The Philosophers were a secret organization founded in the early 20th century, shortly after World War I. Little is known about those who founded the group other than that they were all highly influential people from three countries that were quickly growing in power at that point in history--the People's Republic of China, the Soviet Union, and the United States of America. At the head of the group were twelve key individuals referred to as the "Wisemen's Committee." Beneath them were an unknown number of "sleeper agents," trained in collecting information and using covert tactics to further the organization's agendas. According to EVA, The Philosophers had "charm schools" where children gathered from around the world were raised and trained specifically to be loyal agents.
The original goals of The Philosophers are somewhat hazy, but they clearly sought to influence politics on a global scale. To that end, they assembled a massive fund to finance their collective interests. Known as "The Philosophers' Legacy," this fund amounted to no less than one-hundred billion U.S. dollars, which was split into innumerable pieces hidden away in various banks and financial institutions throughout the world. (How the group managed to hoard such an immense amount of capital and where it all came from is unknown--though it likely involved some amazing acts of embezzlement.) This money was used to research and fund various "black" projects, such as the Cobra unit, nuclear weapons development, and rocket technology. Each branch of The Philosophers controlled a third of the Legacy, thus maintaining the balance of power between them.
However, as the 20th century progressed and the global balance of power began to shift, the internal balance of power within The Philosophers followed suit. All of the original members of the Wisemen's Committee were dead by the end of the 1930s, and their replacements were less interested in maintaining unity. During the chaos of World War II, a deep schism formed between the three branches of the Philosophers.
This split was triggered by one specific event: towards the end of WWII, The Philosophers' chief money-launderer--Volgin's father--used his knowledge of their collective finances to seize the entire Legacy for the Russian branch. He recorded the locations where the numerous pieces of the Legacy were hidden on microfilm, and passed the information on to Volgin upon his death several years later. Volgin used it to build the fortress of Groznyj Grad and fund the development of a number of new weapons.
Once the three branches of The Philosophers turned on one another, their original goal of world unity was completely lost. Each branch became concerned only with holding onto and increasing their own political power. The tool they used to accomplish this was, simply, war. According to The Boss: "The Philosophers of today have no sense of good or evil. Their influence extends to countries and organizations involved in every aspect of every war. They have become war itself. ...The sacrifices of war cause a shift in the times, which increases conflict and, in turn, triggers the next war. ...By consuming me, and you, The Philosophers intend to keep that cycle going forever."
Naturally, the American and Chinese branches of The Philosophers had no intention of allowing Volgin to do whatever he pleased with "their" money. The events of Metal Gear Solid 3 depict what transpired when the three divided branches clashed over possession of the Legacy: by sacrificing The Boss, the American branch was able to acquire half of the missing money (courtesy of their triple-agent, Ocelot). The Chinese branch got away with a fake copy of the Legacy and the Shagohod's test data, which they used to jump-start their country's nuclear and space-exploration programs. With the death of Volgin and the loss of half the Legacy, the Russian branch was greatly weakened--though this didn't stop one of its presumed members, Leonid Brezhnev, from ousting Krushchev and becoming General Secretary of the Soviet Union just a few months later (in October, 1964).
Little is currently known about what became of the Russian and Chinese Philosophers after the events of Operation: Snake Eater. We do know, however, that six years after Snake Eater, in December 1970, the American branch gained the rest of the Legacy and assumed a new name: The Patriots. The story of those events is told in Metal Gear Solid: Portable Ops.
Speculation:
The Boss was the daughter of one of the original members of The Philosophers Wisemen's Committee. To hear her tell it, the group's original goal was to "make the world whole"... which sounds like a nice way of saying they wanted to implement one-world government. Whatever flowery rhetoric they may have used to obscure their motives, The Philosophers clearly weren't shy about using some pretty nasty tactics to steer the world in the direction they wanted it to go--from the very beginning, they were abducting and indoctrinating children to serve as future agents. They even stole away the newborn son of The Boss and raised him from childhood to serve them. That child was named Adamska... later known as Ocelot.
There's also the matter of a certain enigma that would haunt America's collective consciousness for the latter half of the 20th century: the assassination of President John F. Kennedy. On the official series timeline included on the Metal Gear Saga Vol. 2 DVD, 1961 is specifically mentioned as the year Kennedy "falls out of favor with The Philosophers." 1961 was the year of the Bay of Pigs debacle, a botched invasion of Cuba backed by the CIA. Though the invasion was based on faulty intelligence and likely would have failed anyway, the CIA blamed Kennedy because he held back the air support that had been promised to the troops who landed in Cuba (http://en.wikipedia.org/wiki/Bay_of_Pigs_Invasion). In fact, The Boss specifically mentions this to Big Boss at the end of MGS3: "Our weak-kneed President held back their air support. Defenseless, the exiles were annihilated by the Cuban army. All I could do was watch in silence."
As a result of the Bay of Pigs operation, the CIA was publically humiliated, and its founder, Alan Dulles, resigned in disgrace. We know that the CIA at that time was deeply involved with the American branch of The Philosophers. At the end of MGS3, Ocelot calls the director of the CIA to report on his success in obtaining the Legacy. Also, in Portable Ops, Gene refers to the Pentagon and CIA headquarters as "The Philosophers' twin lairs." Factor in Kennedy's famous threat to "splinter the CIA into a thousand pieces and scatter it into the winds," and The Philosophers clearly had a motive to remove Kennedy from power to protect their own interests.
Two years later, in November 1963, Kennedy was assassinated during a visit to Dallas, Texas. Given the annoyance he had caused them already, it's more or less a given that The Philosophers had a hand his death. (If we didn't know for sure that Ocelot was in Russia at the time, I'd be willing to bet he was the legendary "second shooter on the grassy knoll.") Not only did this remove Kennedy as a political threat, it sent a strong message to future Presidents regarding the penalties of defying them.
Links for Further Reading:
Listed below are links to pages containing information on several real-life organizations that may have served as inspirations to Kojima in creating The Philosophers and The Patriots. All of these groups have been the focus of conspiracy theories in their own right. Some of those theories are pretty wacky, but I find it interesting to note the parallels between these groups and their fictional counterparts.
The Trilateral Commission:
http://en.wikipedia.org/wiki/Trilateral_commission
The Bilderberg Group:
http://en.wikipedia.org/wiki/Bilderberg_Group
The Illuminati:
http://en.wikipedia.org/wiki/Illuminati