Now that Zero was too ill to continue running Cipher, Ocelot revealed that Donald Anderson had taken over command of Cipher, as well as the AI he oversaw. The idea came to mind in 1974 when the Mammal Pod penetrated NORAD, but due to what happened during the Peace Walker Incident, the new AI had been given restrictions and its purpose was to filter data it collected before passing it on to people, guiding their decision making. They achieved this by recruiting Strangelove into DARPA. That Zero's last request was for Big Boss to be safe. Anderson's new project was called "the Patriots", which was going to be used to drive society to unify the world.
Prior to 2014, Big Boss's DNA and biometric data was used for the Patriots' ID recognition system, the use of which allowed access to their AI network. The Patriots also declassified documents relating to Big Boss's exploits during the 1960s, which contributed to a resurgence in his popularity, with soldiers beginning to adopt CQC techniques.
Data relating to the location of Big Boss's comatose body was stored in the Patriots' AI, GW. This data fell into the hands of Raiden supplying the information to the Paradise Lost Army led by EVA, now known as Big Mama. Using the body parts of Liquid and Solidus Snake, EVA had Big Boss's body rebuilt, eventually restoring him to his former appearance, though he remained in a comatose state due to the Patriots' nanomachines within him.
However, early on in the game, Big Boss is asked by Para-Medic what his real name is, to which he responds "John Doe" with Para-Medic replying "and they call you Jack for short?" Due to slightly tongue-in-cheek nature of the conversation, as well as Para-Medic jokingly responding that her real name is Jane Doe, most initially thought it was nothing more than a joke. However, at the end of Metal Gear Solid 3, Big Boss also tells Ocelot that his name is John, and in Japan, a Limited Edition release of Metal Gear Solid 3 included a book called R which stated Big Boss's real name was John Doe. The master Patriot AI, which is accessed via Big Boss's biometric data, is also named John Doe (although it is also possible that JD was named as such as a reference to the fact that the last leaders of the Patriots were "no one" (i.e. AIs)). In Peace Walker, when Snake tells Gálvez that Big Boss is just a codename the CIA made up, Gálvez then asks if he would prefer it if he called him John. 2b1af7f3a8