9. Call Of Duty: Black Ops
By its sheer nature, the Call of Duty franchise typically casts the player in the roles of various heroic operators trying to prevent terrorist activity the world over.
But easily the most ingenious rug-pull in the series occurs in the very first Black Ops, where players primarily play as CIA operative Alex Mason.
It's eventually revealed that Mason was a victim of brainwashing at the hands of the game's antagonist, Dragovich, who attempted to force him to assassinate President Kennedy.
Furthermore, most of Mason's perceived interactions with ally Viktor Reznov throughout the game never actually happened. Reznov in fact died early on after hijacking Mason's original brainwashing and using him to assassinate his own desired targets.
Though carrying out Reznov's orders hardly makes Mason a villain, the game's final implication just might.
Before the game ends, we're shown an image of JFK on the day of his assassination, which upon closer inspection also reveals the presence of Mason in the background, blatantly implying that Mason did indeed carry out his original mission for Dragovich.
Though you can certainly see Mason as a victim in his own right, it's pretty tough to be viewed in a favourable light once you've killed one of the most popular Presidents in American history.