In 1999, the terrorist streak of the Central Asian nation of Zanzibarland spiraled out of control. What began with the seizure of nuclear weapon disposal facilities around the globe to gain military superiority continued with an attempt to gain economic superiority through the abduction of the brilliant Czech biologist Dr. Kio Marv, who had developed the OILIX microorganism for refining oil.
Alarmed by the situation, the US government called upon FOXHOUND to initiate Operation Intrude F104. Solid Snake had already retired from active service, but Roy Campbell, commander of FOXHOUND, called him back into action to infiltrate Zanzibarland and rescue Dr. Kio Marv. Snake was provided with a motion-sensing radar and was supported over the radio by FOXHOUND survival instructor Master Miller; Johan Jacobsen, expert on the Zanzibarland wildlife; and George Kasler, who provided intel.
Snake made contact with CIA operative Holly White, who was in the midst of infiltrating Zanzibarland Tower, and Gustava Heffner, who was protecting Dr. Kio Marv. He went on to defeat the mercenaries Running Man, Night Fright, Jungle Evil, Black Ninja, Red Blaster, and the Four Horsemen, and then reunited with Dr. Drago Pettrovich Madnar from whom he finally learned the name of Zanzibarland's military leader.
Zanzibarland's leader was former FOXHOUND commander Big Boss. Big Boss had been defeated by Solid Snake in Outer Heaven only to be revived by Dr. Madnar's Snatcher Project. After surviving the destruction of Outer Heaven, he worked in secret, creating a world of conflict where soldiers would have a reason to live.
Snake learned for Dr. Madnar's betrayal after discovering Dr. Kio Marv's tortured body. After defeating Dr. Madnar, Snake then battled Metal Gear D, piloted by Gray Fox, who had disappeared following the Outer Heaven Uprising. Snake destroyed Metal Gear D then engaged Gray Fox in hand-to-hand combat in a minefield. Their reason to live was to play out on a deadly battlefield.
After he defeated Gray Fox and Big Boss, Solid Snake seemingly vanished from the face of the Earth.