Former Foxhound unit member Solid Snake and Dr. Hal Emmerich follow an anonymous hint to confirm the presence of a new weapon of mass destruction in Chile.

Former Foxhound unit member Solid Snake and Dr. Hal Emmerich have created the NGO "Philanthropy" to rid the world from weapons of mass destruction known as "Metal Gears". Following an anonymous hint, Solid Snake travels to the Andes Mountains in Chile to confirm the presence of a new weapon. In Chile, Snake finds a post-war civil conflict and a terrorist plan carried out by a man called Mongoose and the death squadron "Thug Herd Unit".—Julio Marambio