By 1999, the Cold War had thawed, and nuclear disarmament by the major world powers promised a bright beginning to the 21st century. Despite this, all was not well in the world. A series of shocks to the oil market spurred the development of new high-tech energy sources, including fusion power. However, most vehicles still relied on oil for power.

Oil reserves were at a critical low, and the world community was prepared to take drastic measures, either by drilling into sand and shale for more oil, despite the difficulty -- or moving on to renewable fuels.

Such steps proved unnecessary when Czech scientist, Dr. Kio Marv, successfully bio-engineered a new species of algae, OILIX, that could produce petroleum-grade hydrocarbons with little expense and effort. Marv presented the algae to the World Energy Conference in Prague, and was on his way to a demonstration in the United States when he was kidnapped by soldiers from Zanzibar Land. NATO discovers that Zanzibar Land's leaders plan to hold the world hostage by controlling the supply of oil, and some good old-fashioned nuclear brinksmanship, courtesy of a stockpile of nukes.

I was brought out of retirement by FOXHOUND's new commander, Roy Campbell, and was sent to Zanzibar Land to rescue Dr. Marv.

On the course of my mission, I team up with Holly White, a CIA operative posing as a journalist, and Natasha Marcova (Gustava Heffner in recent versions), an StB agent and Dr. Marv's bodyguard. He is also reunited with Dr. Drago Pettrovich Madnar, the Metal Gear inventor from Outer Heaven, who claims to had been captured once again to build another Metal Gear tank (called Metal Gear D) for Zanzibar Land, as well as oversee mass-production for an army of smaller Metal Gear models. I learn from Dr. Madnar, that Big Boss, my former commander, was alive and well, leading Zanzibar Land's forces.

However, upon reaching the suspension bridge leading to the Detention Camp, Natasha is killed by a missile fired by Metal Gear and Dr. Madnar is recaptured by the enemy. The new Metal Gear's pilot is revealed to be none other than my former mercenary buddy Gray Fox. Determined to accomplish his mission, I fight against Zanzibar Land's elite mercenary force and manage to reach Dr. Marv's cell.

Unfortunately, I arrive too late, as he finds Dr. Marv's corpse, who was unable to survive the repeated torture sessions, along with Dr. Madnar, who was unable to save him. Just before i could retrieve the OILIX formula left by Dr. Marv, Holly reveals via a radio message that Dr. Madnar was not captured after all, but was in Zanzibar Land voluntarily overseeing the development of Metal Gear. After the truth comes out, Dr. Madnar attacks me, but is not successful in killing me.

With OILIX formula in my hands, I am confronted by Gray Fox piloting Metal Gear D once again. After successfully destroying Metal Gear, I find myself in a minefield. we engage in hand-to-hand combat against each other and I eventually emerges as the victor.

After defeating Fox, i am forced to do battle with Big Boss. With no weapons at his disposal, i am forced to improvise and create a makeshift flamethrower consisting of a cigarette lighter and aerosol can. Taking Big Boss by surprise, i defeat him for the second and final time. me and Holly escape and together, they deliver the OILIX formula to Campbell.

With the crisis resolved, i disappear into the Alaskan wilderness, where i lived in retirement for the next six years.