Metal Gear Solid 3: Snake Eater was released in 2004 and still had an emphasis on stealth. It is a prequel to the Metal Gear games and occurs in 1964. Unlike traditional Metal Gear games, this one takes place outside in the Soviet Union.
The antagonist in Metal Gear Solid 3 is Colonel Vulcan. Since it is a prequel, the protagonist is Naked Snake (not to be confused with Solid Snake).
Metal Gear Solid 3 talks about the Philosophers and the Philosophers Legacy as well. The Philosophers are a perverse group of people composed of the US, China, and the Soviet Union. They run the entire world without anyone know it. Ultimately, the Philosophers deteriorated because of quarrels with each other.
The Philosophers Legacy was an exorbitant amount of money that the Philosophers had, and it was concealed at some unspecified locations after the collapse of the Philosophers. The game begins with Snake talking to his colleagues Major Zero and The Boss via codec. The Boss is not the same person that Solid Snake defeated in Metal Gear and Metal Gear 2. In this game the Boss is Naked Snake's former teacher and someone else (who will be revealed later on). After their codec conversation, Snake infiltrates a jungle and locates Sokolov (scientist) because Sokolov is creating a machine called Shagohod. This machine is capable is being immensely harmful and can be utilized as a weapon. Everything goes as planned until, Snake encounters The Boss. She has defected to Colonel Volgin's side, and she hands Volgin two nuclear weapons.
Snake attempts to impede their malicious intentions, but fails miserably. Volgin launches 1 of the nuclear weapons to conceal their escape route and flees with the Shagohod and Sokolov. Since the weapon was launched over Soviet Union soil from an American plane, the Soviet Union interpreted this as an attack. To prevent further bloodshed, United States president Lydon Johnson convinces Soviet leader Nikita Khrushchev that the US is innocent. Furthermore, the US blames The Boss for the nuclear strike and intends to eradicate the Shagohod and The Boss. Seven days later, Snake is sent back into action to accomplish this mission.
While Snake strives to locate the Shagohod, he meets Eva (former NSA agent). A young and impatient Revolver Ocelot enters the picture, and he fails in capturing Snake. Snake and Eva arrive at the facility where the Shagohod is being held. Soon afterwards, Volgin spots Snake and confesses to Snake that he has pilfered the Philosophers Legacy. Snakes hears that the United States actually plans to collect the Philosophers Legacy for their own agenda, and he manages to terminate the Shagohod and Volgin. Eva and Snake blow up the facility and get away unharmed. Unfortunately, The Boss abruptly interferes with their plan to escape.
Snake realizes that The Boss defected in order for the US to have a scapegoat for the nuclear explosion. He swiftly disarms her and completes his mission by killing her.After a long and arduous mission, Eva suddenly leaves but manages to set aside a tape for Snake. The tape divulged that she was a Chinese spy sent to recover the Philosophers Legacy for China. It also revealed that The Boss defected to repossess the Philosophers Legacy for the United States. Here is the big surprise: Naked Snake is awarded with the name "The Boss" for neutralizing the terrorist threat. Meaning that the Big Boss that Solid Snake defeated in Metal Gear 1 and 2 was none other than Naked Snake (the protagonist in Metal Gear Solid 3).