Part 1 – The Philosophers’ Legacy

Metal Gear Solid 3 - Snake Eater                                                                          

1900 - The Philosophers are founded, a secret international governing organization originating from a treaty created by the Wisemen's Committee, a group of powerful figures from America, post-revolutionary Russia, and China.

1922 - A girl, later known as "The Boss" (as well as "The Joy"), is born to one of the members of the Philosophers.

1930 - The last original member of the Philosophers dies. Afterwards, the organization begins to go out of control and the Wisemen's Committee degenerates into a mere shell of its former self.

1935 - John (Jack/Naked Snake/Big Boss) is born.
1936 - EVA (Tatyana/Tanya/Big Mama) is born in Meridian, Idaho, USA.  At some point during her childhood, she is taken from her family by the Philosophers and placed in a joint U.S.-Soviet-Chinese facility to be trained as a Philosopher spy.
Dr. Clark (Para-Medic/Quack) is born in Boston, Massachusetts, USA.
1939 - Donald Anderson (Sigint/DARPA Chief) is born in Nashville, Tennessee, USA.

WW II / The Boss and the COBRA Unit:
1940 - The Boss, now a great warrior and leader, assists the SAS in organizing missions.

1942 - August: The Manhattan Project begins. Dr. Emmerich is assigned to work on the project.

In Stalingrad, the Boss forms the Cobra Unit, an elite special forces unit made up of the Sorrow, the Fury, the Pain, the End, and herself, the Joy.

1944 - 6 June (D-Day): The Allied Forces dispatch the Boss' Cobra unit into Normandy. The Cobra unit partakes in a mission to take down V2 missile installations.

The Boss gives birth to a baby boy, Adamska - the Sorrow is the father. The Boss gets a snake-shaped scar from the delivery.  The baby, later codenamed Ocelot, is taken and raised by the Soviet Philosophers (the Sorrow is a Soviet).

1945 - An atomic bomb is dropped on Hiroshima. Huey Emmerich is born to Dr. Emmerich.

Birth of the Philosopher’s Legacy:  During WWII, a secret pact is concluded between the Philosophers that deals with the construction of world order after the Axis Powers are defeated. The Philosophers of America, China, and the Soviet Union pool their assets in order to secure victory in the War and agree to distribute them amongst themselves after the end of the War.

World War II ends.  Volgin's father, who was in charge of laundering the Philosophers' funds, monopolizes (hides) their assets during the postwar chaos. The Philosophers' "legacy" is dispersed and laundered through banks in countries across the world, including Switzerland, Austria, and Hong Kong. It would later fall into the hands of his son, Colonel Volgin.

Post WW II:
1947 - The Boss disbands the Cobra unit after a 5 year career.  The Boss becomes an adviser/instructor.

1950 - Jack (later Big Boss)  participates in the Korean war.  He also becomes a student of the Boss who teaches him combat, demolition and intel gathering techniques.  They develop CQC (Close Quarters Combat) together.

1957 - September 29th: The Kyshtym Nuclear Disaster in the Ural Mountains: A girl named Elisa is caught in the nuclear fallout and is taken to a lab in East Germany, in which she is subjected to ESP experiments. There, she develops her alternate personality, Ursula.

1959 - June 12th:  The Boss leaves Jack/Big Boss to participate in a secret mission to spy on the Soviet space program and sabotage it.  She gets no help from the CIA (who are afraid of her) and so she uses her anti-Communist Russian Philosopher contacts to plant a sleeper agent.

Jack/Big Boss befriends a fellow soldier/agent named Python.

1960 – Two NSA code-breakers (actually US Philosopher spies), ADAM/Ocelot and EVA defect to the Soviets.  Their real mission is to locate the Philosophers' Legacy for the US Philosophers.  However Tatyana later substitutes herself for the US EVA and is actually working for the Chinese Philosophers, since they want the Legacy for themselves.   Neither know the other’s true identities.

1961 - A scientist named Sokolov designs the multi-engine cluster for the Vostok Rocket Program. Later, he begins designing the Shagohod, a nuclear-equipped tank.

Jack and Python are dispatched into Vietnam by the CIA.  Python is severely wounded.  Later he is given a special “cold suit” and made into an assassin.  His purpose is to kill Big Boss if Big Boss ever rebelled against the CIA.

The Boss’ Soviet sleeper agent turns against the US and the CIA convinces JFK that it is the Boss’ fault.  As punishment, the Boss is sent into space alone and exposed to near-fatal cosmic rays in an effort to beat the Soviets into space.  The mission fails to beat them by only a few minutes, but it is still considered a failure and covered up.

