The 9/11 Commission and the media have accepted the idea that the four 9/11 flights were difficult to track because hijackers had turned off or changed the transponder signals.
The official account held that radar information was lost for three of the four September 11 aircraft because hijackers had, after seizing control of the three flight decks, manually turned off these transponders in order to evade detection and interception by the U.S. air defense system.
This conclusion appears to be based only on circumstantial information — the simple loss of flight data to Air Traffic Control (ATC).
However, to this day, manual deactivations of transponders still cannot be verified by ATC.
The Official Account
On the morning of September 11, 2001, flights American 11, American 77, United 93, and United 175, were taken over by onboard hijackers, who from within the cockpits turned off the transponders for the first three aircraft, and who changed the code transmitted by UA 175’s transponder. 
The 9/11 Commission explained:
- “On 9/11, the terrorists turned off the transponders on three of the four hijacked aircraft. With its transponder off, it is possible, though more difficult, to track an aircraft by its primary radar returns. But unlike transponder data, primary radar returns do not show the aircraft’s identity and altitude. Controllers at centers rely so heavily on transponder signals that they usually do not display primary radar returns on their radar scopes. But they can change the configuration of their scopes so they can see primary radar returns. They did this on 9/11 when the transponder signals for three of the aircraft disappeared.” 
- “At 8:21, American 11 turned off its transponder, immediately degrading the information available about the aircraft. The controller told his supervisor that he thought something was seriously wrong with the plane, although neither suspected a hijacking. The supervisor instructed the controller to follow standard procedures for handling a ‘no radio’ aircraft.” 
- “Because the hijackers had turned off the plane’s transponder, NEADS personnel spent the next minutes searching their radar scopes for the primary radar return. American 11 struck the North Tower at 8:46.” 
- “At 8:51, the controller noticed the transponder change from United 175 and tried to contact the aircraft. There was no response.” 
- “At 8:54, the aircraft [American 77] deviated from its assigned course, turning south. Two minutes later the transponder was turned off and even primary radar contact with the aircraft was lost.” 
- “The failure to find a primary radar return for American 77 led us to investigate this issue further. Radar reconstructions performed after 9/11 reveal that FAA radar equipment tracked the flight from the moment its transponder was turned off at 8:56.” 
- “On American 11, the transponder signal was turned off at 8:21; on United 175, the code was changed at 8:47; on American 77, the signal was turned off at 8:56; and on United 93, the signal was turned off
at 9:41.” 
The Best Evidence
The evidence below shows that changes to the transponder data broadcast by the four aircraft on 9/11 were not necessarily caused by hijackers:
- The 9/11 Commission Report provides no evidence to show that hijackers manually deactivated three transponders to cause the loss of ATC data.
- The National Transportation Safety Board (NTSB) and Federal Aviation Authority (FAA) 9/11 flight studies make no reference dealing with why the transponder signals for these flights were lost.
- Transponder activity is not listed among the Flight Data Recorder mandatory parameters and therefore cannot be established through FDR recordings. 
- A 2001 Christian Science Monitor story reporting how Flight 11’s transponder was turned off was speculative:
“Flight 11’s transponder had stopped working. It was no longer sending a radar pulse … . Still, the controllers hoped that the plane simply had an electrical problem … .The controller speculates that the hijacker may have deliberately deactivated the plane’s transponder … .” 
- In the 2014 disappearance of Malaysian Flight MH 370, news stories overlooked what should have been obvious evidence if proof of manual deactivation were available. For example:
“Kit Darby, a longtime pilot, said Tuesday it was not clear whether the transponder was turned off intentionally.” 
No good evidence has been provided to support the official claims that hijackers manually deactivated or altered the operation of the transponders aboard the 9/11 flights.
Instead, there is a spectrum of evidence to question the reality of the hijackers as having been on the planes at all. 
Accordingly, the transponder claims should not serve as supporting evidence for the alleged takeovers of the 9/11 flights by the accused or even as evidence of their presence aboard the flight decks of these aircraft.
References for Flights Point 3
- The 9/11 Commission Report, July 2004, Chapter 1.
- The 9/11 Commission Report, July 2004, 16.
- The 9/11 Commission Report, July 2004, 18.
- The 9/11 Commission Report, July 2004, 20.
- The 9/11 Commission Report, July 2004, 21.
- The 9/11 Commission Report, July 2004, 9.
- The 9/11 Commission Report, July 2004, 25.
- The 9/11 Commission Report, July 2004, 454.
- Rising Up Aviation. “Federal Aviation Regulations. Sec. 135.152 – Flight Data Recorders,” (showing amendments from 1988 to 2009).
- Mark Clayton, “Controllers’ tale of Flight 11,” The Christian Science Monitor, September 13, 2001.
- Tom Watkins and Steve Almasy, “Transponder’s fate may prove key to solving Malaysia Airlines puzzle,” CNN World, March 13, 2014.
- See for example, other 9/11 Consensus Points: Point Pent-3: “The Claim Regarding Hani Hanjour as Flight 77 Pilot”; Point Flt-1: “A Claim Regarding Hijacked Passenger Jets”; Point Video-2: “Was the Airport Video of the Alleged AA 77 Hijackers Authentic? Official 9/11 Videotaped Evidence”; Point PC-1: “The Alleged Calls of Todd Beamer, Flight UA 93”; Point PC-2: “The Reported Phone Calls from Barbara Olson”.