I had my doubts whether to do some gravedigging or start a new topic, but in the end decided that the subject I'm addressing here is a more narrow one. Since there are bound to be massive spoilers, I suggest that anyone who hasn't yet finished a certain game does a quick search for its name and if they find it here, it's up to them whether to continue reading or not.

So, the title says it all: what were the moments when you played a game, watched the plot unfold and your jaw dropped and you stuttered "N-n-no way t-t-this is happening!"?
I'll start with some of mine.

Star Wars: Knights of the Old Republic
All right, you know how the story goes, there were two great Jedi heroes, Revan and Malak, they turned to the Dark Side, became powerful beyond imagination, then Malak betrayed Revan and left him (her?) for dead on an exploding ship.
And then here comes that scene where you meet Malak face to face and he recognizes you. Big news, pal, you are the Revanchist him/herself! Yep, the savoir of the galaxy and the vile Sith lord who nearly conquered it later is actually you.

Overlord
You fought all those corrupt "heroes", one at a time, reinstalling the rule of Evil over the land. Now, there is only one left, dispose of him - and there will be no more "champions of good" to dispute your rule. Time to die, Kahn!
You return to the Dark Tower victorious... only to find out that its former master is still very much alive and he's in control now. Oh, and he possesses a very powerful wizard as well. All those heroes you killed were once members of an adventuring party questing to defeat Evil - and so were you. Yep, you put your friends out of their misery and your services are no longer needed.

The Bureau: X-Com Declassified
Not a masterpiece, this one, but still playable enough. You play as agent Carter, an operative of a top secret agency fighting aliens from space. Right at the beginning you nearly died when an alien artifact exploded right next to you (and seconds before that you were shot at point-blank range). The explosion caused a strange effect: you recovered from the wound rather quickly and over time developed some abilities not very common among humans (mind control being one of them). You take the fight to the alien planet, blow it up, get out alive. Now victory is a matter of time... right?
Almost. Actually, you weren't playing as Carter, you were playing as an Ethereal, an alien controlling Carter's body and mind. And since the host has become aware of you and is now too hostile to cooperate, the time has come to find another one. After all, you still have a war to win.

That's it for now. Oh, and speaking of spoilers, Laura Palmer was killed by

Amnesia a Machine for Pigs

Mandus' children are dead and he killed them. He even hallucinates about their dead corpses. So the big reveal where he realizes his children are dead is hardly a surprise. The surprise was that he hadn't figured it out already, I thought after the first little dead children hallucination he would stop trying to save his children, but no it takes another half hour.

Edit: whoops I missed the never part in the title for some reason. I think pretty much everyone saw this one coming so here's my replacement one.

Bioshock Infinite

Booker is Comstock but from a different dimension and Elizabeth is his daughter. It was a good enough plot but I really wish it hadn't resorted to Deus ex Machina for the twist.

I'm just going to leave this here: http://www.gog.com/wishlist/site/spoiler_tags_at_the_forum

Voted. :-)

Bioshock 1:

Would you Kindly...
Need I say more :)

Heavy Rain... because of how lame it was :)
Yeah, one of the characters you play as is the killer. He's a fat guy with asthma, who can easily follow his own investigation (for no reason, as he knows the killer's identity), oversee Ethan's tests while having a 'partner' following him everywhere and kill random people for no good reason whie being in another room (antique shop).
Oh yes, and he never thinks about being the killer.

Deadly Premonition, because of how crazy it was.
Kaysen is the killer. And an alien demon from another dimension. And York (the player) is not real. And York \ Zach knew about Kaysen, because Kaysen killed his parents. And so on, until your mind is blown.

System Shock 2 deserves a mention too...
The girl that was helping you is dead. It was Shodan giving you directions all the time.

Seconded! And heartily. At this special scene I sat there open mouthed for several minute with a sick feeling in my guts. Replaying the game I noticed how cleverly they played this for the whole game up to this point.

Prototype begins with the old "you wake up with amnesia" cliché, but it turns out that you didn't have amnesia after all.


[spoiler]



The reason you had no memories is that you didn't exist until that point. You're not Alex Mercer at all; you're a virus hive-mind that developed inside Alex's corpse.



[/spoiler]

Also seconded, although I saw it coming, not all the time but... It was more like premonition, an ugly feeling that something was fishy.

Games I'd like to add:

FF7: Killing my favorite character. And then taking Cloud out of the game for a while.

Planescape Torment Not "the big twist" but a lot of little things like the Circle of Zerthimon's origins and other discoveries of the connections between the Nameless One and the other characters.

Monkey Island 2 The end. Really. There is no Monkey Island 3 or 4...

ROA - Star Trail The end of the Star Trail quest. I felt miserably pranked.

INB4, The Cake is a Lie........

Fahrenheit/Indigo Prophecy. The plot of that game goes on such an outrageous tailspin that I'll buy a burger to anyone who has never heard of the game before and can after, say, two hours, predict with even modest accuracy the general direction that the story is going to take.

The Samaritan Paradox has a rather dark and disturbing twist to it which you kind of don't see coming despite various signs, simply because you don't expect that particular sort of thing in a game.