The Patriots were originally a cabal formed with the funds of the Philosophers between MGS3 and Peace Walker, headed by Major Zero, Eva, and Snake (who rapidly defected when he learned of the Les Enfants Terribles project being ran with his DNA). The Patriots originally existed with the goal of carrying on the will of the Boss, but misinterpreted her belief that humans should be allowed to exist and self-determinate in peace as it being necessary to take down the remaining power of the Philosophers and create a new order to preserve the world from the shadows. The human members of the Patriots gradually either died or turned against the organization, until by MGS1 only Major Zero (now Cypher), remained.
While Zero was elderly and limited, the AI research started by the Peace Walker program had paid out immensely, and the one thing the Patriots did have was an obscene amount of money. As such, Zero gradually replaced the functions of the human Patriots with several AIs, and they at least professed that they were the physical representation of the will of the people (or at least GW, the only AI who ever speaks to humans, does). By MGS2 they'd taken shadow power over all world governments and Major Zero had grown so old that he became vegetative. Without any human controller, the Patriot AIs begin to carry out their directives without hesitation, and gradually become the shapeless and formless power that is the Patriots. At this point they are also framing the Philosophers for their actions in order to throw off suspicion, hence the list of long dead "Patriot" members Snake and Otacon find in MGS2.
By MGS4 the Patriot AIs have integrated all the vital functions of the world into their network and settled on a program of "managed war" both to bleed off human aggression and to create a new economic cycle that to them is rational but to humanity means endless war, controlled and codified down to even individual weapons and the minds of the soldiers who wield them by the SOP system. Ocelot, whom this whole fucking time has
actually been working to destroy the Patriots because he's gay for Big Boss (no, really), intends to kill the Patriot AIs by nuking them with the railgun salvaged from Metal Gear Rex, as it is the only nuclear technology not integrated in the SOP system and thus the only device powerful enough to kill the Patriots that wouldn't refuse to fire on them. Unfortunately, because the Patriot AI's have worked to make themselves the nexus of all power, essentially all global resource management and networks are routed directly through the satellite the AIs are housed on. Were it to be destroyed the grip of the Patriots on humanity would be broken, but the world would also be plunged into a new dark age of chaos as the taps dried up and the crops rotted in their fields. Billions would die and the world would fall into anarchy.
Unfortunately for everybody, Revolver Ocelot is if nothing else a student of Big Boss and sees this arrangement as a paradise where all would be free to determine their own fate and soldiers will always have a place in society. Ultimately, Snake and Otacon stop the launch of the nuke and discover that the late Naomi Hunter created a virus that would "lobotomize" the Patriots, keeping their systems intact but destroying their sapience. It is uploaded by Snake, preserving the world while freeing it from the Patriots. Snake and Ocelot have their final battle, Ocelot dies but proves he is the single greatest Chaotic Evil character in history, Snake goes to kill himself on The Boss' grave so FOXDIE doesn't wipe out humanity but it turns out to be unnecessary, Big Boss is still alive and admits Snake is a better man then him, Big Boss and Zero both die, Snake and Otacon go off to raise Sunny and the hopes of shippers everywhere, Snake probably dies six months later from clonal degeneration.
The End.
RULES OF NATURE!