Warning: Massive spoilers ahead:
Nothing. You can't even ask Father about the abductions. It's a horrible let-down with a nonsensical storyline.
At first we are told by Hancock that Shaun is ten years old. Everything so far leads us to believe that. Then we find out that 60 years has passed. Then why did Hancock say in the vault flashback that he got his orders from the "old man"? It's a mess. It's deliberately engineered so that there is this big reveal at some point, but in doing so any semblance of a logical plot goes out the window.
Then there are the generation 3 synths. The most advanced piece of technology ever. Indistinguishable from a human being except through autopsy. But they aren't treated like that. The Institute treats them like low-value common tools even though that is totally nonsensical. So you create sentient beings that for all intents and purposes are just like human beings and then you treat them like low-value slaves, why exactly? And why were they developed in the first place?
The whole storyline is a disjointed mess, the institute has no discernible sane motives or behaviour and I can't even tell my son to stop replacing people.
Yuck.