1962 - CIA operative "Major Zero" helps Sokolov and his family defect from the Soviet Union to the West.  Unfortunately because of the Cuban Missile Crisis the US government surrenders Sokolov back to the Soviet Union to avoid a nuclear war (apparently the Soviets would rather have the Shagohod, than have a Soviet missile base in Cuba).

On a covert mission in Tselinoyarsk, the Boss finds out that the Sorrow, her ex-Cobra member and former lover, was the Soviet agent who had turned the Boss’ Soviet sleeper agent against her, not knowing it was the Boss he was working against.  The Soviet Philosophers ordered that one had to kill the other, otherwise Adam/Ocelot, their son, would be terminated.  She is forced to kill the Sorrow.
Shortly thereafter, she and Major Zero form the CIA's FOX unit.

1964 - The Boss, using the Philosopher spy network, discovers that Sokolov is nearing completion of the Shagohod.

Tatyana-EVA manages to infiltrate Tselinoyarsk and convinces Sokolov that she is working for Khrushchev’s KGB to obtain data on the Shagohod.  She actually plans to get close to Volgin and the Legacy (as a double-agent for the US Philosophers and a triple-agent for the Chinese Philosophers), expecting Volgin will capture Sokolov and the Shagohod.

The Boss is also ordered by the US Philosophers to defect to the Soviet Union to try and steal the Philosopher’s Legacy from Volgin.   The CIA planned for her to be killed in this mission, since they were still afraid of her charisma and influence.  Later Volgin (under orders from CIA Director Coldman) will fire a nuke in Russia – for which the Boss will become the scapegoat and sacrificial lamb.

In any case, at this juncture Volgin and the Legacy were being targeted by four people: EVE (Chinese Philosophers), ADAM (US Philosophers), the Boss (US) and Big Boss (US, but actually as a pawn of Major Zero).

Virtuous Mission
August 24th: FOX Operation.  Big Boss (here codenamed Naked Snake) infiltrates Tselinoyarsk (with help from support team Major Zero, SIGINT and Para-Medic). He is ordered to retrieve Sokolov and take him back to the West. Big Boss and Ocelot (undercover as a Spetsnaz commander) meet for the first time, though Big Boss doesn't know that Ocelot is actually a US Philosopher spy. Sokolov divulges the existence of the Shagohod, a nuclear-equipped super-tank, to Big Boss. The Boss and a reformed Cobra unit (sans the Sorrow of course) arrive with two Davy Crockett nuclear missiles and defect to Volgin and the Soviet Union, kidnapping Sokolov (and EVA) and severely injuring Big Boss. Colonel Volgin fires a Davy Crockett nuke into the OKB-754 research facility (as ordered by CIA's Coldman). Later, the CIA claims to the Soviets that the Boss fired the nuke and acted alone.  They promise to assassinate her themselves.  Big Boss is extracted and placed in an Intensive Care Unit. The Virtuous Mission ends in failure.

Operation Snake Eater
August 30th: FOX Operation. Big Boss/Naked Snake infiltrates Tselinoyarsk once again, this time under orders from the CIA to assassinate the Boss for her apparent defection and launch of the nuke in Russia. He meets up with EVA who infiltrated Volgin's ranks (during the Virtuous Mission) and pretends to Big Boss that she is the original NSA Codebreaker/US-Philosopher EVA. 
Granin, a rival of Sokolov's, shows Big Boss his plans for a walking tank – a “Metal Gear”.  Sokolov's Shagohod project canned Granin's Metal Gear project.

September 2nd: Operation Snake Eater is declared a success. The Shagohod is destroyed; the members of the Cobra Unit are dead. Colonel Volgin is killed by a bolt of lightning.  The Boss successfully obtains the Philosophers Legacy and gives it to Big Boss, just before she dies at Big Boss’ hand.   
While in Alaska, EVA steals the Legacy microfilm from Big Boss and takes it back to China. It is later found to be a fake. The real Legacy (or at least half of it) is given to the CIA by Major Zero.  The other half of the Legacy is being secretly held by Major Zero, since Zero plans to create his own shadow group, later to be known as the Patriots. Ocelot obtains Granin’s Metal Gear plans and sends it to the CIA. 

(Ocelots 1st loyalty seems to be to the GRU/Volgin, then the NSA, and then the CIA/US Philosophers, making him a triple-agent.  If one counts Zero as his final boss, then he could be considered a quadruple-agent.  EVA’s loyalty is to Volgin/GRU, then KGB, then the NSA, then the CIA/US Philosophers and finally to the Chinese Philosophers.)

