San Heironymo Takeover

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

The two escape and Snake makes his way to a communications base, where he attempts to contact his old CO, Major Zero. Instead, he is greeted by his old FOX comrades Para-Medic and Sigint, who reveal that Snake and Zero are being accused of instigating the revolt and that the only way for Snake to clear their name is to find and apprehend the leader of the rebellion, Gene. To complicate matters, Gene has also convinced most of the Russian soldiers stationed on the base to join their side by simply taking over the chain of command of a former Red Army unit, that was secretly stationed inside the Colombian territory. In order to complete his mission, Snake must persuade enemy soldiers to join his ranks because of the scale of his mission.

Snake and his squad defeat the top members of the FOX unit (if defeated by reducing their stamina to zero instead of their HP, some of the FOX members will join Snake's squad, this includes Null and Python) and eventually they make their way into Gene's guesthouse. Snake learns 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 destroys an experimental model of Metal Gear codenamed Metal Gear RAXA and eventually defeats Gene, destroying the real Metal Gear itself afterwards. After Gene is defeated he gives 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 is awarded for his actions and establishes FOXHOUND afterwards. In the end it is revealed Ocelot kills the DCI and takes the Philosophers documents to "end them". After the credits, Ocelot speaks with an unknown man, (it is very possible that this man is Major Zero, since the unknown man is referred to earlier by Gene is "the man with the same codename as Null") on the phone. Ocelot speaks of using the Legacy to form the Patriots in place of 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 (he and the man on the phone) in their new endeavor - becoming the Patriots.