- Two years after the death of Solid Snake, a rookie FOX-HOUND agent, on his first mission, infiltrates an offshore decontamination facility to rescue the President.
- Two years after the events at Shadow Moses, Solid Snake infiltrates the United States' Marine Corps and sees that the government is trying to unleash Metal Gear upon the world. With the help of Otacon, Snake will expose Metal Gear to the world and try to save the world from the disaster that was the Shadow Moses Incident.—Johnny
- Two years after terrorists seized the nuclear facility on Shadow Moses Island, Revolver Ocelot, the sole survivor of the FOX-HOUND squad that led the terrorists, sells the plans for Metal Gear REX on the black market. Solid Snake and Otacon are now part of "Philanthropy," an independent organization dedicated to eliminating the Metal Gear variants that appear throughout the world. Acting on a semi-anonymous tip, Snake infiltrates an oil tanker sailing through New York Harbor, which is said to be carrying Metal Gear RAY, a new model developed by the US Marine Corps. However, the mission isn't as simple as Otacon and Snake predicted, and the tanker is eventually sunk by explosives. Two years later, terrorists seize the "Big Shell," an environmental cleanup facility placed over the wreckage of the tanker, and take US President James Johnson hostage. FOX-HOUND member Raiden must infiltrate the Big Shell, rescue the president, and disarm the terrorists. As he carries out the mission, Raiden learns the dark secrets behind the tanker incident, Johnson's predecessor George Sears, his own past, and a mysterious organization known as "The Patriots."—Anonymous
- Two years have passed since the Shadow Moses incident, and Revolver Ocelot has leaked the blueprints for Metal Gear REX to the black market. Since then, militaries throughout the world have their own REX for their own military needs. Solid Snake, and now partner and close friend Otacon have founded 'Philanthropy' an organisation based solely on destroying every last Metal Gear REX on Earth. Some time later, Otacon recieves information that a new Metal Gear is being developed, under the codename 'Metal Gear RAY' and is being hidden and transported onboard the tanker 'Discovery'. In turn, Solid Snake, albeit with a mission that involves taking photographic evidence of the new Metal Gear so that Philanthropy can expose it to the world, lands on the tanker via bungie jumping off the Hudson River. Otacon reminds Snake to not kill any personel as the people onboard are "Nice, upstanding Marines, not terrorists". He also tells Snake that the Metal Gear "Should be somewhere down in the cargo holds". Shortly after, he witnesses the takeover of the tanker by Russian Special Forces lead by 'Colonel Gurlukovich'. After finding out where the ship is heading (the middle of the Atlantic), Solid Snake meets and fights 'Olga Gurlukovich' (daughter of the Russian Special Forces leader), rendering her unconscious with a round from his tranquilizer gun.
Before he continues to the location of RAY, Snake spots a hovering photographic device looking at him, taking a picture and flying off. He proceeds down to the cargo hold where the prototype RAY is supposedly being held. Solid Snake sneaks into the holds while a Commander 'Dolph Jackson' ( with the RAY right behind him) gives out a speech to a huge assembly of Marines about how the Marine Corps will lead the world with the RAY, how it will be mass produced and that it is amphibious - able to move on land AND in water, making it more than a match to any REXs that would be used against it. Solid Snake manages to take crucial photographs of RAY that would reveal its existence to the public, and uploads them to Otacon via a computer. Otacon then tells Snake to flee the holds and get off the tanker, just when the speach is wound up. The Marines then salute the commander, but the silence is broken by the sound of clapping. The sound came from a figure which steps out from behind the RAY, and it reveals itself as Revolver Ocelot (his missing right arm now replaced). Gurlukovich's forces then stomr the holds and point their weapons at the surprised Marines, who point their weapons at the Russians. Revolver Ocelot tells the commander that he has come to take back the RAY to 'The Patriots' - its true owners, according to Revolver Ocelot. Out of nowhere, Colonel Gurlukovich grabs hold of commander Dolph Jackson and puts a gun to his head. He claims that "Russia will rise again" and that "Even the technology that gave birth to these weapons is Russian".
Revolver Ocelot then announces that Semtex (an explosive) has been placed in the tanker's key structural points and with a touch of the detonators' button in his hand, he will blow the tanker out of the water. All seems under control until Revolver Ocelot reveals that he has no intention of selling Metal Gear RAY to Colonel Gurlukovich, as he has stated to commander Dolph Jackson that he has come to "Take it back". Colonel Gurlukovich then asks "Have you sold us out?" and whether Revolver Ocelot is still in league with 'Solidus', to which Revolver Ocelot replies "No hard feelings Colonel, but Mother Russia can rot for all I care.
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