*cracks knuckles*
In WWII The USA, China and Russia set up The Philosophers and together they accumulates a fund of $100 Billion dollars in case they ever needed it, the Philosopher's Legacy. When the war was over they squabbled over it and divided it up and hid it all over the place.
(MGS3: Snake Eater)
In 1964 the US sends in Naked Snake to Russia to retrieve a scientist, Sokolov whom they earlier had to give back to the USSR in exchange for the Soviets pulling out of Russia. But this was all a ruse so that their greatest solider, The Boss, could defect to the Soviets. Naked Snake is beaten and nearly drowned but is rescued and sent back in a week later.
He sneaks his shit past the guards and pwns the Boss's comrades, The Cobra Unit. He is told to meet with one of two American fake defectors to the USSR, ADAM (no, not the genetic stuff from Bioshock) but instead encounters EVA, the other one. After this encounter he meets a young Major Ocelot who he inadvertently inspires to take up using revolvers. He encounters a Russian designer called Granin who appears to have plans for something called a "metal gear" but his idea was laughed out for being a walking tank. Later on he learns that the big bad guy, Volgin is the son of a Philospher and as such is privvy to the Soviet share of the money. Volgin kills Sokolov and tortures Snake. Snake escapes and with EVA's help he defeats Volgin and destroys the Shagohod, the massive ICBM launching tank the Soviets were desperately trying to get Sokolov to complete. He ends his mission by retrieving the info on the Philosopher's Legacy and fighting and defeating his mentor and mother figure, The Boss (yes, The Boss is a woman).
However, in his debriefing, EVA steals the Legacy and reveals she is a Chinese Philosophers agent taken at birth from American parents. She also reveals the whole thing was a ruse by the US to get the Legacy and The Boss never did defect, she sacrificed her life and reputation for the sake of her country. Snake is disgusted by this, feeling that soldiers are no more than pawns and harbour no respect from their leaders. However, for succeeding in his mission he is awarded the title of Big Boss. After all this we learn that Ocelot was triple crossing the Soviets and was in fact working for the CIA and is ADAM.
(my summary of MGS: Portable Ops will be a bit hazy, I've not played it personally)
Snake (refusing to use the name Big Boss) is sent in to a South American peninsula to take on members of his former unit who have gone rogue. He pwns more people and saves the life of Frank Jaeger aka Null. Sokolov is revealed to actually still be alive and has designed an Intercontinental Ballistic Metal Gear, which drops off a mech called Metal Gear RAXA. Snake wins and saves the day and becomes more jaded. Ocelot is approached by a man who wished him to join his side and revive the American Philosophers, but rename them The Patriots. This man is none other than Major Zero, Snake's CO from MGS3.
(MGS: Peace Walker...not yet released)
(the following information is largely only revealed in MGS4, but I'll put in here for the sake of chronology)
Zero plans to bring about a New World Order based on a gross misinterpretation of The Boss's dream and needs a public face, Big Boss is reluctant because he does not want to go through with Zero's plans due to his own misinterpretation of said dream so Zero has him cloned and uses EVA as a surrogate. The resulting twins would be called Solid Snake and Liquid Snake. Big Boss leaves the Patriots. Fellow members Revolver Ocelot and Eva are on his side, but stay with Zero as indsiders for Big Boss. Sigint and Para-Medic remain loyal to Zero. Big Boss founds Outer Heaven as a place for soldiers to have purpose.
(Metal Gear)
Young FOXHOUND soldier Solid Snake is sent into Outer Heaven by Big Boss to disarm the terrorist group that has taken over. However, this is actually a manipulation by the Patriots in an attempt to use Snake to take out Big Boss (Snake doesn't know this until MGS4). Big Boss plays along to fake his own death and strike at The Patriots from the shadows. Snake defeats Big Boss, destroys Metal Gear TX-55 and comes home a hero.
(MG2: Solid Snake)
Solid Snake is sent into Zanzibarland to quell a takeover. He finds out Big Boss survived and is again trying to muscle around. Again, this is another Patriots manipulation. Snake has to kill his old comrade Grey Fox (Frank Jaeger). Big Boss is defeated and presumed dead. Metal Gear D is destroyed. Snake retires to Alaska.
I'm guessing it's around here that Zero decided to program his control-the world will into five AIs.
(Metal Gear Solid)
Snake is brought out of retirement to take on his former FOXHOUND comrades. He finds out they are lead by his brother who he didn't know of, Liquid. Ocelot infiltrates Liquid's operation in an attempt to sabotage the Patriots' plans, killing Sigint who is now the DARPA chief. Snake defeats FOXHOUND, confronts and defeats Liquid, destroys Metal Gear REX and saves REX's designer Otacon and his CO's niece (though actually his daughter) Meryl. He also finds out he was injected with a virus called FOXDIE which was used to kill off the people the Patriots wanted dead and would eventually kill him due to tampering on the part of Naomi Hunter, the mission doctor who was the adopted sister of Grey Fox out for revenge. Grey Fox is also revealed to have been brought back to life and used for gene therapy and cybernetics experiments by Para-Medic, whom he killed upon escaping as the Cyborg Ninja. The Patriots are not happy with Snake after this.
