Here again, you can exploit the conventions of video games to mislead the player.
I think this is a great idea. Gamers know lots of things about video games, and they know them very thoroughly. They're used to games that follow these conventions, and they're also (lately) used to games that deliberately avert or meta-comment on these conventions for effect (i.e. Achievement Unlocked), but there aren't too many games I know of that set up convincingly normal conventions only to reveal that the player's understanding is flawed.
Eternal Darkness did a few things in this area. For example, if your character's sanity level was low, you the player might start having unexpected troubles with the interface, i.e. the game would refuse to save on the grounds that "It's not safe to save here", the game would pretend that it was just a demo of the full game, the game would try to convince you that you accidentally muted the television (though the screaming sound effects would still continue), and so on. It's too bad that those effects, fun as they were, were (a) very strongly telegraphed beforehand, and (b) used only for momentary hallucinations, not to indicate that the original understanding the player had was actually the incorrect one.
The problem is that, simply put, such games generally fail on the "fun" meter.
There is a game called "The Void," which begins with the player dying and going to a limbo like place ("The Void"). The game basically consists of you learning the rules of the Void and figuring out how to survive. At first it looks like a first person shooter, but if you play it as a first person shooter you will lose. Then it sort of looks like an RPG. If you play it as an RPG you will also lose. Then you realize it's a horror game. Which is true....
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