Naked Snake earns the title "Big Boss", but leaves FOX shortly thereafter.

Post Snake Eater:
1965 - SIGINT joins ARPA and takes part in the development of ARPAnet.

1966 - Big Boss encounters Frank Jaeger, a child soldier, during the Mozambican War of Independence. After rescuing him, he places him into a care facility, from where he is later taken by the Philosophers for their Perfect Soldier Project (and turned into Null).

A FOX operative (GENE) rescues Elisa/Ursula from the East German ESP lab she'd been sent to since 1957.

1968 - EVA disappears in Hanoi.

1970 - Para-Medic establishes the nation's first paramedic system in Seattle, Washington.

Metal Gear Solid Portable Ops                                                                              

San Hieronymo Takeover and the first Metal Gear:

The Successor Project (involving genetic alteration to make a perfect soldier) ends with GENE as its result.  GENE becomes leader of FOX instead of Zero.

The CIA develops the first Metal Gear, a walking nuclear launch pad, from Granin's plans.

The CIA's FOX unit, headed by GENE, pretends to start a non-sanctioned revolt and takes over the Soviet IRBM facility on the San Hieronymo Peninsula, as well as hijacking Metal Gear during transport.  GENE is actually acting under covert orders of the CIA.  They want to give Metal Gear to the Soviets so that the Cold War could be sustained (the Soviets were actually perceived as lagging behind the US).

However, the Dept of Defense (DoD) was unhappy about the CIA’s influence in the Cold War and wanted GENE to launch Metal Gear at Russia in order to discredit the CIA before the Soviets (nuclear war would be avoided because it would look like the attack came from a Russian base).  They turned ex-FOX agent Cunningham to their side.  However, unbeknownst to the DoD or the CIA, what GENE really wanted to do is launch a nuke at the DoD's Pentagon HQ and the CIA's Langley HQ – this would break the power of the Philosophers and allow GENE to create his own “shadow patriots” and an “Army’s Heaven”.  This also happened to agree with Zero’s plan to flush out the CIA-half of the Legacy, which is why Zero had Ocelot help GENE with the launch trajectory.

Zero and Big Boss are accused of treason, since they were judged to be the only people powerful enough and charismatic enough to instigate such a revolt (ironically, in Zero’s case, this is actually TRUE, tho later he is mistakenly exonerated).

November 2nd: Big Boss is captured by members of the San Hieronymo CIA/FOX unit to try to find out the whereabouts of the missing half of the Legacy.  Big Boss meets Roy Campbell for the first time. Together, the pair set out to take down the renegade FOX unit.  Big Boss battles and then recruits old Vietnam comrade Python from FOX. Big Boss also encounters Null, who it turns out is a modified Frank Jaeger, experimented on by the Philosophers and FOX, battles him and recruits him. Big Boss and Roy Campbell meet Elisa, and they learn about Metal Gear.  Big Boss successfully destroys Metal Gear RAXA (a prototype Metal Gear) with the help of Sokolov (who had previously been rescued from the Soviets by GENE). CIA/FOX agent Cunningham reveals that he is actually serving the DoD to try and discredit the CIA, and is killed by Big Boss.  GENE kills Elisa. Big Boss defeats GENE, who then gives him funds he had amassed for creating an "Army's Heaven." Big Boss later manages to destroy the ICBMG (Metal Gear) before it activates after launching. 

Zero, behind the scenes, gave Ocelot the nuke trajectory data for targeting the CIA and Pentagon so that he could pass it on to GENE.  Later he gives the CIA director the news that a nuke is headed for Langley.  He also anonymously has Ocelot waiting for the Director in the basement.  The Director is caught trying to escape by Ocelot, who obtains the CIA-half of the Philosophers' Legacy from him and kills him. Ocelot finds out that Zero was the one who gave him the tip and promises to give this half of the Legacy to Zero.  With the complete Philosophers Legacy, Zero plans to create his own shadow government and use data from Null/Frank Jaeger/The Perfect Soldier to start a Genome Soldier project.  Additionally, since the CIA Director is now dead, Zero can gather more influence in the CIA itself.  He invites Ocelot to join him.  Ocelot insists that Big Boss be a part of the new "Patriots" as well.
At this point the Philosophers on all 3 sides are effectively crippled: the Russians lost the Legacy in Snake-Eater, the Chinese got a fake one, and now the CIA has lost their half. Only Zero has the complete Legacy data, since he kept half for himself after Snake Eater.  The stage is set for...

PART 2 - The Patriots

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