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
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