Metal Gear Solid 3: Snake Eater was released in 2004 and takes place in 1964. It is the chronological start of the series. Released on PlayStation 2, it shifted the series outdoors and into an open world, stripping players of the Soliton Radar which they had relied upon for the past two games. It introduced a camouflage mechanic that reduces Snake's visibility depending on how well he blends in with the environment. It also introduced a Stamina mechanic that imposes penalties if the Player Character is hungry.
Chapter 1 - Virtuous Mission
A man named Jack, code-named Naked Snake, is dropped via parachute into Tselinoyarsk in Russia. Jack is a former Green Beret now working for the FOX unit of the CIA. His radio support includes the leader of the unit, Major Tom (having taken his codename from one of the secret tunnels in The Great Escape); a doctor, Para-Medic; a technology and weapons specialist known as SIGINT; and his mentor, The Boss. The Boss, formerly operating under the codename The Joy, is the leader of Cobra Unit, the very first special forces group in history. Most of them have supernatural powers, but The Boss, who does not, is in charge, which tells you just how much of a Badass Normal she is. Under her leadership, the Cobras were instrumental in turning the tide of World War II, and they led the charge at Normandy Beach, amongst other things.Snake's mission is to aid in the defection of a Russian scientist, Dr. Nikolai Stepanovich Sokolov, who has been working on a new nuclear delivery system called the "Shagohod". Snake infiltrates the facility, his only real opposition being a GRU Major named Ocelot. Snake defeats him quite handily and takes a moment to criticize Ocelot's training, identifying that his shooting techniques would flourish with a revolver in his hand. After Ocelot retires in shame, Snake escorts Sokolov away... only to encounter The Boss. She announces that she is defecting to Russia — specifically, to Yevgeny Borisovitch Volgin, a rogue GRU colonel who can expel electricity from his body. Volgin is here for the Shagohod, which he hopes to use to oust Khrushchev from power, and The Boss is here to help him. For good measure she throws in the Cobras, who abandon the nations of their birth to fight alongside her, and two Davy Crockett nuclear bazookas
. She breaks Snake's arm and throws him off a bridge into the river below. Volgin recaptures Sokolov and airlifts the Shagohod prototype away, with Ocelot and The Boss by his side. And finally, just to make a bad situation worse, Volgin fires the (American) Davy Crockett nuke at the (Russian) research facility, covering up the situation and pinning the blame on The Boss.
Chapter 2 - Operation Snake Eater
A week later, Snake is kept in a military infirmary as his broken arm is healing. Major Tom meets him there, briefing him on the latest developments in the wake of the disaterous outcome of the Virtuous Mission. During a heated phone call a few days ago, Khrushchev was very blunt with LBJ: while he is willing to believe that the nuclear explosion was the work of Volgin, the Red Army and the majority of the Soviet government blame America and is pushing for retaliation. In order to placate them, prevent a retaliatory nuclear strike, and prove America's innocence, the Soviet Premier demands that Washington take responsibility for eliminating the Boss (so that she can be blamed as the cause of the whole situation) as well as Volgin, against whom Khrushchev cannot move openly due to political limitations. Khrushchev says he can only stall the military hardliners in his cabinet for a week at most, at which point the Americans better have their story and their evidence in order, or else war will happen. The Major explains that the US government want Snake and the FOX unit to carry out the mission, because as they see it, him and Snake haven't yet managed to clear themselves of suspicions of any involvement in the Boss' defection, despite their repeated protestations of their innocence, and taking on the mission would definitely be a step in the direction to do so. He adds that he fears that this is an offer they cannot refuse, because the government has clearly hinted that the alternative to accepting the mission is the two of them being executed as traitors (and to add insult to injury, the higher-ups are also threatening to ruin Para-Medic's career, by revoking her medical license).A few hours later, Snake is on his way to be redeployed to Tselinoyarsk via a D-21 drone prototype. Major Tom, now changing his name to Major Zero out of remorse (he explains to his embarrassment that he had misremembered the plot of The Great Escape, and that "Tom" was the tunnel that the German guards discovered in the film, believing that his choice of codename jinxed the previous mission), commands the mission, with Para-Medic and SIGINT at his side; this time, Snake will have on-site support from two American defectors, codenamed ADAM and EVA, now operating as moles within Volgin's ranks on behalf of Khrushchev.
