with no hope for the other scientists to stop you, you're not a frail old man like Father, you're basically a freakin' super-Courser, in time you could force the Institute to free the synths
If this theory is true it would also explain why Father doesn't just kill you on sight if you go to the Institute but refuse to join, it would explain why he seems to view synth Shaun as a real boy despite his public stance on synths being just machines, it would also explain why he can forgive you if you screw up some missions or openly associate with hostile factions (remember, the SRB is tracking YOU). It would explain the interaction with DiMA in Far Harbor, would explain why you're so good at VATS and combat even before you get your Pip-Boy.
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