The Official Account
The 911 Commission Report holds that American Flight 77, a Boeing 757, was flown by al-Qaeda pilot Hani Hanjour into the Pentagon.  After disengaging the autopilot, he executed a 330-degree downward spiral through 7000 feet in about three minutes, then flew into Wedge 1 of the Pentagon between the first and second floors at 530 mph.
The Best Evidence
Several former airliner pilots have stated that Hanjour could not possibly have maneuvered a large airliner through the trajectory allegedly taken by Flight 77 and then hit the Pentagon between the first and second floors without touching the lawn. 
Russ Wittenberg, who flew large commercial airliners for 35 years after serving in Vietnam as a fighter pilot, says it would have been “totally impossible for an amateur who couldn’t even fly a Cessna” to have flown that downward spiral and then “crash into the Pentagon’s first floor wall without touching the lawn.” 
Ralph Omholt, a former 757 pilot, said: “The idea that an unskilled pilot could have flown this trajectory is simply too ridiculous to consider.”
References for Pentagon Point 3
- The 9/11 Commission Report (2004), pp. 225, 334 (pdf: 242, 351).
National Transportation Safety Board, “Flight Path Study – American Airlines Flight 77” (February 19, 2002). The NTSB video is available on YouTube as “American 77 Final Maneuver”.
- See statements by Cmdr. Ted Muga and Cmdr. Ralph Kolstad at Patriots Question 9/11, where Pilots and Aviation Professionals and “Senior Military, Intelligence, Law Enforcement, and Government Officials Question the The 9/11 Commission Report”
- “Former Vietnam Combat and Commercial Pilot Firm Believer 9/11 Was Inside Government Job,” Lewis News, January 8, 2006.