Best/Most unexpected plot twists in a video game? [Spoilers!]

I love me some plot twists. Who doesn't? (OK, many people don't, but whatever). I was wondering, what are some of the best and/or most unexpected plot twists you've have encountered in video games? I'd love to start a game with some good plot twists that keep the story interesting, or somehow make you rethink everything you thought you knew about it. Two that come to my mind right now are 999 and Spec Ops: The Line. Obvious spoilers follow:

999

The way the plot ends varies with each playthrough, but in the end all these possibilities are revealed to be different scenarios seen by a young June/Akane, who is actually trapped in the last puzzle of the first Nonary Game, an incinerator. She used her psychic abilities to guide Junpei through the best course of action, so he is able to reach the incinerator in the "present", solve the sudoku puzzle and, indirectly, help her solve her sudoku and free her. Pretty wild paradoxes there. The best thing about this is that you realize that all the time you've been playing, you've seen the events of the game unfold through the eyes of Junpei through the eyes of June.

Spec Ops: The Line

Most of what the played had experienced through the game is actually a fabrication of Walker's mind to cope with all the traumatic events he was witnessing, including the killing of 47 civilians with white phosphorus by he himself and his own team. Konrad had been dead for some time and it was Walker's desire to "be a hero" that made things even worse for everyone in Dubai in the end.

The only one that comes to mind at the moment is the one in Oblivion at the end of the Dark Brotherhood involving Lucien Lachance.

Folklore. Keats.

That is all.

Aeris died

For me top place still belongs to MW2 with Ghost and Roach. ='[

I wish I could remember the one in Oblivion @ShadowConqueror mentioned. Damnit brain, wake up!

Tales of Symphonia 1: Kratos turns out to be Lloyd's father? What the fuck!
 
Oh and Revan in KotoR.
Come on, well done.

The Line's "twist" is kinda overrated in my opinion... I actually thought Black Ops 1 had a better crafted twist.

Only because I have been playing it recently, Silent Hill 2 comes to mind. SPOILERS WARNING! I couldn't believe that James had killed his Wife, put the game in a whole new light for me

Revan in Knights of the Old Republic

Persona 3 and 4 had their share of twists that I didn't see coming. Can't really name one.

EDIT: Dunno how I forgot about it but the big twist in Bioshock.

Star Ocean 3 wins this one... completely.

Kid Icarus: Uprising enters total mindfuck territory at a specific point, and it's amazing.

Would you kindly?

Finding out that the Citadel was a relay in ME1 surprised me.

System Shock 2

SHODAN's reveal.

Silent Hill 2

The awful truth.

Fallout 3

President Eden.

Fallout: New Vegas

When you first meet Mr House in person.

The Dark Brotherhood one from Oblivion is really neat, too. Damn, that quest line as a whole is fucking brilliant.

Also, does the "You're a hero..." moment in Fallout count as a twist?

Stranger's Wrath :

Stranger being the last Steef, with its legs bent in its boots.

BioShock :

The Would You Kindly mindcontrol phrase.

Enslaved :

Humans are being brainwashed into thinking the world is a bright and beautiful place.

It's got to be the aknowledgement of aperature science in HL2 episode 2 for me. Besides that I thought the blackops twist was quite good.

I'd say Nier, Folklore and Spec Ops: The Line got them. At least from the games I played.

@Cyrus_Saren said:

Revan in Knights of the Old Republic

@dropabombonit said:

Only because I have been playing it recently, Silent Hill 2 comes to mind. SPOILERS WARNING! I couldn't believe that James had killed his Wife, put the game in a whole new light for me

Only two twists in games I felt particularly stunned by. I immediately wanted to replay them to experience the games again with my new knowledge.

Bioshock and Knights of the Old Republic.

Bioshock and Assassins Creed: Brotherhood

Portal: when you peak behind the testing environment the first time.

Indigo Prophecy / Fahrenheit: everything is fucking crazy nonsense! I love it!

