Technology for Autopilot Override of Pilot Control of Boeing Aircraft Developed Circa 2001
The development of the capability of an aircraft Flight Management Computer (FMC) to take control of an aircraft away from a pilot and turn over control to its autopilot system, including apparently Boeing 757's, was underway circa September 11, 2001. The development of a collision avoidance, control override capability utilizing a Boeing 757 is documented as early as 1999. Boeing 757s and 767s containing common avionics, were used during the 9/11 attacks.
"Ultimately, if required, the system could initiate an automatically flown evasive maneuver. Validation flights were completed at the NASA Wallops Flight Facility and in-flight demonstrations of the system were completed at Minneapolis-St. Paul International Airport in November 1999 for FAA officials and other Government and industry representatives. The NASA B-757 ARIES and a Honeywell Gulfstream IV (G-IV) were used in the flight test effort."
In 2003, "Aviation Week" and Honeywell described the continued development of "ground proximity warning systems" that can allow a GPS-guided aircraft autopilot system to take away control of an aircraft from a pilot during emergencies. Honeywell state-of-the-art Flight Management Systems (FMS) were used by the four aircraft reportedly hijacked on September 11, 2001.
"Assisted recovery builds on existing enhanced ground proximity warning systems (EGPWS), autopilot or fly-by-wire technologies to prevent an aircraft from crashing into terrain or buildings ... If pilots don't respond to warnings within a certain amount of time, assisted recovery directs autopilot or fly-by-wire control systems to steer aircraft away from a crash."
A 2005 report on ground proximity warning systems states that the Boeing 767's that were crashed into the World Trade Center (WTC) relied on navigation databases that contained the exact locations of the WTC towers:
"The hijacked passenger jets that hit the World Trade Center buildings were equipped with EGPWS ... The twin towers were in the database"
 http://www.aviationweek.com/aw/generic/story_generic.jsp?channel=awst&id=news/09265p08.xml&headline=Airbus Shows Interest in Honeywell's Auto Pull-Up Software