In 1999, Snake's former commander, Roy Campbell, called upon him again for another operation in Central Asia. Apparently, a new highly militarized nation called Zanzibar Land kidnapped Dr. Kio Marv, inventor of the oil refining microbe, OILIX. Not only that, but a new Metal Gear was believed to be being developed in Zanzibar Land.
Snake's mission objectives were to infiltrate the seemingly impenetrable wall that surrounded Zanzibar Land and recover Marv. He succeeded in both tasks, and deep in the heart of Zanzibar Land, he destroyed the Metal Gear D. Afterwards, he fought his former ally Gray Fox who piloted the Metal Gear, and successfully stopped the ambitions of Big Boss. Big Boss, the man behind Zanzibar Land, returned for a final battle/test against Snake, but Snake ultimately defeated him using a makeshift flamethrower which consisted of a lighter and an aerosol can.