First, let's get this out of the way: This post is full of spoilers. If you haven't played the games below, the endings and/or best parts will be spoiled. You've been warned. Here are some of the biggest reveals in video game history, in chronological order.
1. Metroid, 1986
At the end of Metroid for the Nintendo Entertainment System, we learn that the hero, Samus, is female. While this should not be a surprise—I'd seen plenty of women as sci-fi protagonists (Ripley from Alien, Sarah Connor from The Terminator, Sarah Jane Smith from Doctor Who and later The Sarah Jane Adventures, etc.)—it threw me for a loop as a kid. I just assumed that Samus was a dude under the armor. This assumption was reinforced by the game's manual (PDF) referring to Samus as "he."
This is a great example of a "twist" that's both dated and sexist. As an eight-year-old in the mid-'80s it surprised me. Today (ahem, Chell in Portal?), it wouldn't be a thing. To make things worse, if the player completed the game quickly, the reveal would include progressively less clothing. Yikes.
2. EarthBound, 1994
In EarthBound you play as Ness. When a meteorite crashes near your house, you enlist the help of Pokey, your annoying neighbor, to check out the meteorite. Along the way, it becomes clear that the evil alien Giygas is in the process of destroying the universe. Thus begins a many-hour role-playing game.
The big reveal is that your annoying neighbor Pokey is really a villain, in league with Giygas. When Ness finally defeats Giygas, Pokey taunts Ness with a letter reading, "Come and get me, loser! Spankety spankety spankety!" In the sequel (Mother 3), Pokey has become an immortal time-traveler. And you thought your neighbors were jerks.
3. Final Fantasy VII, 1997
The Final Fantasy series is huge and sprawling; it's too complex to explain briefly. But one of the biggest moments in the series comes in the middle of the hugely popular Final Fantasy VII, when Aeris, a major character whom you have played for many hours, is suddenly killed. This comes as an incredible shock for the player, as she seems to be set up as an ongoing character. For many gamers, it was a surprisingly emotional moment, and not just because they had spent forever trying to equip and train the character—she was awesome.
The death is so legendary that GameSpot called it "the most shocking moment in video games, the most spoilerific spoiler of all time."
Game designer Tetsuya Nomura created Aeris (also known as Aerith due to the tricky translation from Japanese), and commented on her death in Final Fantasy VII:
"Death should be something sudden and unexpected, and Aerith's death seemed more natural and realistic. When I reflect on Final Fantasy VII, the fact that fans were so offended by her sudden death probably means that we were successful with her character. If fans had simply accepted her death, that would have meant she wasn't an effective character."
4. Star Wars: Knights of the Old Republic, 2003
Throughout KOTOR, you play a Jedi with amnesia, trying to recover his memory. Much of the plot involves making light side/dark side choices, working up to a big battle against the evil Darth Malek, a former apprentice of the super-duper evil Darth Revan.
The big reveal is, you are Darth Revan. You've been brainwashed. When the reveal happens, it's mind-blowing.
5. BioShock, 2007
Throughout BioShock, you're guided through a crumbling underwater utopia by a man named Atlas, speaking over a radio. Atlas seems very helpful, telling you what to do and how to get it done—he's a key part of the game, and you build trust with him over hours of play. But Atlas isn't who or what he seems.
Near the end of the game, it's revealed that the protagonist, Jack, has been brainwashed, and he's been responding to a trigger phrase all along. That phrase is: "Would you kindly?" When the phrase is uttered, Jack does whatever he's told—including kill.
The freaky thing about this moment is that it recontextualizes the whole game. While Jack did have some legitimate choices in the game (for instance, to harvest or save the Little Sisters), for the most part he was being controlled by Atlas, who used the trigger phrase throughout the game to make him do things he might not have chosen to do, had he known what the real situation was. This brings up lots of interesting questions about free will.
6. Portal, 2007
Portal includes another unreliable character communicating via voice; this time it's GLaDOS (Genetic Lifeform and Disk Operating System) guiding protagonist Chell through a series of tests with the promise of "cake" when they're complete.
It becomes obvious early on that GLaDOS is not a friendly machine, but a murderous one. Because of this, it would be reasonable to assume that the cake is yet another lie. After the final fight that leaves GLaDOS in charred pieces, there are two twists: First, the cake was real (despite seeing "the cake is a lie" scrawled on walls earlier), and GLaDOS is "Still Alive":
When Portal 2 was in the works, the ending was changed slightly, retconning in an abduction of Chell. (Arguably a third twist?) The unseen robotic abductor thanks her for "assuming the party escort submission position."
7. Call of Duty 4: Modern Warfare, 2007
In Call of Duty 4: Modern Warfare, a first-person shooter, you played from the perspective of two people: a Marine and an SAS commando. The game swaps perspectives routinely, so you get used to occupying these two guys' points of view. What's shocking is that, in the middle of a mission, one of them is killed off.
In the game, it's a shocking moment—we hear that a possible nuclear threat is nearby, then seconds later the city is nuked and the shockwave crashes the helicopter we're in. The player dies after seeing the mushroom cloud from the ground. His team is also dead. It's the kind of real-world logic that is often defied in video games. We expect that the protagonist of the game will find some way to survive this moment, but nope, that's it.
8. Braid, 2008
In Braid, you play Tim, trying to rescue the Princess from an evil knight. The game is brilliantly complex, and users employ game mechanics related to reversing time to get through puzzling levels. As a platformer, there are many nods to the Mario games, though Tim is no cartoon plumber.
In the stressful final level of the game, the Princess is rescued by the knight. In other words, Tim is the monster pursuing the Princess; he's not the hero—the knight is. It's a bit of a gut-punch. And there's a deeper level to the puzzle, if you go into the epilogue and read up on your nuclear history (I'll leave you to Google that).
9. The Silent Age, 2012-2014
The Silent Age is a point-and-click adventure featuring Joe, a janitor living in 1972. The game begins when Joe discovers a dying man with a time travel device. Joe uses the device to visit 2012, only to find that the future world is a wasteland, devastated by some plague. Throughout the game, you use the time travel device to solve puzzles—jumping between time periods, you can access areas that are blocked in one or the other era.
There are two episodes of The Silent Age, and the biggest twist comes near the end of the second one (released in 2014—the first episode arrived in 2012). The plague is a strain of the flu. What makes it interesting is that Joe was Patient Zero in a global flu pandemic, caught in the future and brought back in time. As he feels the flu beginning to affect him (back in the 1970s), he uses a primitive cryogenic chamber to both freeze and isolate himself, to prevent the pandemic. He wakes up in 2012 to find that although his flu is easily cured (and has not destroyed the world), the world of 2012 is no better than the world of 1972; he still works a boring job, and little has changed for him, despite saving the world. It's a moody game, and the twist makes it that much more delicious. (Note: there are even more twists if you factor in Frank, another janitor who visits the far future, and some details about Dr. Lambert, working on the flu treatment, but it gets very confusing very fast. There's also a suggestion that Joe has been through this whole time-travel trip multiple times.)