The Philosophers were an underground organization bent on global control through current events, controlling the global economy, and starting real war between superpowers. In the events of Metal Gear Solid 3: Snake Eater, the Philosophers' Legacy is in the hands of a madman named Colonel Volgin who wants to use the Legacy in creating World War III between the United States and the Soviet Union but ultimately fails by the hands of Naked Snake. In turn, Ocelot acquires half of the Legacy and later retrieves documents that could possibly reboot the Philosophers. In the events of Metal Gear Solid 4: Guns of the Patriots, it appears that Liquid Ocelot has already rebooted the Philosophers.
United States of America + Russian Empire + China (est. 1900?) | | | The Philosophers | + ---- The Boss (a.k.a. The Joy) | Internal conflict | All original members died (1930s) | | |------The Philosophers' Legacy | Volgin's father captures the Legacy ------| | | Volgin inherits the money | | GRU + Cobra Unit + Brezhnev | |---- Shagohod | Virtuous Mission + Operation Snake Eater | | EVA has the fake Legacy ---|--- Ocelot has half of the Legacy | The Pentagon ----+---- The CIA | % --- San Hieronymo Incident | |--- Cunningham fails | Ocelot retrieves the other half of the Legacy from the CIA Director