I just watched part of a show about 9/11 conspiracy theories (click here for more). Now, I'm no engineer (though have a great deal of related training), so am disinclined to argue the facts on either side of this debate. I lean towards to official story, though, My main criteria for this? For such a secret to be maintained would truly be a revolutionary event. These same people who can't keep secret the next speech are going to keep THIS under wraps? The divergent and conflicting agendas within the federal government will work together in this instance?
Now, if there is some shadow org affecting such actions, the ramifications are amazing. Keeping such secrets with actions that would work across departments is something unique. Perhaps it's possible. It escapes my observations, though.