Military aircraft might not show up on civilian radar if they don't wish to be "seen".
Air navigation is a bit out of my league. But applying critical thinking, with a long experience in surface navigation; I'll make an educated guess.
Air navigation rules, much like her older sister, surface navigation rules; are for safety and apply for all military, commercial, and civilian users of USA air space. Chances are the US DOT has them on-line. Rules logically include assigned ATC radio frequencies, transponder use, navigation lights and traffic separation schemes, such as specific altitudes for direction traveled. On the night of 9/11, the only aircraft over Chicago where the military types, with functional navigation lights.
From my experience with radar, transponders paint a significant picture on radar. The 9/11 hijackers secured transponders, which made it very difficult for ATC'ers to follow four relatively huge radar blips.