Board Thread:General Discussion/@comment-10941901-20130628153213/@comment-4913740-20130628174707

John Doe is used in mortuaries where the victim's body is unidentified. It originated as the name given to unidentified bodies in the battlefield. Snake uses it as a sort of joke when Para-Medic asks for his name. Her response of "Jane Doe" is the female counterpart for this term.

That's why the head Patriot AI is called JD, standing for John Doe. Because the head of the Patriots is unidentified; a nobody.