Two years after the events of the Shadow Moses Incident, Solid Snake and Otacon, working as Philanthropy, receive intelligence of a new type of Metal Gear being transported through the Hudson River. As Snake boards the tanker, it's seized by a group of Russian mercenaries led by Revolver Ocelot, intent on stealing the new Metal Gear.

Another two years later and the Big Shell, the offshore clean up facility constructed in its place is taken over by a terrorist faction calling themselves the Sons of Liberty. New FOXHOUND operative Raiden is sent in to neutralize the threat. However, all is not as it seems.

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Dead Cell

Metal Gear Solid 2 began development in 1999. It was originally going to titled Metal Gear Solid III. The Roman numerals in the title was used to represent the three tallest skyscrapers in Manhattan, the setting of the game. In addition, Hideo Kojima implied that several of the themes he intended to be used in Metal Gear Solid 2 were essentially put into film format by the Wachowskis via their movie The Matrix beforehand.

According to Hideo Kojima in the documentary Metal Gear Saga Vol. 1, the original plot of the game revolved around nuclear weapon inspections in Iraq and Iran. In the plot, Solid Snake was supposed to stop the new Metal Gear while it was located on an aircraft carrier, in a certain time limit. He was also supposed to defeat Liquid Snake and his group, implying that Liquid had faked his death from FOXDIE in the previous game. However, about six months into the project, tensions in the Middle East began to arise, so the development team decided that they couldn't make a game with such a plot. The tanker in the final version is based on the original plot.

Metal Gear Solid 2 was also intended to reference the novel City of Glass, a novel by Paul Auster published in 1985, most notably in the naming of its characters. Raiden's support team originally featured a field commander named Daniel Quinn (simply referred as the "Colonel" in-game); Maxine "Max" Work, an Asian woman who saves the game data and quotes Shakespeare; and William "Doc" Wilson, the creator of GW. All take their names from key characters in the book, and all three would have turned out to be AIs. None of these characters appear in the final version. Their roles were absorbed by other characters, namely the "Colonel Campbell" simulation, Rose, and Emma Emmerich. Peter Stillman, however, takes his name from another City of Glass character.

A two player versus mode was also planned. However, it was dropped for unknown reasons.

Metal Gear Solid 2 is the first Metal Gear game to contain a note at the beginning that states that the events of the story are fictional. The note was presumably added in due to the events of September 11. This would later be repeated in Metal Gear Solid V: The Phantom Pain.

The consistent plot device throughout the game of all the characters either giving lies at least once or otherwise betraying and going to the other side of the conflict, according to Kojima, was based on the film L.A. Confidential.

According to the localizer of the game, Agness Kaku, Konami and Kojima had been insistent that the localized script remain exactly the same as in Japan on a micro-level in a manner comparable to scientific journals and legal documents, meaning she could not remove anything even to keep the flow or reduce repetition.