The blueprints of Metal Gear Rex have been leaked out of the Alaskan Base in "Metal Gear Solid" (for psone). These blueprints have been placed on the black market and bought by a number of countries and private organizations. In response to these developments, an unknown group (FoxHound) has developed a Rex-Killer named Metal Gear Ray. This enormous robot has a tail which it uses to move itself through oceans, seas, and other water enviornments.

It is rumored that Metal Gear Ray, the new Metal Gear prototype developed by the United States Marines, is being shipped to or from New York City. A group of special opperatives from Russia, the Spetsnaz, set an ambush. They infiltrate the oil tanker, and in a matter of seconds, kill the crew and all hands on deck. One man stands between these operatives and their goal of kidnapping Metal Gear Ray. Solid Snake, a member of the new group "Philanthropy", must prevent the capture of Metal Gear Ray. However, there are also other groups/factions iterested in capturing Metal Gear Ray. Some of these people are familiar characters, such as Revolver Ocelot. Other soldiers in the game are working for the mysterous Solidus Snake (the third snake brother revealed in the final credits of Metal Gear Solid).