When Remiel slowly shows himself to be an evil prick. It often happens in JRPGs that the people at the head of a religion turn out to be evil, but the angels themselves, that was new for me. Oh and then God himself descends from heaven and kicks your ass. The writers have cleverly duped me into thinking it was a bland unoriginal story, and then they smacked my expectations in the face and gave me an awesome twisty turny story.
The many plottwists in ToS is why I consider it one of my favorite games.
The many plottwists in ToS is why I consider it one of my favorite games.