On August 24, 1964, an agent of the Cia's Fox unit is flown in on an American aircraft and parachutes onto a Soviet Union base called Tselinoyarsk. This agent , code named Naked Snake, is sent on a solo mission to retrieve Sokolov before he can complet the project of the Shagohod. He must do it in secreacy, for if the Soviets discoved an American soldier was in thier country, they might declare war on the US. Naked Snake works under a man called Major Zero, who he communictes with via codec. Major Zero guides him through his mssion to rescue Sokolov from the Soviets.

     Snake, though, also has contact from another person. His mentor, trainer, and the closest thing he's ever had to a mother. The Boss. Leader of the special forces unit, Cobra. She and the Cobras lead the US to fictory in many battles during WW II. Together Naked Snake and The Boss had developed a hand to hand combat called CQC. Close quarters combat.The Boss had taught Naked Snake all he knew about  combat, war, and stratagy. Now he was glad to have her guide him through this mission.

    Naked Snake travels through the jungle and eventually makes it into the facility where Sokolov is being kept. There is where Naked Snake learns that the Soviets are forcing him to create the Shagohod to have dominence over America in the Cold War. He wants nothing to do with it, but the final tests for he Shagohod have already begun. Naked Snake also learns that the Shagohod is equiped with a SS 20 saber class nuclear missle. On the way back, Naked Snake and Sokolov cross a rope bridge and are meet by a most unexpected person. It is The Boss and she is with Colonel Volgin of the Soviet Union. Volgin is a member of the GRU and he plans to over throw Khrushchev so he can take his place as the leader of the Soviet Union.

  It appers that she has defected from the US. Members of her Cobra Unit come down from a chopper and pick up Sokolov. There is The Pain, a psycich that controls killer bees, The Fury, triple jointed ad can dislocate body parts to jump like a spider, and The Fury, an astonaught with a suit, jetpack and flamethrower. The Boss has taken two miniature nuclear shells with her and she gives them to Volgin as a gift. Snake can't believe what he's seeing. His mentor was betraying her country and him. Volgin wants to know if he is with her and she tells him no. Then Volgin decides he should die then. He tries to comfront her but she is much more skilled than him. She uses a series of CQC moves and breakes his arm. She then flipps him off the edge of the bridge and he plummets to the river below.

     The Boss and her commrads load up and head to the base where they pick up the Shagohod. Volgin then takes the Nuclear missle that The Boss gave him and aims it at he Soviet research facility. A man is with him  called Ocelot, who also one of the higher ranked GRU members and he is the Major of the Ocelot unit of the Spetsnaz. He is armed with dual Mararov PM pisols. Ocelot tries to talk the Colonel out of firing the shell but he fires it regardless of the fact his men where at he base.

    Naked Snake returns to the US, and is  in holding for his next mission. The President of the US is called by the Soviet Unions's leader, Khrushchev. Khrushchev asks the President very concerningly why an American aircraft was in the Soviet's airspace at the same time Sokolov's research facility was nuked. The President explains that The Boss had defected and had taken two nuclear shells with her. Khrushchev doesn't really believe him so he tells the President that they have a week to kill The Boss, proving that she has defected and that America is inocent.

     On August 30, Naked Snake once again lands in Tselinoyarsk and is given the mission to kill his former boss. The Boss. He is the only one who would be able to do it since he was her last apprentice.