All commercial airliners carry two virtually indestructible “black boxes” containing devices to record physical data and pilot communications — a Flight Data Recorder (FDR) and a Cockpit Voice Recorder (CVR).
The FDR records many parameters,  including the plane’s speed, altitude, and course; while the CVR records conversation both inside the cockpit and all the plane’s external communications.
These devices are highly durable and are installed in a plane’s tail section, where they are least likely to be damaged on impact. They are designed to withstand intense heat and violent crashes. 
The Official Account
The 9/11 Commission dealt with two sets of aircraft: those involved in the World Trade Center, and those that were not:
- The black boxes for the two planes that struck the Twin Towers — AA Flight 11 and UA Flight 175 — were never found. 
- The black boxes for UA Flight 93 and AA Flight 77 were found,  but the CVR for AA 77 was badly burned and the information recorded on it was not recoverable. 
- A transcript from UA 93’s CVR was released by the FBI in the 2006 trial of Zacarias Moussaoui. 
- According to the American Society of Engineers’ 2003 Pentagon Building Performance Report, the AA 77 data recorder was “found nearly 300 ft into the structure.” 
The Best Evidence
The official claims above are contradicted by a substantial amount of evidence to the contrary:
- Contrary to the official claim about AA 11 and UA 175, a FDNY fireman who worked in the cleanup of Ground Zero, Nicholas DeMasi, and volunteer Mike Bellone, described their discovery in October 2001 of three of the four black boxes in the rubble of the Twin Towers. 
- A September 18, 2001, memorandum to Governor George Pataki from New York State Emergency Management Office Director Edward F. Jacoby, Jr., reported that “Investigators have identified the signal from one of the black boxes in the WTC debris.” 
- Gen. Paul Kern, the commanding general of the U.S. Army Materiel Command, reported in 2002 that “Radio frequency detectors developed at CECOM [Communications Electronics Command] were used to find “black box” flight recorders from the airliners that crashed into the two towers.” 
- Although the four virtually indestructible black boxes were reportedly never found, the passport of alleged AA 11 hijacker Satam al Suqami was reportedly found near Ground Zero,  and life jackets and portions of seats from AA 11 were reportedly found on the roof the Bankers Trust building. How could they survive when the black boxes could not? 
- Except for the two WTC flights, the black boxes of only one flight over land have ever been lost, and it crashed extremely high in the Andes. (As for flights over water, the only ones that have not been recovered have been over very deep water.)  Just a priori, therefore, it seems unlikely that the black boxes from the two WTC airplanes would not have been found.
- With regard to AA 77, which reportedly hit the Pentagon, the 2003 Pentagon Building Performance Report said that the flight data recorder “was found almost 300 feet inside the structure.”  However, this claim contradicts what was publicly reported. A Newsweek story in 2001 reported that before 4 AM three days after the attack, two firefighters, Burkhammer and Moravitz, discovered them “near the impact site”:
“[They] were combing through debris near the impact site. Peering at the wreckage with their helmet lights, the two spotted … two odd-shaped dark boxes, about 1.5 by 2 feet long. They’d been told the plane’s ‘black boxes’ would in fact be bright orange, but these were charred black. … They cordoned off the area and called for an FBI agent, who in turn called for someone from the National Transportation Safety Board (NTSB) who confirmed the find: the black boxes from AA Flight 77.” 
- Likewise, Arlington County spokesman Dick Bridges said that members of the FBI’s evidence response team found the two recorders “right where the plane came into the building.” 
- According to a file released by the NTSB in response to an FOIA request from Aidan Monaghan, the flight data file for American Flight 77, which was based on this FDR, was created at 11:45 PM on Thursday, September 13. This is a serious contradiction within the official story: According to the Pentagon, the FBI, and even the NTSB, the FDR was found early on the morning of Friday September 14, and authorities later in the day were hoping that information on it could be recovered. And yet according to the NTSB file released only after there was a FOIA request for it, the file based on flight data file for AA 77 had already been created the previous day. How could the file based on the AA flight data have been created a day before the FDR itself was found? 
- According to an NTSB investigation handbook, accident investigators are required to list the manufacturer/model, serial number, and maintenance readout of the Flight Data Recorder.  However, there have been no serial numbers published for any of the recovered black boxes from the four flights.  Retired Air Force Colonel George Nelson, a specialist in aircraft accidents, reports that every plane has many “time-change parts” which must be changed periodically because they are crucial for flight safety. Each time-change part has a distinctive serial number. These parts are virtually indestructible, so an ordinary fire resulting from an airplane crash could not possibly “destroy or obliterate all of those critical time-change parts or their serial numbers.”  That the serial numbers on the AA 77 black boxes were not reported is another serious problem with the official account.
