Radar and IFF are total different from each other.
The Interrogator, land based, transmits a signal challenge to the aircraft's transponder and receives a signal back which is processed by maybe the TPX-42 system and finally sent to the radar scope
in FSK (frequency shift key) format. One frequency for a 1 and a higher frequency for a 0.
This video is called secondary video.
If a plane turns off it's transponder you will receive and display nothing on the scope
. (except raw video if the radar is on and the plane is close enough usually within 60 nm)
A raw radar return is the bounce back of the transmitted signal that was transmitted by that radar which is receiving the bounce back which is received during transmitter dead time on a pulse radar before the next transmit pulse.
Secondary video is processed etc during dead time also. There is a separate IFF antenna
on the radar antenna for IFF.
Mode C is for altitude. Usually the selector on the scope (Air Traffic Control, ATC) will be set to mode 3C.
Civilian and military aircraft IFF is the same during peacetime operations which allows some military based airports to also accept civilian airliners and visa versa. Example MCAS Yuma, AZ. Civilian airliners, UPS, DHL, etc also land on Naval Station Norfolk's runway the same used by the F18's, E-2's, C2's, and so on.
We had FAA Rep's and sometime Customs
at the RATCF (Radar Air Traffic Control facility) on base with us in Yuma, AZ and I'm sure it's the same at Naval Station Norfolk these days