Snake, returning to Tselinoyarsk, encounters EVA, a motorcycle-riding, extremely-breasted blonde (though he's much more impressed by the customized M1911 she gives him). ADAM is nowhere to be found, but EVA, posing as Sokolov's girlfriend Tatyana, ends up being quite sufficient. Snake fights his way through the Russian jungle, handling the members of the Cobras as he goes. Each is named after the emotion they bring into battle, and has powers to match: The Pain controls bees; The Fear is double-jointed and can move like a spider, attacking using poisoned crossbow bolts; The End, a fearsome sniper, can photosynthesize; The Fury, a disfigured cosmonaut, wields a flamethrower-slash-jetpack that runs on rocket fuel; and The Sorrow, a medium who can speak to the dead, is not fought because he died in 1962. Like every other Cobra, he landed on Normandy Beach, paying special attention to The Boss, who was pregnant at the time. She gave birth by emergency C-section, delivering a healthy baby boy, who was kidnapped by unknown forces. After the war, The Sorrow and The Boss returned to their home countries: she to America, and he to Russia. This was how the two of them ended up meeting as enemies in 1962, right here in Tselinoyarsk, ordered by their countries to slay each other. This was incredibly painful for both of them, as The Sorrow was not only The Boss's friend, but her lover, and the father of her wayward son; it is eventually revealed that he sacrificed himself to her, as someone behind the scenes—someone pulling the strings in both the USA and the USSR—claimed to have possession of their son, and was threatening to kill The Boy if both The Sorrow and The Joy survived their battle. Though deceased, The Sorrow is present throughout the game as a ghost, visible at certain times through first-person view.
Snake also continues to encounter the Ocelot unit, led by Revolver Ocelot, who has taken Snake's advice and now wields the weapon he is named after. There is a clear competition between the two men, but it's just as clear that Ocelot looks up to Snake. He also looks up to The Boss, and as the game progresses it is revealed that Ocelot is in fact her stolen son by The Sorrow, though it is unclear if either of them is aware of this fact. That doesn't stop The Boss from mothering him, but then she's Team Mom to everyone—treating "Tatyana" with respect, mourning her lost comrades, interceding on behalf of Sokolov, providing accurate but ignored warnings about Jack's progress, and even forcing Volgin to back down on occasion. And when you consider that Volgin's an Ax-Crazy, Depraved Bisexual, lightning-wielding sadist who is happy to nuke his own country, you figure out just how much of a Badass Normal The Boss is.
Snake makes his way to Grozny Grad, Volgin's personal fortress, along the way learning the nature of the Shagohod. Like most Metal Gears, it has a unique way of launching nuclear weapons. Specifically, it's a rocket tank, using itself as the first stage of an ICBM. He handles most of the Cobras: The Pain is fought in an underground cave, where Snake can dive beneath the water to avoid bees; The Fear takes a stand in a dense forest where he can use his climbing mobility to great advantage; The End is fought in an arena so large that it consists of multiple areas, any of which he could be hiding in. (Of course, the player can also engage in Breaking the Fourth Wall by simply turning off the console and waiting a week, during which time The End, who was born in the 1860s, will simply pass away in his sleep.) After defeating The End, Snake must climb an extremely long ladder, during which time the gloom and boredom is alleviated by only one thing: one of the greatest main themes of all time.
Upon reaching Grozny Grad, Snake is discovered and tortured for information by Volgin. Though he ultimately escapes, he loses an eye, trying to protect EVA from Ocelot, who now suspects that she is a double agent. (During his escape, Snake wades down the river and "fights" The Sorrow, who narrates as the souls of all those Snake has killed over the course of the game come screaming at him. Depending on how effectively the player has pursued a Pacifist Run, the "opposition" may not consist of anyone except The Cobras, who will self-immolate even if defeated by tranquilizer weapons.) Snake must now get back into Grozny Grad and destroy the Shagohod. To do so, he must handle The Fury, who is hanging around in an underground cellar where his rocket-fuel-powered jetpack gives him an enormous advantage.
