I may get pummel for this but the pilot episode of the Lone Gunmen, the X-Files spinoff (6 months before 9/11) was the story of a shadow agency inside our government planning to fly a commercial jetliner into the towers.

This from Wikipedia:

Pilot episode "predicts" 9/11

In a foreshadowing of the September 11, 2001 attacks, subsequent conspiracy theories, and the 2003 invasion of Iraq, the plot of the March 4, 2001 pilot episode of the series depicts a secret U.S. government agency plotting to crash a Boeing 727 headed for Boston into the World Trade Center via remote control for the purpose of increasing the military defense budget and blaming the attack on foreign "tin-pot dictators" who are "begging to be smart-bombed." This episode aired in Australia less than two weeks before the 9/11 attacks, on August 30

I'm just saying......