In The Boys, when Billy Butcher (Karl Urban) came so close to getting his wife back, only to have her slip through his fingers, he fired the boy. Although not certain, this could spell the beginning of a supervillain arc for Ryan.
Homelander showed him anger
Homelander (Antony Starr) opened a well of anger inside Ryan. He kept taunting Ryan because he thought it would put his son on his side instead of Becca’s (Shantel VanSanten), but he did the opposite in The Boys.
Ryan (Cameron Crovetti) took advantage of a vengeful fury directed at his father that allowed her to kill for the first time in his life, and the ending of The Boys never offered closure for this moment.
Will be in a hostile environment
He was taken into the custody of Grace Mallory which means that he probably won’t be in the same warm and welcoming environment that Becca Butcher gave him, and as a result, Ryan’s anger could grow into something more malicious.
Billy Butcher views Ryan as a weapon, but has a harsh approach to showing it: he sends Ryan to live with Mallory, who is a complete stranger to him. Since a super killed his grandchildren, Mallory probably sees it the same way too.
He is easily manipulated
The Boys season 2 finale makes Ryan start a new life with just these dangerous ideas in his head. Ryan is still quite young, which makes him easily impressionable.
So if Ryan is told that he is a weapon and he treats him like that enough, he will believe it. If he does indeed believe that it is a weapon, he will probably start treating his powers that way.
That belief, combined with the rage that’s been bubbling up inside him, could easily drive him to use his powers for evil in The Boys. With Becca gone, there won’t be anyone left to get the goodness out of her. Therefore, it is very possible that he disappears.