In case you're wondering, the AIs are just AIs
that thought a bit too highly of themselves, and in the end, the Patriots weren't even controlling them anymore. The men dead for over a hundred years are actually from an earlier
Ancient Conspiracy known as the Philosophers; the Patriots took over the American branch of the Philosophers and used the identities of its founders as a cover. All the original members died off by the 1930s, and the last people with any connections to them were killed by the end of
Snake Eater - those two being
Colonel Volgin and
The Boss, whose fathers were both members of the Philosophers. The actual Patriots turn out to be
Big Boss and his partners from
Snake Eater, but they had a falling out over the final wishes of The Boss which caused Big Boss to turn against the group alongside EVA (who turns out to be the surrogate mother of Solid Snake and Liquid Snake). In fact, two of the original Patriots were killed in
Metal Gear Solid, and they were none other than the unseen Dr. Clark (who was
Para-Medic from
3, and was killed by Grey Fox before the Shadow Moses Incident) and the DARPA Chief (who was Sigint from
3, and was killed during the Shadow Moses Incident by Ocelot and impersonated by Decoy Octopus because Sigint was aware of Ocelot's true identity). By
Metal Gear Solid 4 the last one (Zero) is little more than a vegetable, later revealed in
The Phantom Pain to have been infected with a precursor to FOXDIE by a disgruntled former operative known as Skull Face; the AIs were running the group by this point, and the idea behind them came from the CIA Director who orchestrated the events depicted in
Snake Eater and later nearly caused a nuclear holocaust during the events of
Peace Walker. Ocelot turns out to be one of the original Patriots and although he pretended to be loyal to them,
he actually sided with Big Boss - though he cooperated with the Patriots in order to protect a then-comatose Big Boss from Skull Face from 1975 to 1984. Ocelot's possession by Liquid was part of a larger plan to fool the AIs and last member of the Patriots, and
at some point Ocelot began faking he was possessed. (It's also suggested Ocelot's original possession was tied to his father, The Sorrow, being a spirit medium.) Oh, Rosemary is real, Vamp had a natural
Healing Factor enhanced by nanomachines, and Fortune... Actually, we don't learn what happened with Fortune, but
Psychic Powers do exist in this universe. Doesn't it all make sense now?
