Update, 9/10/08: I wrote this post a long time ago when i was more "Truthy," but in fact there was probably NOT a wargame called Vigilant Warrior on 9/11 - see comments below. For reference purposes at least however I'll leave this post up. Just read "probable" as "faintly possible," and so on...
USA Today reported in April 2004 article also cited a NORAD press release: “Numerous types of civilian and military aircraft were used as mock hijacked aircraft. These exercises tested track detection and identification; scramble and interception; hijack procedures…”  These “mock hijacked aircraft,” otherwise called “live-flies,” are used sometimes in air-based war games involving hijacking scenarios. They are actual planes of a variety of makes, in the air (manned or under remote control), pretending to be hijacked for the benefit of effective training.
Ruppert asked some questions, some regarding live-flies, of Major Don Arias, NORAD press spokesman who was on duty and involved in the response the morning of 9/11. Arias at first dismissed Ruppert as part of the “grassy knoll” crowd, but later gave him some good information in a phone interview and follow-up e-mail. He confirmed Vigilant Guardian, and provided clues on the meanings of nicknames.
“Vigilant or Amalgam means it is a HQ NORAD sponsored exercise. Guardian means it is a multi-command CPX, or command post exercise (no live-fly). So on 9/11, NORAD was conducting a NORAD-wide, multi-command, command post exercise with no live-fly. Other exercise terms include: Warrior = JCS/HQ NORAD sponsored FTX, or field training exercise (live-fly).” 
Arias thus confirmed that JCS-connected “Warrior” exercises would involve live-flies faking symptoms of a hijacking. Ruppert further speculated that “warrior” and “guardian” exercises would be conducted jointly in an offense/defense simulation, a possibility he was unable to verify. But whatever its relation to the other war games, there is evidence of at least one “warrior” exercise taking place on the morning of 9/11.
Richard Clarke said in his book Against All Enemies that acting JCS Chairman Richard Myers told him in their videoconference on 9/11 “not a pretty picture, Dick… We are in the middle of Vigilant Warrior, a NORAD exercise.”  This does not seem to be a confused reference to the already admitted Vigilant Guardian, since that did not involve JCS – but a “Warrior” FTX would have Joint Chiefs involvement – and live-flies. Chalk up another (probable) exercise, this one putting extra “hostile” aircraft in the skies amid the attack.
 Ruppert, Crossing the Rubicon. p 345
 Ruppert, Crossing the Rubion. p 368
 clarke, Against All Enemies. p 5