After a few days, his last message being "Metal Gear..." Gray Fox was missing in action. Taking the situation seriously, the top men of the "West" again called for FOX-HOUND. Big Boss selected Solid Snake, who had recently joined FOX-HOUND, as the agent and entrusted everything to him.

Successfully making a solo infiltration to Outer Heaven, Snake got in touch with local resistance members Schneider, Diane and Jennifer. With their co-operation, Snake succeeded in rescuing Gray Fox. Gray Fox laid out the terrifying facts about "Metal Gear" Metal Gear was the development name of a nuclear warhead-equipped two-legged walking tank. It can walk over the toughest terrains that would stop normal tanks. It can conduct local warfare by itself with unique weapons like its vulcan-cannon and anti-tank missiles. It was indeed a new type of weapon that can conduct a nuclear attack against any place on the face of the Earth from any land surface...

With Metal Gear, Outer Heaven was trying to establish its military superiority over the entire world. In order to destroy Metal Gear, Snake rescued Metal Gear's chief engineer Dr. Pettrovich and his daughter, Elen, who was taken hostage to force her father to continue with his development. Snake hears from Dr. Pettrovich how to destroy Metal Gear. However, as Snake approached the heart of Outer Heaven and Metal Gear, well designed traps were set all around Snake - as if his actions were being leaked to the enemy...

In the midst of the escalating battle, the leader of the resistance, Schneider, fell into the hands of the enemy, and Snake himself was injured through the deadly battles with Outer Heaven's best mercenaries. But Snake's indomitable spirit lead him to the 100th floor basement of the secret base where Metal Gear was developed. Evading the powerful defence system that wipes out all intruders, Snake ultimately succeeded in destroying Metal Gear.

Snake tried to escape from Outer Heaven upon completing the mission. However, during the escape he was confronted by one man- FOX-HOUND's commander-in-chief Big Boss. Big Boss laughed at the astounded Snake and told him the truth behind his mission. While serving as commander-in-chief of FOX-HOUND, Big Boss also ran a mercenary dispatch company utilising his connections and capitals from his own years as a merc. He was planning to build this company into a larger military establishment with Outer Heaven as its base. His purpose for sending the rookie Snake was to cause information confusion amongst the west. However, Big Boss miscalculated. He never thought Solid Snake would make it this far...

Having lost Metal Gear, Big Boss activated the self-destruct system of the underground base. While the countdown to destruction continued, his scream echoed in the emptiness "YOU HAVE GONE TOO FAR. TOO FAR!!!" On the 100th floor basement, the battle between the 2 men commenced - free of ideology and politics. The armed fortress nation Outer Heaven collapsed. The impenetrable fortress made from the best military technology and occupied by the toughest mercenaries burned in flames. Behind him, the flames reached skyward as Outer Heaven fell leaving Solid Snake all alone...