They could be at any point of the story. Could have even quit right after his "dark past" was revealed.
"It's almost as if sometimes the character you're in control in of a VN can be wrong and are their own person, or something"
This trips me every time though. Because a lot of times authors use MC as the way to portray facts or it's a self insert. So the rare time the mc is wrong, you end up being completely fooled.