Fallout 4 spoilers

My theroy of [SPOILER]SHAUN[/SPOILER] and [SPOILER]FATHERS[/SPOILER] lies

This whole entire thing is going to be a wall of spoiler text get ready! GOOOO!
Note: there is a reference of a last of us spoiler within but is marked by brackets

[SPOILER]I have spoken of my theroy of this before but I played a little deeper and learned a bit more, I am grasping inconsistencies in the story they happen far too often, I will not cover them all as I am not a theory nut but here we go...

[B]MISSION: Dangerous Minds[/B]
[I]Memory lane - kellogg's memories[/I]
By clicking on your pod kellogg speaks of you being backup and mentions being OLD MANS decision. I believe he is revering old man as father...

In the final memory he mentions old man again, Amari mentions this being a VERY RECENT memory, and the radio gives us exact date, Piper just released the article about the mayor, thus leads to her being locked out of diamond city.

before my old theory was still that was Shaun making father impossible to be Shaun, one mentioned that could of been the synth shaun, and the boy does say "Are you taking me back to my father." neither that was shaun that was lied to or was the synthboy.

My two possible theories
Shaun was killed by the institute they needed sacrificed the boy like [Ellie was going to be killed to find possible cure.] this falls apart a little with father repeatedly claiming to be Shawn and look the part.

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