In 1964, the CIA sends Big Boss, who was then called Naked Snake, to a secret Soviet airbase in Pakistan. He is sent to rescue Sokolov. Sokolov is a Soviet scientist who left the Soviet Union with his wife and daughter. The United Stated sent him back to the USSR because US wanted the USSR to take nuclear missiles out of Cuba during the Cuban Missile Crisis. He is then forced to build a secret weapon called the Shagohod. This is a tank that can fire nuclear missiles in places that would otherwise be hard to do so. This building of this weapon is being overseen by Volgin. He is a Soviet officer who wants to destroy both the KGB and the Western world. Naked Snake almost completes his mission until his mentor, the Boss, betrays him. She does this by changing sides from the United States to the Soviet Union. After the mission fails, he is brought back to America.