San Hieronymo Incident

Six years after the events of "Operation: Snake Eater," Naked Snake's former unit, FOX, had broken their allegiance with the CIA and gone renegade. Snake himself was also targeted by the FOX Unit, which sent renegade FOX Unit soldiers to attack and capture him. Snake was captured and brought to an unknown location before being tortured and interrogated by one of the members of FOX, Lieutenant Cunningham, who was trying to locate the whereabouts of the missing half of the The Philosophers' Legacy. He explained that the United States Government had already acquired the other half of the Legacy from the Soviet Union at the conclusion of Snake Eater and they had suspected that Snake had stole the other half. Snake was imprisoned in a cell next to Roy Campbell, the sole survivor of an American Green Beret team sent in to investigate the base. Snake learned through Campbell that they were on the San Hieronymo Peninsula, the site of an abandoned Soviet missile silo in Colombia.

The two escaped and Snake made his way to a communications base, where he attempted to contact his old commanding officer, Major Zero. Instead, he was greeted by his old FOX comrades Para-Medic and Sigint, who revealed that Snake and Zero were being accused of instigating the FOX revolution, and that the only way for Snake to clear their name would be to find and apprehend the leader of the rebellion, Gene. To complicate matters, Gene had also convinced most of the Russian soldiers stationed on the base to join his side by simply taking over the chain of command of the former Red Army unit that was secretly stationed inside the Colombian territory. In order to complete his mission, Snake was forced to "persuade" enemy soldiers to join his ranks, due to the scale of the mission.

Snake and his squad defeated the top members of the FOX unit and eventually they make their way into Gene's guest house. Snake learned many things on his way. Cunningham was working for the Pentagon and wanted Snake to push Gene into launching a nuke to Russia to prolong the Cold War, so the Pentagon could keep their importance over the CIA. Gene was actually aware of this plan the whole time from information from Ocelot. Gene himself wanted to launch a nuke at America to destroy the Philosophers and to make his nation of soldiers, "Army's Heaven". Snake destroyed an experimental model of Metal Gear codenamed Metal Gear RAXA and eventually defeated Gene, destroying the real Metal Gear itself afterwards. After Gene is defeated he gave Big Boss the funds, equipment, personnel, and all other information regarding Army's Heaven, telling him that one day, he will need to use them. On his return home, Snake was awarded for his actions and established FOXHOUND afterwards. In the end it was revealed Ocelot killed the DCI and took the Philosophers documents to "end them". After the mission had ended, Ocelot spoke with Snake's CO, Major Zero, on the phone. Ocelot spoke of using the Legacy to end The Philosophers. Ocelot actually wanted the trajectory data of the nuke to point to the DCI so he would bring the documents right to him. Ocelot requests Big Boss be able to 'join' them in their new endeavor - becoming The Patriots.