Metal Gear Solid 2 ending
Major spoilers ahead!
The main plot of Metal Gear Solid 2: Sons of Liberty (excusing the opening where Solid Snake fails to stop Revolver Ocelot from stealing Metal Gear RAY and gets framed for the whole mess) starts out fairly straightforwardly with the main character Raiden on a mission to rescue the President from a group of terrorists that have taken him hostage. Even the plot twists (that America is actually run by an Illuminati-like group called the Patriots, and that one of Raiden's allies is actually Solid Snake incognito) were rather routine for a series known to have plenty, and heavily hinted at.
About eighty percent of the way through the game, though, a side character dies, and Raiden is double-crossed by Solid Snake (as an aside, Solid Snake is one of three characters in the game with the codename "Snake", but he is the only character to be called simply "Snake" on a regular basis, even by others with the same codename. Every time you see that, it's him. This is one of the least confusing parts of the game). After being double-crossed, Raiden is captured and stripped naked.
At this point, everything becomes extremely surreal. Veiled references to the previous game become blatant, with two rooms reproduced almost exactly from Metal Gear Solid, and both Raiden's CO and girlfriend transform from allies to identity-less manipulative agents to ersatz constructs composed of AI, nanomachines, and the contents of Raiden's own psyche. Said constructs then go all insane from a computer virus and proceed to Break The Fourth Wall (if there is one at this stage) and spout incomprehensible gibberish. Meanwhile, Snake reverses his double-cross and, in an effort to keep Raiden sane, tries to convince Raiden that his (Raiden's) girlfriend is real - even though Raiden is the only character to have ever met her. Snake mentions that he is counting on having infinite ammo from a bonus item attained in Metal Gear Solid; either the fourth wall has had it, or the player must confront the idea that the series accepts the literal existence of every once-thought Joke Item contained within it.
After a Marathon Boss fight against unmanned Metal Gears on top of a supercomputer-cum-battle-station-cum-submersible-cum-VR-training-environment, much of the remaining cast is gathered. This looks bad, because the heroes (Raiden and Snake) are outnumbered by the villains (Fortune, Revolver Ocelot, and Solidus Snake). However, Ocelot's Chronic Backstabbing Disorder acts up, and then all three villains reveal previously-unimagined motives and admit that they were all manipulating each other to the point where it can no longer be discerned who the biggest villain is (or, for that matter, if there is a villain anymore). Ocelot also reveals the S3 Plan (Solid Snake Simulation) that was meant to test if putting a person through something similar to the Shadow Moses Incident would create a soldier as skilled as Snake. Hence why the situation Raiden finds himself in is so similar to the Shadow Moses Incident, from the basic setup of "terrorists led by a Quirky Miniboss Squad have seized control of a remote Metal Gear facility disguised as some kind of treatment facility, they have taken several important people hostage and will bring about a catastrophic terrorist attack if their demands are not met" right down to individual setpieces, boss battles and character relationships. Due to how well the game is designed, the player can control Raiden as well as or better than they could have controlled Solid Snake in Metal Gear Solid. Fortune's seemingly supernatural ability to intercept bullets is Hand Waved as magic technology, but she displays her powers even after her Phlebotinum has been demonstratively turned off. She dies just in time to miss what happens to Ocelot: his transplanted arm takes over his mind (for the second time... but possession by the dead is actually one of the most sensible concepts portrayed, all things considered), and he manifests the consciousness of Metal Gear Solid's Big Bad, Liquid Snake. Ocelot-controlled-by-Liquid's-arm takes flight in a submersible robot, and in a symbolic move (in the author's view, breaking free of his own backstory), Snake breaks the handcuffs he was restrained with, and dives into the sea in pursuit. Then the VR AI nuclear battlestation goes crazy: its pilots are the AIs which were just infected by the computer virus. It begins sailing full pelt towards New York City, with no plans to stop.
