Most surprising plot twists

Ace Attorney spoilers warning (Investigations 2 and Dual Destinies)

Spoiler

Simon Keyes being the mastermind in Investigations 2 and Bobby Fulbright being the Phantom in Dual Destinies. Holy crap they seemed like just average people who were just there for you to help out or in Fulbright's case be the main detective of the game. Did not see these coming AT ALL.

 

In Mario and Luigi Super Star Saga, there is a point in the story in which Mario devises a scheme to get princess peach back from Bowletta. Everything seems to be going as usual with the storyline, but then out of no where, another princess peach appears when Mario confronts Bowletta with the actual Princess Peach. Bowletta is suspicious, so she steals the other peach, thinking the one she has is an imposter. The next thing you know, you get a cutscene on Bowletta's ship and Princess Peach keeps covering her face. Eventually she laughs and you see a mustache on her face. The whole time, Princess Peach was actually Luigi wearing a dress pretending to be her so that Mario could get the actual one back!

 

Mass Effect 3, which gets bonus points in my book for making a plot twist self-inflicted.

Throughout the series, you're asked to make choices that shape the story. Often, these choices boil down to "paragon" (save as many people as you can, do what's right, protect the people in danger even if it means greater risks down the line) or "renegade" (Do what's necessary, make the hard choice so that you can save the galaxy, sacrifice some for the sake of many, many more). As someone who favored renegade options, I found myself making some morally questionable decisions throughout the series.

Spoiler

This came to a head on the planet Tuchanka. The civilization native to that world, the Krogan, were a militaristic, expansionist society. Hundreds of years ago, they'd been brought into galactic society by the Salarian civilization, to fight a war the Salarians were losing. They won, completely exterminated their enemies, and promptly started to expand across the galaxy in a wave of conquest, turning on their former allies in the process.

The Krogan came from an incredibly dangerous world, where they'd adapted by developing a high birth rate. On more tranquil worlds, this meant that the Krogan population could grow at an astonishing rate, leading to their civilization's rapid expansion. The Salarians responded with a bioweapon that caused only one in a thousand Krogan births to survive, reducing their birthrate to original levels. In the third game, the player is asked to cure this plague to secure Krogan military support, and is given the help of Mordin Solus, skilled doctor and friend from the previous game.

Now, a renegade player like myself will quickly realize the problems with this plan. Curing the plague means securing much needed Krogan military support, at the cost of their expansion down the line. At this point, the Salarian military offers a deal: fake the cure, thus securing Krogan support while ensuring they don't become a threat down the line. In exchange, the Salarians would provide additional support for the player as well.

Naturally, I chose this option. Throughout the following missions, I gained the trust of the Krogan, developed a cure, and prepared to deploy it into their homeworld's atmosphere. The device that would spread the cure, however, had been damaged in such a way that the cure would be destroyed on deployment without the Krogan knowing. Everything was going according to plan... and then Mordin Solus found out.

Mordin had been with me for the past two games. He'd fought by my side, offered advice, and nearly died for me on a number of occasions. He expressed deep sympathy for the Krogan, and was always extremely intelligent and quick to solve problems. With all the evidence at his feet, it's no surprise he figured out my plan, and as we made ready to deploy the cure, he confronted me. Determined to cure the plague, Mordin planned to repair the deployment system whether or not I liked it. There would be no talking him down, no stopping him from trying to help the Krogan... so, in that moment, the game gave me a choice.

I shot him twice in the back.

Mordin Solus, trusted friend, genius, and dedicated ally, died by my hand for his beliefs. The game didn't let me know he'd caught on until I thought I was in the clear. There was no obvious warning, but I should've known. Because he wanted to do the right thing, he had to die. I killed a friend to save the galaxy.

 

The good aul' twist towards the end of Jak 3, for one. Always a fun one to rewatch.

In more modern games, maybe the revelation about Dust's origins in Dust; An Elysian Tail is a bit noteworthy. I suppose the evil ending of Infamous: Second Son is another one to mention too. I know Delsin is supposed to be all hardcore, anti-authoritarian and all, but even that crossed so many lines.

I honestly thought Beyond: Two Souls was gonna deliver a killer twist regarding the identity of Aiden in the end, and whilst we got some answers and there was good stuff there in the end, it kind of let me down too.

Oh and let's not forget to mention just about every Metal Gear Solid game to date. <3

 

It's recent-ish, but I love the plot twists in Resident Evil Revelations. Double-cross after double-cross. The story at first was very unclear and hard to decipher until later when it was a little better explained. I legitimately thought Parker died in the game, they made it seem very convincing. I was overjoyed to later find that he actually survived.

 

Ah yes, this one. This one is great, though I prefer the one in Jak II where

Spoiler

old man Kor turns out to be the Metal Head Leader.

In hindsight, the signs are actually pretty obvious, but you know what they say about hindsight being 20/20.

 

Everyone shut your eyes because I'm about to spoil Xenoblade Chronicles! (This is better presented in Video form)

Spoiler

Brief overview of what's happened so far:

Shulk is an 18 year old Homs able to wield the legendary blade, the Monado. He was found and raised by a figure called Dickson who also thought alongside Dunban to fend off the Mechon in Sword Valley. He constantly supplies the party with useful weapons. Shulk wields the Monado to grant revenge on the Mechon, but at this point in the game, he's grown pass that and has instead been tasked to kill the Machina's corrupt, vengeful leader, Egil, who wants revenge on the Homs (and all Bionis lifeforms). Shulk and his squad confront Egil and stop him from destroying Bionis, using the Monado's power which was fully unlocked by the creator of the Bionis (Shulk's home), Zanza, who Egil doesn't seem to like. Lady Meyneth, the creator of Mechonis, is trapped inside Shulk's "girlfriend", Fiora, and also seems to show negativity towards this Zanza guy, who helped Shulk so much on this journey in 1 simple action. At first you might think this is just spite, but then... THIS HAPPENS. Just as Shulk and Egil are making peace (Shulk and Egil together resist their desire for revenge and decide to unite the 2 races once more)... DICKSON SHOOTS SHULK IN THE BACK. And then...

http://www.youtube.com/watch?v=Afy6KOXoIUY

 

I have two!
The one in PMD Explorers of Time/Darkness/Sky:

Spoiler

DARKRAI WAS THE BAD GUY ALL ALONG OMFG

And the one in Professor Layton (that one game in which they travel to the future. I don't know its English name, but in Dutch, the game is called "De Verloren Toekomst". That must mean the game is titled Professor Layton: The Lost Future in English? XD) :

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ADULT LUKE TURNED OUT TO BE THE MASTERMIND BEHIND THE UNDERGROUND "FUTURE" ALL ALONG OMFG U F*GGING BASTARD

 

When I played Bioshock, the part where

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I found out that the phrase "would you kindly" controlled your actions. That kind of freaked me out, tbh.

 

Mmm! That was a good one, too. And also;

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Frank Fontaine reveals himself as Atlas.

 

Let's see...

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2nd Phoenix Wright game last case when you figure out that your client is insane

 

Plot twist? Tales of Xillia 2's ending. You literally get to choose between the good ending and the bad ending, besides mentioning the game itself is one huge plot twist.

 

The identity of the final bosses of Megaman Zero 1 and Zero 3 were shocking to me. 1 was because of "Wait, I have to fight you, of all people?", and 3 was because of "So that explains why you're so (many, many colorful and bad words in all caps) hard to beat!"