*BIG SPOILERS! READ AT YOUR OWN RISK!*
In this article, we will also talk about real events that happened in real life and real organisations of real countries and will be shown in blue.
After the end of World War II, the world was split into two – East and West. This marked the beginning of the era called the Cold War. During the Cold War, the United States and the Soviet Union embarked on a frantic race for the conquest of space and new military technologies.
Nikolaï Stephanovitch Sokolov, a Russian scientist, is working on a top secret weapon project for the Soviet Union: the Shagohod. The United States, scared that the Soviet Union will take the lead, sets up an infiltration mission to recover the scientist.
24th August 1964: Virtuous Mission
This is the first combat mission of the FOX Unit which is composed of the leader Major Zero, Para-Medic, John and The Boss. John, codenamed Naked Snake for this mission, is helped by all of them through radio and receives orders from Major Zero to infiltrate Tselinoyarsk and rescue Sokolov.
During this mission, he will meet Major Ocelot and his unit, a Spetsnaz elite group under direct control of the GRU, itself controlled by Colonel Volgin. Ocelot tries but fails to take Sokolov back from Snake just after he finds him.
Just before accomplishing his mission, Snake meets his mentor again, The Boss, who he hasn't seen for several years. She violently hurts him and leaves him for dead, telling him that she has gone over to the other side and reformed the Cobra Unit for the occasion. She then re-captures Sokolov and defects to the Soviet Union with Volgin, Ocelot, Tatyana (a potential KGB agent posing as Sokolov's lover who has been captured) and the Shagohod.
One of the two Davy Crocketts, an American nuclear-headed missile, brought by The Boss to Volgin, is launched on Sokolov's design bureau, OKB-754. The Virtuous Mission is a failure.
Davy Crockett's Explosion
Nikita Sergeyevich Khrushchev, leader of the Soviet Union, uses the “Red Telephone” to call US President Lyndon Baines Johnson who has to explain why an American missile exploded on Russian soil. To avoid retaliation, a third World War and to be wiped of any suspicion, the US government has no choice but to listen to the Soviet Union's ultimatum which is to kill Volgin, who is made responsible for the disaster, and kill The Boss, who betrayed her country. The US government is also made to retrieve the second Davy Crockett and rescue Sokolov. Naked Snake will be the man for this mission!
Sigint joins the FOX Unit for the mission which is their last chance to be wiped clean of the previous failure. If they do not succeed they will be disbanded. ADAM and EVA, two former-NSA agents, are sent to Tselinoyarsk by Nikita Sergeyevich Khrushchev as KGB agents and, there, Snake will have to ask ADAM the question “Who are the Patriots?” for which his correct answer will have to be “La Li Lu Le Lo”.
Operation Snake Eater
30th August 1964: Operation Snake Eater
During this mission, Naked Snake is helped through radio by Major Zero, Para-Medic and now Sigint. A few minutes after arriving on site, he meets The Boss who tells him to go back home after having defeated him with some CQC (Close Quarters Combat). She then leaves. Later on, he meets the KGB agent EVA who helps him to defend himself against Ocelot and his unit and tells him where is Sokolov. On his way, Snake has a duel against Ocelot, comes out victorious and then meets and kills the first member of the Cobra Unit, The Pain.
Instead of finding Sokolov, Snake meets Aleksandr Leonovitch Granin, another scientist, who is responsible for developing the first concept of a bipedal tank: Metal Gear. He tells Snake that he and his concept have been disregarded by Volgin in favour of the Shagohod, Sokolov's own concept for a tank. Granin also tells Snake that Sokolov is now detained in the military base Groznyj Grad. On his way, Snake meets two other members of the Cobra Unit, The Fear and The End, that he kills after fierce combat.
Snake arrives close to the military base where he meets EVA who tells him that she is a double agent pretending to be Tatyana, Sokolov's lover. Just before reaching the inside of the base, Snake witnesses Granin's death during Volgin's 'interrogation' and fights against The Fury, killing him.
After infiltrating the base, Snake surprises Sokolov giving Shagohod's experimental data to EVA. After a conversation with Sokolov about the Shagohod and Tatyana, who is actually pretending to be Volgin's lover after all, Snake is spotted and captured by Volgin.
