It really bothers me that in the memory from Kellogg it references the "Old Man," and that he claims he only took Shaun 10 years ago. Really not much point to that lie. So here is my idea, I posted it earlier, but think the title was misleading. Sorry for the bad grammar. I probably have typos as well. It's long, so read on if you are interested.

Spoilers follow





I'd like to see another twist to the main storyline, that keeps your quest for your son from being pointless.

Shaun is still alive. Father was a synth, and an imperfect one at that. The female scientist, shown in memory, who assisted Kellogg in the abduction had a crisis of conscience. She had known they were going to collect a clean “sample” from a vault, but did not count what that would entail. Wrapping a child from the arms of his parents and then seeing them shot while the other watched on in horror took its toll on her. Knowing the rest of the inhabitants would be left to die was too much. She had to do something….anything.

On returning to the institute she was instructed to begin harvesting DNA from the child, as much as possible even if it meant killing him. Unable to bear the thought of now murdering a helpless infant she came up with a plan. Telling the Old Man it would take a while to prep for extraction, she began her work. Using some old date on advanced cloning techniques and cancerous cell growth she was able to extract a small sample of cellular material and accelerated its growth exponentially.

Now, the infant, Shaun. He wouldn't be safe in the institute, they would corrupt him or kill him it they knew he survived. With help from her husband a small cryogenic chamber was constructed, fueled by several dozen fusion cores, and transported to room in a collapsed wing, sealed off long ago during a construction accident.

The old man referenced in the memory is the same as father. But why does he look like you and your spouse? The Doctor, now experimenting with Shaun’s DNA, was tasked with creating a new body for the Old Man who was dying, and could no longer be sustained by implants. To do so, she would have to create a perfect Gen 3 synth. She succeeded, and in the process of transferring the memories of the Old Man into the new body, transferred some saved imprints from the infant Shaun. Images of his father and mother over his crib. This would help further her plan for at least partial redemption.

When the transfer was complete the Old Man took on a new moniker, calling himself Father. Years passed and some obvious health issues began to arise. While longer lived than most humans, Father still seemed to be getting ill. Upon completion of a thorough medical exam, the Doctor discovered the method used to quickly acquire genetic material and avoid harming the infant had damaged some strands of DNA. She was able to correct it in the samples she still possessed, but any synths created using Shaun’s DNA exclusively could not be saved, and would eventually die of an aggressive form of cancer.

When confronted by Father she blamed the problem on the rush to create a replacement body, and general scientific trial and error. Father,though angry, tasked her with growing a new body with the now supposedly greater understanding of the process. She set to work, but father had her cut short the growth of the new synth, intent on stretching it's potential life as long as possible before needing a new transfer.
The process began to transfer Father into the now 10 year old body of the synth. However, even to her surprise, the process failed. The damage that was causing the cancer was preventing the transfer as well. She discovered that it would also prevent the use of any implant suspended aging as well. Father was dooomed.

Father was furious, and probably afraid of death. Who could be worthy of running the institute after his passing? No one! The Doctor had a plan though. Everything she had done, every step she had taken over the years had been waiting for this opportunity. Father had left one of the infant Shaun’s parents alive. To be used as a backup plan. Slowly, over months of subtle manipulation and a few intentional remote stimulations of Father's synth brain, she was able to convince him to release the other parent. The constant flashes of the imprints from Shaun caused him to unconsciously begin to see infant's parent as a worthy successor.

But how could he convince them. He decided to play a role. Using his failed synth replacement body, he would lure the parent to the Institute, then he would claim to be the child they had lost so long ago, after seeing the devastation and brutishness of the wasteland he was sure they would take up his cause.

The Doctor, now well past 100, was beginning to feel the effects of old age. Her implants, prototypes of those given to Kellogg, could no longer sustain her. Nor did she want them to. In her final days she set messages and instructions to be delivered to the Sole Survivor when they finally made it to the Institute and after Father had passed. These would detail the what had been done, why so many details seemed forced, why the Sole Survivor still felt their son was alive somewhere out there. Finally, it would detail how, after all these years, and all the searching, to finally be reunited with their son.

He said "taking care of the kid was the old man's idea" he was referring to the Synth as the kid not Shawn. I don't remember him saying "10 years ago" at any point

This would remove 99% of the story's pathos.

Yep, when X6-88 takes the kid Kellogg is sent after Virgil who has only been gone from the institute for a couple months.

Maybe I am misremembering. Back to memory den!

And true, but honestly I really hate the plot twist, maybe it's just having a kid of my own, but the plot twist makes it feel like all the work I did was for nothing and from there on I just want to watch the world burn, not save it. Maybe if you had found out at the beginning and he was already dead, so the game was instead about vengeance and coming to terms with your loss. Don't say loss of spouse. I'd have shot them myself for a few bottlecaps. Sorry for crappy sentences. On phone...

I would feel less motivated by revenge than I would be to try to find my living son. Yes, the revelation that he has already grown up and then promptly dies makes you feel bad and that your quest to find your son the way you wanted ultimately failed, but it is better than go find and kill the people who killed your spouse and your son. You still have to come to terms with your loss, it is just after seeming your son old and then dying, rather than just at the start.

I like it, because you have to mourn your spouse throughout the story, you get vengeance when you kill Kellogg, but then you are twisted and have to mourn your son and/or get vengeance too.

Probably would have made the destruction of the institute a tougher decision if Shaun was a grandfather at this point and you got to meet your great grandchildren. Bethesda could have even had some fun with a random appearance for Shaun's spouse and then extrapolating the appearance of the children and grandchildren.