You were right about your death all along.
You've been trying for three games to figure out the identities of an evil organization, only to find out that 4/5ths of them died shortly before or during the first game.
You killed her and are merely repressing the memories of it.
They were not intended to protect people, but to conduct a mass psychology experiment.
The device you've been looking for the whole game is standing in plain sight right in the middle of town square.
The game never actually happened.
What game does that sound like? Those are supposed to be spoilers of a game, but they didn't give out the game title out... It's from here.
http://www.gamefaqs.com/boards/genme...5773803&page=3