The anti-Patriot faction was the unofficial organization of three renegade founders of the Patriots that sought to kill the power hungry members of the organization and end it once and for all. The three renegade members consisted of Big Boss, EVA and Revolver Ocelot.
In 1970s, when Big Boss was growing tired of being used as a pawn for Zero's plan to gain power and influence over the United States, Zero feared that he would leave the Patriots, so he enlisted Dr. Clark to create two clones with EVA serving as the surrogate mother. The project was called Les Enfants Terribles. Ironically, Big Boss left the Patriots when he found out about the project. While EVA and Ocelot stayed with the organization, they began to drift away.
In 1999, after Solid Snake "killed" Gray Fox and Big Boss the Patriots recovered the two, who were seriously wounded, but alive. They had Big Boss placed in a nanomachine-induced coma, while Fox was given to Dr. Clark. who experimented on him and later transformed him into a Cyborg Ninja. After Fox's transformation, EVA and Ocelot finally saw how twisted the Patriots had became. They decided to form a long term plan to destroy the Patriots, one that would not be complete for another 15 years. During this time, Ocelot used his position in the organization to keep tabs on their activities.
In the early 2000s, EVA and Ocelot enlisted Naomi Hunter into their organization to help them kill Dr. Clark, as she was Dr. Clark's assistant and Fox's adopted sister. Under EVA and Ocelot's instructions, she freed Fox, who killed Dr. Clark partially out of revenge but mainly for EVA and Ocelot. After Dr. Clark's death, Naomi covered it up as a lab explosion and helped Fox go into hiding.
During the Shadow Moses Incident in 2005, Ocelot was ordered by President George Sears to gain the Metal Gear REX data without Liquid Snake knowing his true intentions. When Ocelot was torturing Donald Anderson, he intentionally killed him because Anderson knew who he really was and used an opportunity to kill another member of the Patriots.
With Anderson and Clark dead, Zero was the only major member left. Ocelot decided to use nanomachines and hypnosis to make himself think he was Liquid to fool the Patriots, who by that time was controlled by the Patriots' AIs, while Philanthropy destroyed them, making EVA think that Ocelot was lost.
Between 2009 and 2014, EVA now going by the codename Big Mama, founded the Paradise Lost Army and with help from Raiden, recovered Big Boss comatose body and used the brain dead Solidus Snake as a decoy. It was also around this time the war economy was created.
In 2014, Ocelot, who was now known as Liquid Ocelot, came up with an elaborate plan to distract the Patriots into focusing on him and his insurrection, while Philanthropy inevitably destroyed them. The Patriots had Drebin 893 inject Snake with a newer version of FOXDIE to kill the renegade members of the Patriots and had Rat Patrol Team 01 help Philanthropy take down Liquid.
After Liquid gained controlled of SOP through GW, EVA's death at the hands of the Patriots hands via FOXDIE, and Liquid's control of REX's rail gun to destroy JD and gain control of the Patriot's AIs through GW, Snake managed to upload a virus made by Naomi and Sunny called FOXALIVE that, not only stopped Liquid, but also destroyed all of the Patriots' AIs, while keeping necessary elements like water, transportation, and electricity intact for civilization.
Liquid revealed to Snake that this was his plan all along. After a final fight with Snake, Ocelot regained his original personality. Ocelot died shortly after coming into contact with the newer version of FOXDIE, and Snake's final mission was finally over.
One month after the attack on Outer Haven, Snake attempted to commit suicide to stop the old strain of FOXDIE from mutating and infecting those around him. Big Boss then appeared behind Snake after waking from his fifteen year long coma. He explained the long history of the Patriots to Snake, until he killed Zero himself.
A few minutes later, Big Boss told Snake that it was the new strain of FOXDIE that killed EVA and Ocelot. Just then, Big Boss started to feel the effects of the new FOXDIE. He told Snake that he would not have to commit suicide to stop the old strain as the new strain had cancelled it. A few moments later, Big Boss died. With Big Boss' death, the Patriots were no more.