You mean nothing to him (remember that he and the institute are moustache-twirlingly evil) until you find the institute and he realizes he can use you He knew he was dying and probably let you out from guilt, never imagining he would actually meet you. He serves as the primary antagonist of Fallout 4 unless the player character chooses to side with him The answer to every question is that Shaun never intended any of what happened.
After the Kellogg boss fight, you're told by Valentine and Piper to go to Goodneighbor and use the Memory Den to explore Kellogg's memories Shaun, also known as Father, is the son of the Sole Survivor and is the leader of the Institute in 2287.
The answers to this lie in the Great Green Jewel itself, Diamond City.
