I had always assumed that the F-16s that were scrambled were planning to (tragically) shoot down commercial airliners. I did not know that the planes were unarmed.
http://www.washingtonpost.com/local/f-16-pilot-was-ready-to-give-her-life-on-sept-11/2011/09/06/gIQAMpcODK_story.html

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