"Sneaking Mission":
In 1995, the Western powers received intelligence that a weapon of mass destruction was supposedly being constructed deep within Outer Heaven, a heavily fortified state founded by a legendary mercenary in the late 1980s, 200 kilometers north of Galzburg, South Africa. The U.S. Government called upon High-Tech Special Forces Unit FOXHOUND, commanded by the legendary soldier Big Boss, to infiltrate the enemy fortress, assess the situation and neutralize whatever threat the weapon posed to the West.
The mission was carried out by Gray Fox, one of FOXHOUND's top agents. After successfully infiltrating Outer Heaven, Gray Fox scouted the first building of the fortress, noting the locations of the inner courtyard, cameras and elevators, along with various weapons and equipment, such as card keys and Beretta handguns. Sometime afterwards, he stumbled upon information relating to the new weapon being developed. However, the mission ended in failure when Gray Fox was captured, though not before relaying some of the details of his reconnaissance back to FOXHOUND. His final words before his transmission was cut were simply: "Metal Gear..."
"Operation Intrude N313":
A few days later, rookie operative Solid Snake was called in for his first assignment for FOXHOUND. His commanding officer, Big Boss, briefed him on the situation, and after handing him a classified document detailing Gray Fox's infiltration route, ordered Solid Snake to perform a follow up mission entitled Operation Intrude N313. His mission objectives were to rescue Fox, and to find out the truth behind Metal Gear. After dispatching him to the rough area of Outer Heaven's location, Big Boss contacted Snake via his wireless radio and reminded him that what he was about to experience is nothing like what he has experienced in battle before.
Snake infiltrated Outer Heaven via an underwater insertion, and proceeded into the base, eventually managing to locate Fox with intel provided by Outer Heaven's prisoners and the Resistance leader Kyle Schneider. To get there, Snake allowed himself to be captured, and then after being thrown into a prison with all his weapons and equipment confiscated, he managed to break through a weakened wall under Big Boss's advice to get to Fox's cell next door. Gray Fox then revealed to Snake the true meaning behind Metal Gear: a walking battle tank capable of launching a nuclear missile from any kind of terrain. Luckily it was still in a hangar within the fortress and had not yet been activated. Fox told Snake to find Dr. Drago Pettrovich Madnar, the creator of Metal Gear and the only person who knew how to destroy it, explaining that he should be in a prison cell at the courtyard. After breaking out of the cell, he ended up encountering the prison's warden, Shotmaker, who attacked Snake while declaring that no one had ever escaped from the prison. Snake was forced to retreat into an unlocked room due to not being able to attack Shotmaker without his equipment. After retrieving his confiscated belongings, as well as getting rid of a transmitter that was planted among his belongings, he then managed to fight Shotmaker.
"Mercenary":
After fighting his way through Outer Heaven mercenaries Shotmaker and Machinegun Kid, Snake traversed the rooftop of Building 1 in order to reach the inner courtyard via parachute, also donning a bomb blast suit to bypass the wind barrier. Before he could reach the veranda, however, he had to fight off a Hind D gunship stationed in his path. After destroying it with a grenade launcher, Snake parachuted down into the courtyard, arriving at Dr. Madnar's cell, only to find it empty. However, he saved another hostage who revealed to him that Dr. Madnar was still alive, but that he had been relocated to the basement of the Building 2. While crossing the interconnecting desert between the two buildings, Snake was forced to battle a tank that had been recently deployed, using land mines to destroy it.
Afterwards, Snake arrived at the entrance to Building 2. However, he discovered a few guards stationed near the entrance making it virtually impossible to sneak past. It turned out that the Outer Heaven personnel had become aware of FOXHOUND's attempts at infiltrating the base, so they set up a checkpoint in case anyone tried to infiltrate Building 2. Big Boss then contacted Snake and suggested that he use a disguise to get past, and also mentioned that his radio frequency has been changed to 120.13 from that point on. Snake managed to procure an enemy officer uniform and used it to sneak into the building. Afterwards, he snuck through a waterway towards a nearly submerged door and encountered an armored bulldozer, which he managed to defeat using a grenade launcher. Proceeding to the basement, he eventually found "Dr. Madnar", who immediately revealed himself to be a decoy and activated a suicide trap. Snake quickly avoided the trap and, confused, continued his search for the real Dr. Madnar, encountering and defeating the mercenary Fire Trooper on the way.
