The story...

The initial response of various Norad and Air Force staff prove that the 9/11 war games involved scenarios involving hijacked planes.

"First thing that went through my mind was, 'Is this part of the exercise? Is this some kind of a screw-up?'" said Air Force Maj. Gen. Larry Arnold, who was at a command center at the Tyndall Air Force Base in Florida.
http://www.billstclair.com/911timeline/2002/abcnews091402.html

Sgt. Jeremy W. Powell of North American Aerospace Defense Command's (Norad) Northeast Air Defense Sector (NEADS) in Rome, N.Y., took the first call from Boston Center. He notified NEADS commander Col. Robert K. Marr, Jr., of a possible hijacked airliner, American Airlines Flight 11.

"Part of the exercise?" the colonel wondered. No; this is a real-world event, he was told.
http://billstclair.com/911timeline/2002/aviationweekspacetechnology060302.html

At 8:40, Deskins noticed senior technician Jeremy Powell waving his hand. Boston Center was on the line, he said. It had a hijacked airplane.

"It must be part of the exercise," Deskins thought.

At first, everybody did.
http://www.newhousenews.com/archive/story1a012802.html

Our take...

Does this claim really stand up? We don’t think do. Here’s why.

Problem #1 is that the quotes don't all support this scenario at all. Someone saying "'Is this part of the exercise? Is this some kind of a screw-up?'", for instance, doesn't sound like it's a call they were expecting to us. 

Likewise with Jeremy Powell of NEADS, whose taped response to Boston Central's hijacking report was "Is this real-world or exercise?". If he was expecting a hijacking call then why would he even ask? And why in such an unspecific way? You might expect Powell to ask "Is this a part of Vigilant Guardian?" or whatever the exercise was, but he doesn't.

Boston Central certainly don't appear to know of any related exercise. Instead of saying "This is nothing to do with todays exercise", we hear "this is not an exercise, not a test". "A", not "The" -- they're not referring to anything specific. From these few comments there's no evidence Boston Central knew of any hijacking-related exercises at all. And if they didn't, then why would Powell expect them to be involved?

Problem #2 is that there could easily be an alternative explanation for these quotes. Maybe Norad include unexpected events during war games, for instance, as well as a main, preplanned theme. (After all, you don’t fully test staff and procedures if they know exactly what’s coming up). Therefore, if you're in the middle of an exercise, and you receive a call that relates to something unusual, then plainly it'll be natural to wonder if this is just a part of the war game. 

This isn’t just conjecture, either. Here’s Major General Larry Arnold testifying before the 9/11 Commission (our emphasis):

As you know through previous testimony from Gen. Eberhart to Congress, we were in the middle of a NORAD exercise at that particular time. Which means, that basically our entire staff was focused on being able to do the air operations center mission, which was our job to do. We had just come out of a video teleconference with the NORAD staff and with our folks at that particular time when I was handed note that we had a possible hijacking in Boston Center. And it had come from the Northeast Air Defense Commander Col. Bob Meyer (phonetic) who is commander up there and he had requested that I call him immediately. And I was upstairs in our facility. I immediately went downstairs and picked up the phone, asking on the way to my staff, is this part of the exercise? Because quite honestly and frankly, we do do hijacking scenarios as we go through these exercises from time-to-time. But I realized that it was not – that this was real-life.
http://permanent.access.gpo.gov/websites/www.9-11commission.gov/archive/hearing2/9-11Commission_Hearing_2003-05-23.htm

He wondered if this might be a part of the exercise because, occasionally, hijackings are. However there’s no evidence it was a planned element in this case.

Problem #3 is that even if a hijacking was scheduled to be a part of the war games, there's absolutely no evidence to suggest that multiple hijackings were involved, that they involved flying planes into buildings (as some sites claim), or that they had any significant effect on the Norad response. In fact, the articles stated claim the precise opposite:

The Federal Aviation Administration has evidence of a hijacking and is asking for NORAD support. This is not part of the exercise.

In a flash, Operation Northern Vigilance is called off.
http://www.911truth.org/readingroom/whole_document.php?article_id=92