The most brilliant kind of twist in a story is the kind where, if you just had this or that little bit of information, you'd be able to blow the whole thing wide open. But you don't, and that one missing piece keeps you from being able to put anything together until the game pulls the rug out from under you.
Video games, being an interactive medium, have the tools to do this better than anyone else, but often stumble due to how genuinely difficult it is to pull off a twist like this well.
You have to give the audience enough information to come to one conclusion, while keeping away one or two bits that alter literally everything. This requires a deft hand, mastery of planting and payoff, and a red herring effective enough to throw even the keenest eye off the scent.
These games managed to make you think you had everything all figured out before making you realize that you were staring at the truth the whole time, but just not thinking about it correctly.
10. Shaun Is The Leader Of The Institute - Fallout 4
At the bottom because, due to the fanatically secretive nature of The Institute, there's only so much that the game can hint at the true identity of the guy running the place. But sure enough, there are more than enough hints hiding in plain sight through conversations and even the opening cutscene of the game.
When you emerge from Vault 111 for the first time, all you know is that someone has taken your baby, and that some time has passed since then due to the cryogenic container re-freezing you after that happened.
However, you have absolutely no idea of exactly how much, so when the game at first seems to tell you that it's been about 10 or so years through showing you a 10 year old Shaun, you have no reason to not believe it. Making the moment when the truth hits all the more brutal.
Turns out, it's been over 60 years, and Shaun is not only older than you now, but is also the man at the head of The Institute.