Though Snake succeeds in sabotaging the Shagohod's hangar with C-4 set on a 30-minute timer, he is once again captured. Volgin this time goes on his Villain Monologue: he is a son of one of "The Philosophers," a group of very rich men from America, Russia and China who banded together during World War II in an attempt to guide the world from behind the scenes. Alas, after the war, they began to fracture, and their cache of funds, a $100-billion pool called the "Philosophers' Legacy," was split into bank accounts around the world. Volgin has now gained possession of these accounts, though America is also trying to get their hands on it. (During this rant, if the player jumps into 1st-person view, they will see The Sorrow holding up a digital clock showing how long remains until the C4 goes off.)
Volgin engages Snake in battle, first hand-to-hand and then (after Snake knocks him unconscious and escapes) aboard the Shagohod itself. Ultimately, he is felled by a bolt of lightning out of a clear blue sky. Snake and EVA retreat to Rokovoj Bereg, where an escape aircraft is hidden. However, there The Boss is waiting for them. She explains that the agent America sent after the Philosophers' Legacy is herself. She has succeeded—EVA now has the intelligence she collected. Now, The Boss declares, Snake must kill her in the traditional end-game Duel Boss fight, to complete his mission, exonerate their nation and prevent the outbreak of a deadly nuclear war. This is, of course, no easy feat, as The Boss is a pale-skinned blonde wearing a white jumpsuit in a field of white flowers, and has an assault rifle with infinite ammo. There's also bombers coming to blow the place up in 10 minutes. Afterwards, The Boss, Facing Death With Dignity, tells Snake to do it... And the game won't let you progress until you pull the trigger yourself.
(If you hit R1 to jump into first-person view after you kill The Boss, you can see her and The Sorrow, Together in Death, fading away.)
Finally, Snake and EVA's plane is boarded by Ocelot, but after an inconclusive fight, he admits defeat, acknowledging that the world is more interesting with Snake in it. The two trade first names (John and Adam), and Ocelot jumps out of the plane, allowing the Americans to depart, but not before telling Snake that he is sure they will meet again some day.
Snake and EVA escape to Alaska, where they share a night of tumultuous passion. But the next morning, Snake finds that EVA has left while he was sleeping, taking the data on the Philosophers' Legacy with her. She leaves only a tape recording of her confession. She is actually a triple agent working for China, with orders to obtain the Legacy for them as well as the data on the Shagohad project (the latter of which will jumpstart China's own nuclear weapons program). The Boss also told her (EVA) the truth about her mission: she was a Fake Defector, ordered to join Volgin in pursuit of the Legacy. After Volgin's nuke became a Spanner in the Works, the CIA chose the path of plausible deniability and declared her a "real" defector; her new orders from Langley were to sacrifice her own life at the hands of Snake to prove America's innocence. Thus her life, just like that of The Sorrow, was thrown away for the convenience of the nation she served. She ultimately went to her death knowing that, despite her Undying Loyalty, she would be remembered only as a Scapegoat, Rewarded as a Traitor Deserves. EVA adds that despite having orders to kill anyone who knew about her status as a triple agent — and that she could have done so while Snake was sleeping — she have chosen to spare his life, insisting (perhaps a bit too strongly) that her decision wasn't based in her having fallen in love with him, but because she had given the Boss her word that she would protect him.
For his valor, Snake is awarded the Distinguished Service Cross by President Lyndon Johnson; and the CIA bestow on him the codename "Big Boss" in recognition of his triumph over the (now, clearly, lesser) Boss. Zero, along with the intel team, also up to congratulate him, but Snake, knowing the truth, disdains their praise, and is unable to look anyone in the eye, and quietly leaves the ceremony, as the government bureaucrats speak amongst themselves about how they could use more men with Snake's skill, wanting him to train and head up a new unit. After ducking out, Snake visits Arlington National Cemetery and salute the grave of the franchise's Big Good: a headstone marked only with "In memory of a Patriot, who saved the world." Trying yet failing to hold back tears, he is now irrevocably broken: he realizes that soldiers are cast aside as mere pawns and treated like dirt by their governments when they are no longer needed. His Start of Darkness as the Big Bad of the franchise's first two games has begun.
In the traditional end-of-game phone call, Ocelot confirms to the Director of the CIA that no one suspected that he, ADAM, was a triple agent the entire time, and that the Philosophers' Legacy was in fact in the hands of the CIA, as EVA actually stole a fake copy of it from Snake. However, the disc containing information on the Legacy only had details on half of the total amount of monies...
