Some other plot twist that totally suprised the hell out of me was

Tales of Vesperia-Alexei was behind everything that happen throughout the game.

Chrono Trigger-When Crono got killed by Lavos.

Shadow Hearts:From The New World-Johnny was not 16 he was 21 but stayed 16 because he died and was resurrected by the Emigre Manuscript. 

I also was very suprised when I found out that

MAJOR SPOILER MAJOR SPOILER MAJOR SPOILER

Xenogears-Gears were made out of Humans

5. Highlord Bolvar lead the charge at Angrathar the Wrath Gate along with Saurfang Jr. ~ WOW wotk
4. i threw my xbox controller to my xbox deliberately after learning the most lazy ass ending ~ KOTOR 2
3. Theresa asked you to leave the spire because it belongs to her now ~ Fable 2
2. Darth Revan remove his mask revealing his true identity ~ KOTOR
1. Kaim Argonar learn about his daughters faith + with grandchilds crying ~ Lost Odyssey

 Good List

It's moment like these that makes the RPG Genre so great you feel me?

I was pretty shocked when Isara was shot in Valkyria Chronicles. It was a beauitiful moment ;_; before Rosie ruined it with her awful singing.

 I agree with you.

what can be more shocking than this unforgettable moment:

mario RPG the legend of the seven stars: bowser is not the final boss

KOTOR - Revan
Mass Effect - Soverign
Phantasy Star II - Termi...I think that's her name.

1. Final Fantasy VII: Aeris's death. Totally did not see that coming but when it did it hit me like a ton of bricks. Yea....I cried like a girl. Also the fact that Aeris could see the outcome of the world way before it actually happened. She knew she would die, she welcomed it. Dying meant that her prayer to save the planet would reach it quicker(this is assumed from the opening and secret ending scenes of Aeris).
2. Final Fantasy VIII: Ultimecia is actually Rinoa, years down the line after Squall was long gone. Squall promised her that even if she became the sourceress he would protect her. He became Griever, Ultimecia's Gaurdian Force.
3. Kingdom Hearts: Ansem, the man everyone was looking to for an answer to the heartless, was actually the man who unleashed the heartless upon them. To make matters worse, he did it on purpose.
4. Final Fantasy X(X-2): Probably not the one everyone else was thinking but. Machean, the old man that always tells the long history stories, is actually dead. That the Fayth developed the idea for Tidus and Yuna from previous Star Crossed lovers, Lenne and Shuyin. They used this to predict their actions and minipulate them.
5. Persona 4: The man that had been helping you solve the crimes by mistake had actually been decieving you on purpose. He had been manipulating you the whole time. Depending on how you progress throught the game, you can obtain the bad ending where he tricks you into killing the wrong suspect.

If this was a thread on simply the Most Shocking moments period in any game....

MGS4: The fact that the villain that you have been persuing for 4+ games, the one came so close to world domination, isn't really the "villain" at all. He is actually the game's ultimate hero. He is also secretly "The Boss's" only biological Son. While Big Boss and Zero tryed their hardest to achieve what the The Boss wanted, only Ocelot succeeded. Brilliant!!!!