As Captain Kirk eventually learned in the Star Trek episode "Obsession," his failure to act in a crisis of his past would have made no difference in the outcome. The same goes for the lack of fighter defense coverage in the 9/11 case.

As I pointed out in an earlier post, even had the interceptors suddenly appeared at the side of each airliner the moment they were hijacked, I don't believe that they would have asked for, much less been able to get, the authority to shoot down passenger-filled planes prior to the first WTC impact. The second WTC impact was fifteen minutes later, so going through even the most rapid channels to try and clear shooting down the second plane before it reached an inhabited area would have been nearly impossible.

The attack on the Pentagon was 35 minutes after the second Tower hit, so a case could be made that in this time surely a shoot-down order could be processed. Unfortunately, this assumes that Flight 77 would have been identified as a missile plane in that period of time, during which it was flying without a transponder and all eyes were currently on New York.

The last plane, Flight 93, is really the only one that could plausibly have been intercepted and shot down in the time frame given, even assuming fighters were right on the spot. Some people (not me) think this was actually done. Had some target in Washington been its goal, it wouldn't have gotten there until almost an hour after the Pentagon strike, which means that by then everyone would have been fully aware of the situation and a shootdown order through channels would be highly plausible, although probably political suicide.

This knowledge of the situation, transmitted to Flight 93's passengers on cell phones, is why they, unlike the passengers in the other planes, finally took matters into their own hands.