A new Metal Gear prototype (codename Gander) has been stolen by a separatist guerrilla group in the region of Gindra in Central Africa. The group, known as the Gindra Liberation Front (or GLF), plans on using the prototype as a means of achieving victory in an ongoing civil war. Solid Snake, the FOXHOUND operative responsible for the destruction of the original Metal Gear seven years before, is brought back from his retirement in Alaska. His mission is to infiltrate the group's headquarters Galuade, the fortress that was formerly Outer Heaven.
During the course of his mission, Snake teams up with Chris Jenner, a surviving member of the Delta Force that was sent before him to retrieve Gander. His main adversaries are Black Chamber, a group of mercenaries with abilities and codenames resembling those of FOXHOUND. In the end, he uncovers a conspiracy involving the GLF and US Government.
