 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."