(MGS2: Sons of Liberty)
Snake and Otacon travel the world sabotaging and exposing Metal Gears. Snake sneaks into a tanker to prove that the Marines are developing an amphibious Metal Gear called RAY. This is a trap by the Patriots to smear their names however. Ocelot, still playing the role of The Patriot's agent, hijacks the RAY and sinks the tanker but not before being taken over by Liquid's psyche which is trapped in his arm, which is transplanted onto Ocelot after Ocelot lost his to the Ninja in the previous game. The Patriots then send a crude-filled tanker to the area and sink that too to stage a disaster to frame Snake for. They use the spill as an excuse to begin constructing the Big Shell, a guise for their ultimate weapon Arsenal Gear.
Raiden is sent to the completed Big Shell to defeat terrorists that have taken it over. The terrorists' leader turns out to be Solidus Snake, the third Big Boss clone created later on. Raiden slowly learns his mission was a construct by the Patriots in an attempt to shape a normal soldier into one on par with Solid Snake. The AI in charge of the assignment, GW, is stored on Arsenal Gear. It didn't count on Solid Snake showing up though, due to Snake and Otacon using Liquid to fake Snake's death. Snake's appearance throws their plan into a disarray and Snake, Otacon and the mercenary leader Olga Gurlukovich use Raiden to infiltrate Arsenal and upload a worm cluster to GW, causing to start acting erratically. Olga reveals she is being blackmailed at the expense of her daughter's life by the Patriots to keep Raiden alive, before being killed by Solidus. Liquid takes over Ocelot again and uses Ocelot to hunt down the Patriots, leaving in a stolen RAY. Arsenal crashes into New York and Raiden kills Solidus in a sword fight atop Federal Hall.
After the Big Shell incident Raiden becomes an absent alcoholic and leaves his pregnant girlfriend, Rose. Rose fakes a miscarriage and marriage to Snake's CO Roy Campbell in an attempt to draw attention away from them and thus protect Raiden from the Patriots. Raiden and EVA break into Area 51 to rescue Olga's daughter, but Raiden is caught and experimented upon, resulting in his head and spine being placed in a robotic body. Olga's daughter, Sunny, is left with Snake and Otacon. Ocelot replaces Liquid's arm with a prosthetic but mentally conditions Liquid's personality onto his own in order to make the Patriots think they are dealing with Liquid Snake which allows him to hide his true intention of bringing them down from the inside (he had the whole plan laid out before committing this, he's good that way). Under the Liquid Ocelot guise he used the funds he raised from selling Metal Gear REX specs on the black market to set up the world's four largest PMCs and control them under one dummy corporation, Outer Heaven. With these he fights in the Patriots new perpetual war they use to spurn economy and sneak in the Sons of the Patriots battlefield control system which will eventually allow them to control human will, something not even Zero wanted of the Patriots (Zero by this time was wheelchair bound and on life support, so couldn't stop them). Snake starts aging rapidly for unknown reasons.
(MGS4: Guns of the Patriots)
Snake is hired by Roy Campbell to kill Liquid. Snake follows him around the globe, learning most of what I've already told you along the way. He meets his mother, whom dies of New Foxdie (given to Snake by the Patriots via Drebin the arms dealer). Snake learns from Naomi that the Patriots created him to age rapidly around 40 so that he couldn't be taken by the enemy when past his prime and used to create their own super soldiers. Liquid uses what he believes to be Big Boss's DNA (but is actually Solidus', an identical copy unlike his brothers)as the key to gain access to the SOP system via the reconstructed GW. Once in control of SOP he heads after the Patriots' head AI, JD. Since SOP controls all in-commission military weapons he steals REX's pre-system railgun in attempt to use it to launch a nuke at the JD satellite. The Patriots had anticipated this and thus had counted on Snake stopping him. They did not count on Ocelot's plan however. Ocelot used Naomi to get in close to Snake and provide him the means to take out the Patriots altogether. With a little tweaking from Sunny to only remove the malevolent systems, Snake succeeds in uploading the program to GW which Otacon used as a foothold to destroy the Patriot's control once and for all. After the Patriots are wiped, Snake faces Liquid Ocelot whom he fights until Ocelot, having had the brainwashing beaten out of him, dies of New Foxdie.
In the epilogue we learn that Big Boss is still alive and was kept artificially alive without concious thought by The Patriots. He was reconstructed using bits of Liquid and Solidus when Ocelot got a hold of GW. He explains many things to Snake before turning off Zero's life support, killing him. He realises that even in death Zero still gets his wish of taking out Big Boss when he feels the effects of New Foxdie. Big Boss dies sitting on The Boss's grave with his last son by his side, ending the Patriots for good. Snake vows to spend the rest of his days living happily as a man.
*collapses back in chair*
