An IFF interrogator sends out two pulses modulated on a 1.03 GHz carrier. To interrogate Mode 3/A, the pulses are 8 microseconds apart. To interrogate Mode C, the pulses are 21 microseconds apart.
The aircraft transponder replies on 1.09 GHz with 12 pulses giving the requested information, with each pulse providing a "0" or "1" bit giving a total of 4,096 codes.
3/A and C modes are common to both civil and military aircraft, but the military also has other modes reserved for its own use. In Mode 1, two pulses are sent by the interrogator 3 microseconds apart, and the IFF transponder responds with an 8-bit response enabling 64 codes that indciate the type of mission . In Mode 2, the two pulses are sent 5 microseconds apart, and the aircraft provides a 12 bit reply, returning an airframe assigned code.
Mode 4 is similar to Mode 3/A, but the challenge and response are encrypted.
Mode S is more recent and a bit more complicated.
Mode 3 was the precursor to 3A and was limited to 2 digits/64 codes. Some jets still had them fitted well into the 80s. I remember the Italian F-104s visiting Leuchars and ScATCC complaining they wouldn´t squawk the last 2 digits.
There also used to be a military emergency button on the old aircraft IFF boxes which, when pressed, transmitted the currently set Mode 3 code 4 times giving a 4 bar indication on the tube but still allowing the controlling unit and position to be identified. Only visible at the older ADGE sites however....