Snake came into contact with Jennifer, another Resistance member, who helped him locate the real Dr. Madnar and provided him with a rocket launcher, which he could use to defeat the seemingly invincible Bloody Brad cyberoids, who were guarding the area near to where Dr. Madnar was being held. After destroying Bloody Brad, Snake entered Dr. Madnar's cell. However, Dr. Madnar would only tell Snake how to destroy Metal Gear if he rescued his daughter, Ellen, who had also been imprisoned. Snake made his way back to the basement of Building 2 where he was contacted by resistance member Diane, who advised him on how to locate Ellen. She was in the basement of Building 1, but luckily the two basements were connected by an underground passageway, though it was filled with pit traps, which Snake had to avoid. Eventually rescuing Ellen, she told Snake that her father had been forced to develop Metal Gear against his will.
"Metal Gear TX-55":
After Snake retraced his steps, Dr. Madnar informed him that Metal Gear TX-55 was located on the 100th floor basement of Building 3, located 20 km to the north. In order to destroy it, Snake needed to place plastic explosives on its feet in a specific order. Determined to destroy Metal Gear, Snake headed to Building 3. Once there, he was ambushed by enemy forces, but managed to slip by and made his way to the elevator. However, as he drew closer to the underground base, Big Boss started to act strangely, providing faulty information that would have delayed Snake's progress, and eventually ordering him to abort the mission.
Reaching the 100th floor basement, Snake found he didn't have the right card key to continue further. Contacted again by Jennifer, she informed Snake of a wall he could destroy in order to locate an oxygen tank that he could use to swim through the drainage duct in Building 2 in order to find the required card key. Jennifer also told Snake to save her brother, and threatened not to help him anymore if her brother was harmed.
After making his way through the drainage duct, Snake was challenged by Dirty Duck who was holding the card key Snake needed. Duck hid himself behind POWs and used boomerangs to attack Snake. Snake awaited his chance to attack and took it, defeating Duck at close range. Rescuing the POWs, one of them revealed himself to be Jennifer's brother, who thanked Snake and gave him information to aid in his escape from the fortress.
Heading back to the 100th floor basement of Building 3, Snake was contacted by Schneider regarding the truth behind Outer Heaven's leader, but his transmission ended prematurely after he fell into the hands of the enemy.
Although injured after the deadly battles with Outer Heaven's best mercenaries, Snake pressed on and found himself in Metal Gear's hangar. Placing explosives on its feet as per Dr. Madnar's instructions, while avoiding gun cameras, Metal Gear was ultimately destroyed. Immediately afterwards, the fortress's self-destruct sequence was activated.
"Escape - Beyond Big Boss":
While making his escape, Snake came face-to-face with the leader of Outer Heaven, who revealed himself as Big Boss. Snake was informed that he had only been sent in to gather false information. However, because Snake had achieved too much, he had crushed Big Boss's ambitions and the legendary mercenary vowed he would not die alone. After a ruthless battle, Snake defeated Big Boss and quickly made his way for the escape route, with the timer for the self-destruct sequence ticking away.
After successfully escaping, and with Outer Heaven exploding behind him, Solid Snake called back to HQ, informing them that Metal Gear had been destroyed, and that Operation Intrude N313 had been a success. Shortly thereafter, the South African radio station, KNK, reported breaking news of an earthquake occurring in the Galzburg region before sunrise.
"Just Another Dead Soldier":
It was later revealed that Big Boss had survived, while the "phantom" who was killed in Outer Heaven was actually his body double. The conclusion of Operation Intrude N313 saw NATO launch a massive aerial bombardment, wherein a pinpoint strike was executed on Outer Heaven's nuclear weapons facility using bunker-busting bombs. There were even reports of nuclear blasts in the aftermath, but the truth was hidden from the media, and few people ever learned of what really happened.
Outer Heaven was wiped from the face of the earth, killing many within the area, regardless of their ties to the regime or not. The multinational forces deemed this as an acceptable loss since the war orphans and refugees were considered a liability in their eyes. However, those who survived the bombings were rescued by Big Boss, including Resistance members who had initially been opposed to him, such as Schneider.
Big Boss later vowed that he and Solid Snake would meet again...