Actually, NORAD was involved with multiple exercises that day. More simultaneous exercises than ever before. Then, the Secretary of Transportation heard Dick Cheney give an override order. The exercises were supposed to provide all the cover the Bush junta would need in order to claim "confusion and incompetence," but at the last moment Cheney had to do a bit of tweaking. And it was witnessed by the Secretary of Transportation. Others have talked about stand down orders too:

"Then we (at CENTCOM) see the other plane come in and hit it and at that point everybody is standing up. The air force had commanders in contact with NORAD. The plane, or whatever, hit the Pentagon and then we were like 'Why aren't they scrambling jets?' We were asking, there was eight or nine people... Colonels and Lieutenant Colonels asking the Lieutenant Colonel in charge of the air force 'why isn't NORAD scrambling jets? and he said 'we received an order to stand down''. And that just perplexed everybody."

http://infowars.net/articles/September2006/260906Chavez.htm

Here's a page of links to sites that talk about the stand down, or whatever you want to call it:

http://www.911myths.com/html/stand_down_links.html