Well, I wasn't supposed to reveal this, but too many have silly conspiracy theories like yours and seems it's time for the truth to come out.
The whole event you all call "9/11" was the fault of the ETs of Rigel.
Seems they were peeved your USA's FTC wouldn't grant them exclusive export rights on geoducks to the gourmet market of Tau Ceti.
So in a fit of rage, the Rigelians teleported the crew and passengers of those airplanes to their secret base on the far side of the Moon to become slave labor in their colony and mines.
Then they teleported some biologic robot drones onto those planes to simulate the hijackers and pilots, then crashed them into the buildings and ground.
This all has been kept secret for fear revelation would spark an interstellar war in this arm of the Galaxy.
However that war has started already and now we are focused in keeping the Alpha Centaurians from seizing this star-planet system for a base to serve their operations in this intra-galactic war.
We will need to keep this secret for a while so as not to tip off their agents operating on Earth that we are on to them and their schemes.