Problems with the story [SPOILERS]

[Moraelin]

1. The Institute's actions don't make sense.

 

Piper talks about kidnappings and the sort by the institute throughout the commonwealth but there is no mention or explanation of it anywhere, you can't ask Father about any of this stuff, nor do you find any evidence of human experimentation in the environment.

 

If you actually found the FEV lab, to retrieve Virgil's serum, and actually read the terminal, you'll see they were experimenting on humans with FEV. All those supermutants in vats were not captured supermutants, but people who had been infected with FEV, and then documented their resulting level of aggression and whatnot. Virgil apparently even begged father to stop the experiments, and assured him that nothing more can be learned there, but apparently Father insisted to continue anyway.

 

Also, you can find plenty of evidence of very recent (as in, RIGHT NAO) people being replaced with synths. E.g., the Art vs Art encounter, Roger Warwick, etc.

 

 

 

9.Father says that he let the player out, but he lets his Corsers to kill the player. Even though we know that in this world no normal human could defeat one of those. Does Father want to outright kill the player? He even lets the Player face Kellogg when we also know that Kellogg has been playing this game for over a hundred years there's basically no chance the player will come out on top from the game word's perspective.

 

You can actually ask him on the roof after the Battle Of Bunker Hill, and he's quite candid that it's just that

 

A) They didn't need you as a backup any more, so no point in keeping you on ice, AND

 

B) it was his idea of an experiment to see how long you can survive in the new hostile world.

 

Seriously, his only interest in his one surviving parent was some curiosity to see how long until you're killed.

 

 

 

10.Vault 111 is full of subjects from before the war, somehow the Institute kills all of them so that the Player can be special.

 

Whether it makes sense or not, Father actually answers that on the first encounter. An infant was the best source of pristine DNA for gen 3 synths, and they wanted one backup source, related to the first one, in case they need it. Everyone else was killed.

 

Even Kellogg in the memory questions why did they have to kill everyone instead of refreezing them, but assumes it's the Institute head's idea of tying loose ends.

 

Presumably if the player's spouse would have let go of the baby, then the spouse would have been refrozen, and the player killed too. They needed just one backup.