The Patriots are a secret organization in the Metal Gear universe. An offshoot of the Philosophers, the Patriots initially organized after the events of Metal Gear Solid 3: Snake Eater under Major Zero. The other founding members included Big Boss, EVA, Revolver Ocelot, Sigint and Para-Medic. Zero used his power and influence to turn Big Boss into a popular, almost messianic being with which the Patriots could gain more popular support and influence, and thus more control over the world.
However, Big Boss grew tired of his role as organization figurehead, believing that Zero had misinterpreted The Boss's vision. He split from the group, eventually founding a mercenary company and working alongside Kazuhira Miller. In the 1980s, he founded Outer Heaven, his interpretation of the Boss's final wish. After Big Boss left, EVA and Ocelot began to drift away from the group as well, although Ocelot remained within their ranks as a spy.
Over time, Zero became more and more power hungry; as he grew older, he became more reluctant to pass power down to the next generation, believing they would not be able to fulfill his vision. For this reason, he created the four AIs: TJ, TR, AL, and GW, named for Thomas Jefferson, Teddy Roosevelt, Abraham Lincoln, and George Washington, the four presidents on Mount Rushmore. A fifth, JD (John Doe), was designed as the head. The AI network would assume control of The Patriots from Zero once he could no longer fulfill his duties as leader of the organization.
Between the events of Metal Gear 2: Solid Snake and Metal Gear Solid, Para-Medic became the first founding member to die. Under the name of Dr. Clark, she had revived Gray Fox using cybernetic technology, but was killed by him as he mounted an escape with Naomi Hunter's help. Then, just prior to the Shadow Moses incident, Sigint, real name Donald Anderson and the head of DARPA, was captured by FOXHOUND. Revolver Ocelot, still an anti-Patriot spy, killed Anderson to remove him from power and made his death look like an accident as a result of a too-strenuous torture interrogation.
In 2007, during the Big Shell Incident, it was discovered that the construction of the Big Shell and all the events surrounding it had been orchestrated by The Patriots so that they could create Arsenal Gear under the cover of secrecy. Arsenal was to be used as their new means to completely control global information flow. GW was was housed inside Arsenal, and the whole point of the S3 Plan (Selection for Societal Sanity) was to collect data so that The Patriots could improve their AIs. They used Raiden as an unaware test subject, but in the end GW and Arsenal Gear were both destroyed.
By the events of Metal Gear Solid 4: Guns of the Patriots in 2014, The Patriots were completely controlled by the remaining AIs. They began to propagate and mutate, leading to the creation of a war economy. Out of this sprang a world which had no morals, no ideologies, and no loyalty, the aspect which The Boss treasured most. The Patriot AIs managed to manipulate Meryl's Rat Patrol, and their agent Drebin to help Snake in his mission to kill Liquid Ocelot. The AIs did not foresee that Snake would destroy them in the process as well.
They were destroyed by FOXALIVE, a worm cluster computer virus named in reference to FOXDIE. The virus was engineered by Naomi Hunter and Sunny Gurlukovich, and once uploaded, it infected the core components of The Patriot AIs' systems. Sunny, however, managed to block infection from regions of the AIs that controlled vital infrastructure such as water, food, and transportation so that the negative impact on society would be minimized.
With the AI network destroyed, the Patriots finally came to an end when Zero, now over a century old and in a senile, vegetative state, had his oxygen supply cut off by Big Boss. Big Boss, the last surviving founder, then succumbed to the new version of FOXDIE the Patriot AIs made Snake unwittingly carry throughout the mission, and which had previously killed the other surviving founders, Ocelot and EVA.