Snake being tortured by Volgin with The Boss, EVA and Ocelot present
Naked Snake now has to go through a torture session at the hands of Volgin who wants to know if he is here for the Philosophers' Legacy, a large amount of money gathered by the wealthiest men of the United States, Soviet Union and China in 1918. He reveals at the same time where the microfilm is located, on which are all the transactions of the Legacy scattered across banks around the world. EVA (undercover), Ocelot and The Boss are all there. Snake loses his right eye during the interrogation while saving EVA's life. Snake is then thrown in jail.
Snake manages to escape, jumps from a waterfall and, because he is close to death, meets The Sorrow's “ghost”, once a member of the Cobra Unit, in a kind of waking dream in which he encounters the souls of the ones he previously killed. He extricates himself from the nightmare and heads to a cave where he meets EVA who gives him some C-3 which will prove to be useful later.
Snake then goes back to Groznyj Grad, places the C-3 in the warehouse where the Shagohod is but, just after having set the timer, he is spotted by Volgin who is with Ocelot, The Boss and EVA who has been caught looking for the microfilm. Now knowing that EVA is a spy, Volgin asks The Boss to hide the microfilm somewhere else, which she agrees to straight away, taking EVA with her to dispose of her. Snake defeats Volgin, gets out of the warehouse and finds EVA who is waiting for him in her side-car motorcycle. She tells him that The Boss let her run away and that she's waiting for him close to the lake.
They escape together on the motorcycle but are soon followed by Volgin who, still alive, has taken the Shagohod before the explosion of the C-3. Snake destroys the Shagohod and defeats Volgin who is then hit by a bolt of lightning.
Snake and EVA finally arrive at the lake where The Boss is waiting. Before the final battle, The Boss destroys Groznyj Grad and Granin's Research Facility with the last Davy Crockett and explains to Snake her vision of the world as she would like it to be. She talks about the Philosophers and their first and true objective: maintain peace on earth. She also talks about her suffering and sacrifices as a soldier and about her pain as a mother whose child was taken away from her at birth – several elements show that this child is none other than Ocelot. She finally talks about when she had the vision of a unified world as she travelled into space for the Mercury Program. Her dearest wish is a world without any borders, which was the original purpose of the founders of the Philosophers.
Snake defeats The Boss after a long and bitter battle. Before dying, The Boss gives a microfilm to Snake and asks him to fulfil his purpose and to put an end to her misery.
Naked Snake kills The Boss
Snake uses The Boss' gun, a Patriot, and kills her. He then joins EVA who is waiting with a seaplane close to the lake and, after one last duel against Ocelot, they leave.
They spend the night together, but when Snake wakes up, EVA is gone. She left an audio-tape explaining everything: she is not the EVA who left the NSA for USSR in September 1960, but a spy in charge of retrieving the Philosophers' Legacy for the Chinese branch of the Philosophers. (The Boss knew all of this so she let EVA run away with a fake microfilm). She also explains everything about The Boss' real mission to Snake:
The Boss was actually sent by the CIA to retrieve and secure the Philosophers' Legacy. Her defection to the Soviet side was actually an order from the US to allow her to contact Volgin. The only unexpected event was the launch of the Davy Crockett on the laboratory infrastructure by Volgin. The Boss had to give her life and be seen, in everyone's eyes, as a traitor to her country. This giving the chance for the US government to save face. The truth is that she has been a true patriot, a real hero who sacrificed her life and honour but will go down in history as an official war criminal.
Naked Snake becomes Big Boss for having brought the Legacy back and having defeated his mentor, The Boss, but leaves the FOX Unit after gaining knowledge of all this masquerade.
A salute from a hero to another
As a final twist in the tale, Ocelot is found to be a triple agent. As he said to Snake, he was a member of the GRU, but he was also spying on Volgin for the KGB as ADAM, the NSA's agent who had allegedly defected the US, and given the mission to overthrow the Soviet First Secretary Nikita Sergeyevich Khrushchev. Nevertheless, his "real" employer is the Director of the CIA, a Philosophers' organisation, who asked him to recover the Philosophers' Legacy for the US. For that, he has been helped by The Boss, and Naked Snake of course. Ocelot tells the CIA that only half of the Legacy was on the microfilm and that the other half might still be in the hands of the KGB. Somehow after these events, he will manage to recover the other half, and keep it for himself. He also gives them the blueprint of Granin's Metal Gear concept.
A tear for The Boss from Big Boss