Wait, wait, wait... Not only did the original in-game character manage to become strong enough to rival the in-game protagonist and his companions, but he also has two of the strongest bloodlines in the story. Not just that, he also surpassed every person in the duchy, including his father, who is regarded as one of the strongest descendants under the God of War. He's a bonafide son of Heaven.
Just to point out how ridiculous it is to try and maintain the whole 'he's an extra!' trope even with all the info we have now, let me give you a comparison. Imagine if I said that Dumbledore from Harry Potter was just an extra. That is the equivalent of what the author is trying to do.
Also, why exactly is the main character planning on stopping the in-game protagonist? Sure, I could see why you'd be disappointed and upset that the story had a bad ending when you were just a paralyzed hospital patient. Who doesn't hate bad endings to a story? But... it isn't a story for him anymore.
One would argue that the in-game protagonist wasn't even necessarily wrong. Yeah, he destroyed the world, but he then rebuilt it from scratch and revived damn near everyone that shouldn't have died. It's probably a paradise, so why try to rewrite that ending? Does the main character think he can do better? Because even if he stops the protagonist, he won't be able to stop the people seeking out the godly power that comes from solving the puzzle forever. He isn't immortal.
The only reason that I can imagine in which he'd try to stop the in-game protagonist is because the in-game protagonist was secretly evil, but given the information we've been given, that isn't the case... so why? It doesn't exactly make much sense. If the in-game protagonist was secretly evil, I feel like that'd be vital information to tell us so that we'd be more understanding of the real main character's motivations to stop him.