My third time playing through this game and I finally took the time to talk to all the scientists in the Institute past introducing myself to them. In the Bioscience division, you hear a couple of scientists talking about the Warwick Homestead Initiative and the replacement of Roger Warwick. You can read a http://fallout.gamepedia.com/The_Institute_terminals#Warwick_Homestead_Initiative in the division that gives more background to the whole program. My question is simply: what the hell?!
I entered the Institute set on giving it truly a fresh look. I listened to everything Father had to say, and I felt the same unease at some of his responses, but I was more considerate of the time gap and tried to be understanding. I talked to all the scientists, read every terminal, and paid close attention to the random encounters (the one where the courser is interrogating the synth about terminal use is always a little unsettling). I got into the Bioscience division and managed to catch the conversation about the Warwick Initiative and when I found the terminal and read about it, I almost couldn't believe it. The program involves kidnapping the patriarch of the Warwick family, Roger, and interrogating him "intensively" and then replacing him with a synth to grow new strains of crops and collect data. Once the mission is complete, the evidence is to be "purged" which is a strong indication that they are just going to kill them all.
I get the argument that the FEV stuff is probably not known by anyone but the upper echelon of the Institute, even though the FEV lab is not that isolated and it always struck me as odd that no one (except for Dr. Li) bothers to ask what happened to Virgil, but it is plausible. This however, is in plain sight. Everybody has to know about this, unless they are being willfully ignorant, and after reading it (I'm not sure how I missed it the first few times) I don't think I could ever support the Institute. I think they are all psychopaths, with a few exceptions.
I'm just curious about what other people make of this.