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The game is set in 2005, where FOXHOUND and a genetically enhanced next-generation special forces unit lead an armed uprising on a remote island in Alaska's Fox Archipelago. This island, codenamed Shadow Moses, is the site of a nuclear weapons disposal facility. The forces that seized this island have acquired the nuclear-capable mecha Metal Gear REX, and are threatening the US government with a nuclear reprisal if they do not receive the remains of the "legendary mercenary" Big Boss within 24 hours.