- the strong official evidence contradicting the extraordinary claims that:
- the two sets of black boxes from the World Trade Center were never found and that
- the Cockpit Voice Recorder from the Pentagon Flight AA 77 was too damaged to be readable;
- that the flight data file for AA 77 was made before the FDR itself was reportedly found;
- that the official report contradicted the public stories about where the black boxes were found (by 300 feet); and given
- the failure to provide the required serial numbers for any of the allegedly retrieved black boxes,
the official account’s claims about black boxes from the 9/11 planes appear to be false.
References for Flights Point 4
- Rising Up Aviation. “Federal Aviation Regulations. Sec. 135.152 – Flight Data Recorders,” (showing amendments from 1988 to 2009).
- “Flight Recorders,” Wikipedia (accessed August 6, 2014).
- “The CVRs and FDRs from American 11 and United 175 were not found,” The 9/11 Commission Report, p. 456, note 76 (no ref. given by Commission); Brian Dakss, “Speed Likely Factor in WTC Collapse,” CBS News, 25 February 2002.
- The 9/11 Commission, “Memorandum for the Record: John S. Adams, Special Agent, FBI, November 3, 2003,” “Flight 77’s black box was found on the first floor near the A&E Drive by the night shift team”.
“3:29 PM UAL 93 black box located at Sommerset [sic], PA.,” 9/11 Commission, Chronology of Events, undated.
“Flight Data and Voice Recorders Found at Pentagon,” PBS Online Newshour, September 14, 2001.
“Feds Would Have Shot Down Pa. Jet,” CBS News, September 12, 2001.
- “The CVRs and FDRs from American 11 and United 175 were not found.” The 9/11 Commission Report, p. 456, note 76 (no ref. given by Commission).
- Transcript of Flight 93’s Cockpit Voice Recorder.
- ASCE, Pentagon Building Performance Report, 40.
- Gail Swanson and Robert Nahas, eds., “Behind-the-scenes: Ground Zero … A Collection of Personal Accounts” (2003); Will Bunch, “New Coverup Revealed? 9/11 Black Boxes Found,” Philadelphia News, October 28, 2004.
- Edward F. Jacoby, Jr., “Sept. 18, 2001, memo to Gov. George Pataki.” OEM FOIL Sec. 4, p. 16. Edward Jacobi was the director of the New York State Emergency Management Office, responsible for marshaling 22 state agencies and nearly 17,000 personnel, including 5,200 National Guardsmen and 500 state police officers.
- General Paul J. Kern, “AMC: Accelerating the Pace of Transformation,” AUSA: Army Magazine, February 1, 2002. Kern headed the US Army Materiel Command from October 2001 to November 2004, Wikipedia, (accessed August 30, 2014).
- National Commission on Terrorist Attacks Upon the United States, “Public Hearing, January 26, 2004.”
- Ronald Hamburger, et al., “WTC1 and WTC2,” FEMA World Trade Center Building Performance Study, Ch.2, FEMA, n.d., p. 2-16.
- “List of Unrecovered Flight Recorders,” Wikipedia (accessed August 2014).
- ASCE, Pentagon Building Performance Report, Section 6.2, p. 40; passage quoted in David Dunbar and Brad Reagan, eds., “Debunking 9/11 Myths: Why Conspiracy Theories Can’t Stand Up to the Facts,” New York, Hearst Books, 2006, 70.
- “Washington’s Heroes: On the Ground at the Pentagon on Sept. 11,” Newsweek (MSNBC News), September 28, 2001.
- “Black Boxes from Hijacked Plane Found at Pentagon,” Associated Press, Sept. 14, 2001;
“Flight Data and Voice Recorders Found at Pentagon,” PBS Newshour, September 14, 2001.
- Aidan Monaghan, “Pentagon 9/11 Flight ‘Black Box Data File’ Created Before Actual ‘Black Box’ Was Recovered?” 911blogger.com, May 18, 2008.
“Searchers find Pentagon black boxes,” usatoday.com, 09/14/2001.
- National Transportation Safety Board. Vehicle Recorder Division. “Flight Data Recorder Handbook for Aviation Accident Investigations: A Reference for Safety Board Staff,” December, 2002.
- Aidan Monaghan, “9/11 Aircraft ‘Black Box’ Serial Numbers Mysteriously Absent,” 911blogger.com, February 26, 2008.
- Colonel George Nelson, USAF (ret.), “Impossible to Prove a Falsehood True: Aircraft Parts as a Clue to Their Identity,” Physics 911, April 23, 2005.