I know nothing about aviation, so help me out here. Let’s assume there is no foul play involved. That being the case, is there any legitimate reason for the crew to turn off the transponder?
9/11 Military Notification and Response.
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.
http://www.9-11commission.gov/report/911Report_Ch1.htm
At NEADS, the report of the hijacking was relayed immediately to Battle Commander Colonel Robert Marr. After ordering the Otis fighters to battle stations, Colonel Marr phoned Major General Larry Arnold, commanding general of the First Air Force and NORAD’s Continental Region. Marr sought authorization to scramble the Otis fighters. General Arnold later recalled instructing Marr to “go ahead and scramble them, and we’ll get authorities later.” General Arnold then called NORAD headquarters to report.118
F-15 fighters were scrambled at 8:46 from Otis Air Force Base. But NEADS did not know where to send the alert fighter aircraft, and the officer directing the fighters pressed for more information: “I don’t know where I’m scrambling these guys to. I need a direction, a destination.” 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. Shortly after 8:50, while NEADS personnel were still trying to locate the flight, word reached them that a plane had hit the World Trade Center.119
Radar data show the Otis fighters were airborne at 8:53. Lacking a target, they were vectored toward military-controlled airspace off the Long Island coast. To avoid New York area air traffic and uncertain about what to do, the fighters were brought down to military airspace to “hold as needed. “From 9:09 to 9:13, the Otis fighters stayed in this holding pattern.120
Electrical fire involving the transponders, according to so-called experts on CNN.