Best plot twists in games

[Fragony]

Obviously spoilers but as little as possible

A few of my favorites;

Finding out where you are in Deus Ex, major wtf moment that makes you question everything. You know what I am talking about.
System Shock 2, the introduction of my old arch-enemy left me breathless for a while, and I really felt like all hope was gone.
Knights of the old republic, shame on me, I didn't see it comming. It was awesome to learn who I really am, on par with 'I am your father'

There are more great plot-twists in games so add your favorites

[rvg]

Finding out who was the real arch villain in the 1st Witcher.

[rajpoot]

Witcher 2, Saskia turning out to be the dragon Saesenthessis.
Deaths of player characters, specially the one killed by the backstabbing general in COD MW2.
Saren's ship turning out to be sentient in Mass Effect.

[easytarget]

Much of Bioshock Infinite was a bit of a twist. Particularly the ending and I liked some of the cultural references. My personal favorite being the references to the movie Rosencrantz and Guildenstern Are Dead.