In SO3, they don't gradually, or slowly learn they're actually in a game. It happens very suddenly.
See, I might almost envision it as paralleled through our own experiences as humans.
Perhaps a trilogy. The first would be largely dominated by religion and exist in a very traditional RPG world. Your character perhaps acts to fight the church and it's suppression of science. Insert "magical" element for sake of separation from our own reality and to establish an actual sense of godliness within the game.
Then the second game details the world's tumultuous evolution into a more scientific world. Perhaps there's a hyper progression of scientific achievement through preparation for an unavoidable catastrophe. Maybe your character works to unify the world by mid game. Get crazy with the end boss being symbolic of religious ideologies and you can only defeat them with physical attacks. Game ends with the founding of the first space colonies.
Final game is entirely sci-fi with absolutely no "magical" element, no trace of god. Until the very end when the presence of a god being is almost too certain. Only for that god being to end up being us.
Star Ocean 3 isn't exactly what you're looking for.
Spoilers.
The main characters do eventually get the revelation that they, and the entire universe they know (the 3D universe) are actually a massive MMORPG played by 4D beings. They don't find out that they are within an actual PS2 game and being controlled by a player. ---