The game is divided into two missions. The first is SolidSnake?'s infiltration of an 'oil tanker' sailing through the New York harbor that secretly carries a new MetalGear prototype. What started as a mission to photograph the prototype and expose its existence goes awry as a group of Russian mercenaries simultaneously invade the ship in attempt to steal the MetalGear for themselves. Things get even worse when RevolverOcelot? betrays the Russians and steals the MetalGear for his own purposes, escaping from the ship's hold by ripping the ship apart, drowning everyone inside.
The second mission takes place several years later, on the giant oil-cleanup facility called 'Big Shell' that was constructed around the site of the sinking of the oil tanker. During a visit by the president, the facility was seized by a group of terrorists known as 'Dead Cell', and Raiden is sent to stop them. The leader claims to be Solid Snake himself, who was blamed for the sinking of the tanker but thought to have died in that incident.
As it turns out, the Big Shell is a cover for the construction of MetalGear Arsenal by a shadowy group known as the Patriots (they're not not the Illuminati). The terrorists are lead by SolidSnake?'s other brother, Solidus Snake, the former US President who is now attempting to acquire Arsenal and use it to destroy the Patriots. SolidSnake? is quite alive and has disguised himself as one of the SEAL team members sent in to help but get killed in the first five minutes (except for SolidSnake?, of course). (He's SolidSnake?; he can't die. Period.)
So of course Raiden and SolidSnake? attempt to disable Arsenal, which acts as both an impenetrable fortress (it carries 20 other MetalGears inside it) and a central Internet censorship system. Their attempts using a computer virus fail, but they manage to learn the names of the leaders of the Patriots. (Arsenal's computer core, 'GW', knows which names to delete. No relation to GW Bush.) In any case they all end up inside Arsenal, which is now on a collision course with New York City, and Raiden single-handedly takes out the entire MetalGear defense fleet and ends up fighting Solidus on the roof of some monument (I can't remember the name right now).
The one redeeming part of the ending is Hal (SolidSnake?'s sidekick, sort of) following up on the names he found. Several were major benefactors of Philanthropy (their anti MetalGear group), and all have been dead for more than 100 years. So yup, the Patriots win again. Or something.
I thought the game was really good right up until things start getting weird (to say the least) towards the end. The graphics and controls were awesome, and the boss fights and gameplay were well done, and I liked almost all of the puzzles, but things fell apart right around the time Raiden is captured and starts having hallucinations suggesting that he turn the game console off. (Not to mention the 'Fission Mailed' screen, which is a fake 'Mission Failed' game-over screen.) From that point on I don't know what the game designers were thinking. The final boss fight is cool, but by that time the two of you are on the same side (or ought to be), so it doesn't make much sense.