After a scene of cityscape destruction that was removed due to 9/11, we find Raiden atop of Federal Hall in Manhattan, along with the only remaining villain, possible-Big Bad Solidus. Both Raiden's crazed AI commanding officer and girlfriend mock him and reveal that they, the Patriots, were manipulating the whole situation, not only to reproduce and exploit the historical, cultural, backstory "memes" that had created Solid Snake, but to use said methods to control all cultural information flow. It's revealed that they are not AI per se, but something more like an incarnation of a far older consciousness which built up over centuries in the arena of U.S. politics. Also, Ocelot was wrong about the S3 Plan; it is really the Selection for Societal Sanity. The objective is to see if they can control a person in an extreme situation; the Shadow Moses Incident is the most extreme situation on record, so they simulated that. The test subject is the player, and it worked perfectly: by programming the player with VR reconstructions of the Shadow Moses incident (that is, with the first game in the series), they were able to convince him or her to follow every one of their instructions in the Big Shell simply by presenting them with a superficially similar façade. Because Solidus has been trying to take them down ever since he was President of the United States, they want Raiden to kill him. Solidus also admits that he killed Raiden's parents, condemning Raiden to child soldierhood and the Orphan's Ordeal, which might've been a Moral Event Horizon if we weren't so mind screwed that we don't know left from wrong anymore. Raiden questions why he should even fight Solidus even after this reveal, to which the Patriots respond that Raiden's nanomachines are the only remaining link to the Patriots, so Solidus is going to attempt to kill him to gain said machines regardless of what he does. So it's either Raiden (who is you) or Solidus. Guess who wins.
We find ourselves in front of Federal Hall. Snake shows up as if from nowhere and rhetorically breaks the bond between the player's avatar-Raiden and the character Raiden: the personal information you input before the game started is on a dog tag Raiden is wearing; he throws it far away and declares he is creating his own identity. As Raiden turns to ask what, exactly, he is to do with his new life, Snake is gone, but Raiden's girlfriend Rose shows up (please note that at this point it is still unclear whether or not she actually exists). The lovers are reunited (also, if you turn the camera at a certain point, you can see that Vamp, another villain thought to have been killed twice before, seems to be both still alive and hailing a taxi). The credits roll, and then it is revealed, in a phone conversation between Snake and Otacon as the logo is displayed, that the Patriots are already dead and have been for over a hundred years.
Metal Gear Solid 4: Guns of the Patriots had the dubious honor of having to explain, retcon, and tie up all this confusion somehow—and the amazing thing is that it did, but just by the skin of its teeth. However, it can be argued that this is also the reason as to why Metal Gear Solid 4 had approximately nine hours of cutscenes. In case you're wondering, the AI's are just AI's that thought a bit too highly of themselves - and in the end, the Patriots weren't even controlling them anymore. The men dead for over a hundred years are actually from an earlier Ancient Conspiracy known as the Philosophers; the Patriots took over the American branch of the Philosophers and used the identities of its founders as a cover. The actual Patriots turn out to be Big Boss and his partners from Metal Gear Solid 3: Snake Eater, but they had a falling out which caused Big Boss to turn against the group. In fact, two of the original Patriots were killed in Metal Gear Solid, and by Metal Gear Solid 4 the last one is little more than a vegetable; the A.I.s were running the group by this point. Ocelot turns out to be one of the original Patriots and although he pretended to be loyal to them, he actually sided with Big Boss. Ocelot's possession by Liquid was part of a larger plan to fool the A.I.s and last member of the Patriots - and at some point Ocelot began faking he was possessed. (It's also suggested Ocelot's original possession was tied to his father being a spirit medium.) Oh, Rosemary is real, Vamp had a natural Healing Factor enhanced by nanomachines, and Fortune... actually we don't learn what happened with Fortune, but Psychic Powers do exist in this universe. Doesn't it all make sense now?
- A 15 part analysis/essay about this ending (seriously).
- Junker HQ's line-by-line analysis of the ending
- Penny Arcade's take on it.
- An analysis of the details of the story including the ending, from Super Bunnyhop