I did NOT know that old dude was my son. I got to the Institute, after ages of side quests, and I am gearing up to kill everyone in the place for the Brotherhood. I find this little kid, who I THOUGHT was Shaun. The one that was stolen from me. Coincidentally I was using Kellogg's pistol, cause I like V.A.T.S. Then an old, vaguely brownish guy, who looked kinda like my (now dead, thanks to Kellogg) wife.
He did a thing, and my child got all slumpy. For a moment I was shocked that Bethesda would kill a child on screen. Then I queued up every V.A.T.S. shot I could on the man's face, even before he could speak. Then I made it look like he had a heart attack that violently removed his extremities, leaving him on the sofa. Fought my way out, did some more Brotherhood stuff, and then.
I do a little preemptive Googling for my options from here, and I found out the child was a robot, and the old man I ruthlessly, systematically dismembered for "murdering" a child was my son!
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#Offtopic
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Plot twist, the institute stole Shaun even earlier than you thought and swapped him out for some other random baby just to mess with you. Kellogg was Shaun all along and you murdered him in cold blood.