A conspiracy theory of that time was that Bush was behind 9/11 because he wanted a causus belli to shore up his tanking popularity in the leadup to his re-election. Basically, fitting the plot of Wag the Dog to the facts of the day. The theory remains unsubstantiated.

Another was that the collapse of the world trade center towers was due to planted explosive charges. That one has been roundly refuted.

Of course, people continue to believe what that will, but there's a pretty big gap in the amount of evidence behind those theories and confirmed conspiracies.