JD
From the Metal Gear Wiki
JD was the name of the head AI which governed the organization known as The Patriots. JD had top priority, and kept command over the four other AIs which made up the organization. These four other AIs were codenamed GW, TJ, TR, AL.
"JD," housed in a satellite orbiting the Earth disguised as debris, is an abbreviation of John Doe, most likely named after Big Boss.
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Early Construction
After Big Boss had left the Patriots, Zero lost his faith in humanity and commissioned the construction of AIs to command the organization after his death. JD was to watch over and command these AIs. It is unknown when exactly they were commissioned, or when they went active, although GW was in the final testing stages in 2009, and JD itself appeared to be fully active at this time.
The Manhattan Incident
See the Tanker Incident and the Big Shell Incident
During the events of The Manhattan Incident, Raiden, Solid Snake and Otacon, were able to upload a worm cluster virus into GW's cerebral core through the help of Emma Emmerich, Otacon's younger sister and lead designer of Arsenal Gear. After the destruction of GW aboard Arsenal Gear, the AI, under the disguise of both Colonel Campbell and Rosemary, began to glitch and error itself out. After crashing in lower Manhattan, Raiden was contacted by yet another AI disguised as Campbell and Rose, although this time it was JD, the main AI, doing the talking. Unlike GW, which had a more mission-based tone, JD spoke with an almost unworldly presence, with a condescending tone to the human race in general. JD told Raiden the true nature of the S3 Plan, a plan in which The Patriots would control the world through the digital flow of information. Giving Raiden his final mission, JD instructed him to defeat Solidus Snake in battle, which he had no choice but to do. JD was never heard from again and its whereabouts were a mystery to both Raiden and Philanthropy.
Liquid Ocelot's Insurrection
See Liquid Sun, Solid Sun, Third Sun, Twin Suns, Old Sun and Naked Sin
After the incident, Liquid Ocelot managed to reconstruct GW using its broken pieces, allowing himself access to the neural network of Patriots AIs and subsequently being able to control the SOP system. GW, now linked directly to JD and the other three AIs, became a sort of data haven. Liquid discovered that JD was not a terrestrial being at this point, it had actually been sent into space and was orbiting the Earth attached to a satellite. Liquid decided that stealing the railgun still attached to Metal Gear REX and launching a nuclear warhead at JD would be the only way he could fully take control of the system with GW, as when JD was eliminated GW would take its spot as the priority AI, controlling the entire system in the process. However, Solid Snake and Otacon were able to upload the FOXALIVE virus into GW, and unbeknownst to them it spread into JD and the other AIs, eliminating them all and successfully defeating The Patriots and Liquid Ocelot simultaneously.
