So I just met Shaun and found out that he was taken 60 years ago. And my OCD kicked in... If you recall Kellogg's memory, he was sent to deal with Virgil and Shaun (10 years old) was taken to the Institute. So we go to Virgil and he thought it was Kellogg coming to end him, but it was 50 years ago!!! Was he waiting it that cave for 50 years? And he just forgot to mention that? I dont get it. Am I missing something or there is a hole in the plot.

I think babby shaun was the synth shaun.

Yeah, the ten year old Shaun you see in the flashback is the synth.

You can hear him say "Are we going back to Father now?" Which means the real Shaun is actually Father during that sequence. Not sure why Father had the Not!Shaun being looked after by Kellog though...that's kind of weird.

Escaped or taken maybe?

Beacause he wanted to go see father as in shaun

Nah, its clear he was supposed to be taking care of SynthShaun but it just seems odd why Father would have allowed that when he clearly had a disdain for Kellogg.

I mean, maybe he was taken by somebody and Kellogg was sent to get him back.

I think Elder Shaun had Kellog taking care of Synth Shaun because he wanted the kid raised in an environment away from his fellow Institute members and Kellog is the only person who knows what it's like to live outside Tomorrowland.

Every other Institute member would treat Synth Shaun like a child-shaped toaster.

True, except possibly Dr. Lee as there is a terminal post about how another scientist believes she may be to attached to Synth Shaun.