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Nah, neither of those. Tomato in the Mirror definitely fits the last one but it's not what I'm looking for. Evil All Along isn't it either because you aren't necessarily playing as a bad guy. In the Professor Layton example Don Paolo is actually a good guy during the course of that particular game, You just don't find out you were playing as him until after you're done playing as him.
The point is you're playing as one guy and the game switches who you're playing as at some point without the player realizing it due to either a disguise or just two characters who look alike. It happens often enough to qualify as a trope but I can't find it. Maybe take it to YKTTW?
Well, at the very least it's a Tomato Surprise, since the player is being deceived about what's going on when they could reasonably have expected to know they were playing as someone else, given that (as convoluted as this sounds) they are playing as someone who presumably knows that they are not the person the player thinks they are.
I do think this is distinct enough to be its own Sub-Trope, given enough examples, though.
^ Definitely relevant. This could be a specific variant/Sub-Trope of Playing The Player. I was actually thinking of the Assassins Creed III example (playing Haytham at the beginning) that's on that page, though of course it's not an example of what the OP is talking about.

WARNING: SPOILERS FOR THE FOLLOWING. Record of Agarest War 2, Professor Layton And The Unwound Future and Disgaea 2
Is there a trope for when playing a game one of the player characters including possibly the main character is temporarily replaced by an imposter but the player continues to play as them without knowing that they are playing as an imposter? I can think of at least two instances.
in Professor Layton And The Unwound Future there is a bit where Layton runs off and you play as Luke for a very short while. You immediately meet up with Layton again and continues playing as him with him even being the designated puzzle solver for a few puzzles and the player for a puzzle boss. Then the real Layton shows up and it's revealed that you've actually been playing as Don Paolo.
in Disgaea 2 there is a single battle during the game where this happens. You have full access to all of your party members but after the battle it is revealed that one of your party members that you were still able to control had actually been left behind by mistake and was replaced by a ninja in disguise for the entirety of the battle even mimicing his stats and skills along with somehow gaining experience for that character.
In Record of Agarest War 2 you fight a boss as soon as you start the game and then get back stabbed. Stuff happens and you're still alive. You later find out that the guy at the beginning died and you've been playing as amnesiac version of the series main villain throughout the ENTIRE GAME.
Edited by SpoonElemental