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MGS 2 Ending
What the hell?—Solid Snake, summing up the audience's reaction in the final line of the game
Major spoilers ahead!
The plot of Metal Gear Solid 2 Sons of Liberty starts out fairly straightforwardly with 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 a legendary soldier named "Snake" in disguise) 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, Raiden is double-crossed by MGS1's player character Solid Snake. (As an aside, Solid Snake is one of three characters in the game with the Code Name "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 MGS1, 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 MGS1; 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.
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. 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 MGS1. Fortune's seemingly supernatural ability to intercept bullets is Handwaved 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 MGS1'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 A Is 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 Snake. 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 US 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. 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. 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 seems to be both 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 (and arguably frightening) thing is that it did, but just by the skin of its teeth (which frankly is a Crowning Moment of Awesome in itself). However it can be argued that this is also the reason as to why MGS4 had cutscenes of up to an hour of dialogue.
- A 15 part analysis/essay about this ending. (Seriously.)
- Metal Gear the unofficial site's take on it, in it's original context
- Penny Arcade's take on it.