Braid: the ending

To the Moon: oh that's why he wants to go to the moon. The rabbits! Best story ever.

Silent Hill: Shattered Memories: oh, I'm not really who I think I am, that's neat.

@Cyrus_Saren: @Owlright: @SeanFoster:

Revan in KotoR was mentioned multiple times, I'll never play this game so would you please spoil what's the twist? I'm curious :]

Bioshock and AC 2. Come to mind quickly

@Morrow: Sure!

It sounds really trite writing it out like that but it's fantastically well done in game. The impact it has on your interactions with party members and how you reevaluate your character and play style is pretty excellent.

@Owlright said:

@Morrow: Sure!

SPOILER WARNING: Click here to reveal hidden content.

You play through the game hearing about a terrible Sith Lord called Darth Revan, and their apprentice Darth Malak, who launched an armada against the Republic and split the Jedi. You spend the game trying to stop Malak, as Revan disappeared/was thought to have been killed by Malakin an act of betrayal. Eventually you find out that you're in fact Darth Revan, brainwashed by the Jedi Council after they found you injured by Malak.

It sounds really trite writing it out like that but it's fantastically well done in game. The impact it has on your interactions with party members and how you reevaluate your character and play style is pretty excellent.

Oh yeah, I can imagine that played out very well :) Great idea!

From way back in the day I thought the Bagus/Janus revel was cool. (looking back it was fairly obvious but I was young)

I would say the big one at the end of "Heavy Rain" but that one is a little controversial.

By far the coolest one that sticks out to me is "would you kindly"

Folklore was cool though I felt that it kind of violated the rules that they'd established about how the afterlives worked.

Star Ocean 3's might have been better if I enjoyed the game more or hadn't already seen the same twist done in a movie.

Infamous is probably my favorite.

Star Ocean 3 wins this one... completely.

The ending of FF9. I can't even remember what it was now, I just remember being surprised.

I remember the twist in Breakdown (for the original Xbox) blowing my mind when I first saw it.

Nier

MGS 2

I have a feeling a lot of people will disagree with me on this one, but Mass Effect (1).

Am I the only one to be surprised by the appearance of the Flood in Halo 1? Also for me: Bioshocks "Would you kindly" and just why Johny wanted to go To The Moon... Almost made me cry.

Tear Ring Saga deciding that it best end like a combination of Earthbound and a 1990s dating sim.

Oh yeah.. How has nobody said yet... "Samus is a WOMAN?!"

Would be Revan in KOTOR but some fucker intentionally spoiled it for me.

Bioshock takes the cake for me.

@Zuldim: This one blew my mind aswell! Made me fall in love with the game so much more!

And like everyone else has said. The whole Revan thing was amazing.

Resonance

Spec Ops The Line, most recently. DAMNIT OP STOLE MY ANSWER LOL

KOTOR was the first one.

The Darkness (Jenny's death).

@TaliciaDragonsong: Ah yes, that made my day when that happened. And then the whole thing with the child angels and ending the world or something. If I didn't recall that correctly, it's evidence that I didn't understand the what da fuq was going on once you went to that "pseudo-heaven."

@themangalist said:

The Line's "twist" is kinda overrated in my opinion... I actually thought Black Ops 1 had a better crafted twist.

It's surprising how similar the twist in both the games is. I never realized until I read your post.

The upside down castle in Castlevania SoTN. Blew my mind the first time i found out how to get there. But, continues to get played out every time another Castlevania does it now.

I really liked BioShock.

Heavy Rain , when essentially my favorite character betrays another very emotional main character. I just taught oh shit. I love that game with all of it's flaws.

@Jay444111 said:

Star Ocean 3 wins this one... completely.

That was a fucking insane twist that way to few people will ever experience. I don't feel like it's super good executed, its just fucking insane

Binary Domain has a pretty good one. Just to add to all the ones people have mentioned here.

Nier, Folklore, and Infamous 1.