The Official Account
The The 9/11 Commission Report holds that four airplanes (American Airlines flights 11 and 77, and United Airlines flights 93 and 175) were hijacked on 9/11. 
The Best Evidence
Pilots are trained to “squawk” the universal hijack code (7500)  on a transponder if they receive evidence of an attempted hijacking, thereby notifying FAA controllers on the ground. But leading newspapers and the 9/11 Commission pointed out that FAA controllers were not notified. 
A CNN story said that pilots are trained to send the hijack code “if possible.”  But entering the code takes only two or three seconds, whereas it took hijackers, according to the official story, more than 30 seconds to break into the pilots’ cabin of Flight 93. 
The fact that not one of the eight pilots performed this required action casts serious doubt on the hijacker story. 
References for Flights Point 1
- The 9/11 Commission Report (2004), Chapter 1.
- “To facilitate NORAD tracking, every attempt shall be made to ensure that the hijacked aircraft is squawking Mode 3/A, code 7500.” Source: Federal Aviation Administration, “Order 7610.4J: Special Military Operations, Chapter 7. ESCORT OF HIJACKED AIRCRAFT,” July 12, 2001. “
Hijack Code a Secret Signal of Distress,” ABC News, June 3, 2005.
- The Christian Science Monitor reported the failure to squawk as an “anomaly” (Peter Grier, “The Nation Reels,” Christian Science Monitor, September 12, 2001).
- “Flight 11 was hijacked apparently by knife-wielding men. Airline pilots are trained to handle such situations by keeping calm, complying with requests, and if possible, dialing in an emergency four digit code on a device called a transponder. … The action takes seconds, but it appears no such code was entered.” (“America Under Attack: How could It Happen?” CNN Live Event, September 12, 2001).
- According to the purported tapes from the cockpit recorder of United 93, it took over 30 seconds for the intruders to break into the pilot’s cabin (Richard A. Serrano, “Heroism, Fatalism Aboard Flight 93,” Los Angeles Times, April 12, 2006). Flight 11’s failure to squawk is discussed here. It clearly would have been “possible” for the pilots to have squawked the hijack code. According to a famous Sherlock Holmes story, the theory about an intruder in a racing stable was disproved by “the dog that didn’t bark.” The intruder theory about the 9/11 airliners, one could say by analogy, is disproved by the pilots that did not squawk.
- For discussion, see David Ray Griffin, The New Pearl Harbor Revisited, 2008, pp. 175-79.