After Ryan had rejected Homelander and chose Butcher over him, he started to listen in to the higher-ups at Vaught. He heard whispers and got sideways glances. They had guilty expressions, and it was obvious they were hiding something.
So John had started snooping around, in all the places he wouldn't look. They knew him, but he knew them better. He ended up in one of the main file rooms. If he were to look for something hidden, it wouldn't really be hidden.
He started to look through the files until he came across one that looked recently opened. He pulled it out, seeing it was one of the test Supes in the lab. But under one of the categories it said ‘Kin of Homelander.’
He didn't believe, or understand it. A kid? His kid? It only made sense. Why would Ryan be his only offspring? This didn't just mean Vought would burn. They did hide his kid and test on them for god knows how long. It also meant he had a second chance, as a father.