He was kidnapped. One of the earliest missions is finding out that he is at least 10 years old inside the Institute. The next step is to head to the glowing sea but you are level 14 so fuck that. You decide to build up some settlements so he will have a safe place to live once you re-kidnap him, a few more months in the institute won't matter.

So you help the local radio host with his confidence, steal the money and drugs from a deal, help an immortal vampire of sorts, end up retaking the castle, do some menial tasks for the railroad and brotherhood of steel, stop killer robots from killing humans, head to Far Harbor and end up solving their problems in one way or another. You're trip on Far Harbor makes you forget what you were originally doing so by time you get back to the mainland you are once again distracted by a Vault in need of assistance but also some man his family has been abutted by Raiders or whatever at an old amusement park.

Now you are the saviour/destroying of Far Harbor, A BoS Knight, saviour of the Railroad, General of the Minuteman, overseer of vault 88, the overboss of a bunch of raiders and so much more. After all that you go.. oh yeah my son right as you venture into the glowing sea naked as by now rads no longer harm you. Finally the story can continue.