It has been the consensus of informed observers that the loss or alteration of Secondary Surveillance Radar (SSR) information for the four September 11 flights was caused by accused hijackers allegedly seizing control of the aircraft flight decks and manually turning off or adjusting each plane’s Mode S (Mode Select) transponder. This was presumably for the purpose of evading detection and interception by U.S. air defense systems. However, this view appears to be based only on circumstantial information - the simple loss or change of SSR flight data to Air Traffic Control (ATC) – and seems unsupported by conclusive facts. Following these transponder operation changes, ATC was still able to tag and track the primary radar returns of three flights and estimate their locations, directions, ground speeds, and even altitude changes.
http://www.journalof911studies.com/implications-of-september-11-flight-transponder-activity/