The year is 1995, and Special Forces operative Grey Fox is sent into Outer Heaven, a fortrified state founded by a "legendary mercenary". The mission Grey Fox was given was to infiltrate, assess the situation, and eliminate any threat he found. After a few days all contact with Grey Fox was lost, his last transmission stated nothing more then "Metal Gear". Because no one truely understand the meaning, and all contact with Grey Fox was lost, Solid Snake a rookie to FOXHOUND was sent in to rescue Grey Fox, and to eliminate "Metal Gear".

Upon ariving Snake meets Diane, Jennifer, and Schneider while on his mission to rescue Grey Fox. Once he reaches Grey Fox, he learns that "Metal Gear" is a codename given for a nuclear equipped bipedal walking tank, which can launch a nuclear attack from anywhere at any time. The leader of Outer Heaven plans to use "Metal Gear" to impose itself as the new world superpower.

Snake then heads to rescue the lead designer and enginner of Metal Gear, Dr. Pettrovich and his daughter. Once Snake rescues them he is given the information he needs to defeat "Metal Gear".

On his way Snake realizes that too many traps are being set for precisely him, and no one else. This makes Snake wonder how information on him is being tracked. During this time Schneider is abushed and loses contact with Snake, thus Schneider is assumed dead.

Snake is able to defeat "Metal Gear" upon breaching the base, as he makes his way out of the compound's basement area he is confronted by the leader of "Outer Heaven", and his commanding officer Big Boss. Big Boss reveals he was using his connections to the military to establish his own mercenary force, and to fund his force. Big Boss also reveals that it was his aim to have Outer Heaven become the world's great superpower. The reason Big Boss sent Snake in, was to gather false information and feed it to the authorities.

The final boss battle of Metal Gear is against Big Boss himself, Big Boss initiates a self-destruct sequence for all of Outer Heaven and he promises Snake that he will not die alone and that Snake will join him. Upon defeating his former leader and fleeing the base as it is detonating, Snake successfully completes the mission. At the end of Metal Gear the credits show a message from Big Boss stating that he will meet Snake again some day.