In 1995, 200km north of Galzburg, South Africa, lies Outer Heaven, a fortified state founded by a legendary mercenary in the late 1980s. Word had gotten out to the western world that deep within the Outer Heaven stronghold, a weapon of mass destruction was being constructed. Government officials order the high-tech Special Forces unit FOXHOUND to infiltrate the fortress, assess the situation and neutralize the threat. In a mission known as "Operation: Intrude N313," FOXHOUND operative Gray Fox infiltrated the Outer Heaven stronghold. Days later, contact with Gray Fox is lost and his last transmission simply reads "METAL GEAR..."

Operative Solid Snake, FOXHOUND's newest recruit, is ordered by leader Big Boss to rescue Gray Fox and carry out his mission.

Upon insertion into Outer Heaven, Snake makes contact with local resistance members Kyle Schneider, Diane, and Jennifer. Using all of his skills and the equipment he procured on site, he manages to rescue Fox. He learns from Fox that Metal Gear is the codename of a nuclear warhead-equipped bipedal walking tank, which can engage and dominate in all forms of combat as well as launch its nuclear warheads from any location. Outer Heaven plans to use Metal Gear to impose itself as the new world superpower.

In order to destroy Metal Gear, and topple the Outer Heaven mercenaries, Snake rescues the lead engineer of Metal Gear, Dr. Drago Petrovich Madnar, and his daughter, Ellen. Armed with information on how to destroy Metal Gear, his skill and indomitable spirit, Snake fights through the entire Outer Heaven force. He begins to notice that traps being set for him are too precise, and wonders how information on his activities is being tracked. Moreover, Schneider is wounded by hostiles and is presumed dead after losing contact with Snake.

Upon destroying the powerful Outer Heaven defense system, Snake is able to neutralize Metal Gear. As he makes his way out of the compound's basement, he is confronted by the mysterious mercenary leader of the Outer Heaven forces, who turns out to be Big Boss himself.

Big Boss has been using his connections in the U.S. government to establish his own mercenary force, corrupt and steal military intelligence, and fund his activities. It was his aim to have Outer Heaven become the world's most powerful nation, with him at the top. He had the rookie Snake sent in, hoping to have him captured and feed the U.S. government misinformation, but had underestimated Snake's capabilities.

Having lost Metal Gear and much of his force, Big Boss starts the self-destruct sequence for the compound, and an underground battle ensues between Big Boss and Solid Snake. Despite injury, Snake defeats Big Boss and escapes the Outer Heaven compound as it crumbles in flames behind him. Big Boss stays behind and is presumed dead after the explosion.

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.

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

On the course of his mission, Snake teams 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. Snake learns from Dr. Madnar, that Big Boss, Snake's 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 Snake's former mercenary buddy Gray Fox. Determined to accomplish his mission, Snake fights against Zanzibar Land's elite mercenary force and manages to reach Dr. Marv's cell.

Unfortunately, Snake arrives 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 Snake 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 Snake, but is not successful in killing him.

With OILIX formula in Snake's hands, Snake is confronted by Gray Fox piloting Metal Gear D once again. After successfully destroying Metal Gear, Snake finds himself in a minefield. The two engage in hand-to-hand combat against each other and Snake eventually emerges as the victor.

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

With the crisis resolved, Snake disappears into the Alaskan wilderness, where he will live in retirement for the next six years.