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When looking at conspiracy theories don't forget that there is a concept in spy (i.e. "intelligence") circles of the "smoke screen".
The idea is that when you launch a secret operation you should expect that people will be curious, and you should prepare several storylines ("smoke screens") in advance for the curious to pursue. The curious will get busy investigating the false leads you planted. Even if they do later stumble on part of the truth, it won't be distinguishable from the "smoke screens".
The beauty of the "smoke screen" concept is that you might not even have to create the false leads yourself -- the more paranoid observers will often do it for you.
Consider that old classic, the JFK assassination. For generations everyone heard about the grassy knoll, the magic bullet and the extra shot. Who knows how much time has been wasted on these issues. And while everyone focused on whether Oswald was the only shooter, they mostly ignored the core question: who hired him? Whether or not Oswald was the lone shooter, there is no evidence that he would have undertaken an assassination on his own. There is plenty of evidence of groups who wanted to see Kennedy replaced with Johnson.
You see? A smoke screen. The important question was ignored while everyone focused on distractions.
Similarly, on 9/11 the key question is not whether there were explosives in the towers or whether the Pentagon was hit by a plane or a missle. It's "who knew enough in advance to make the massive short sells of American and United Airlines". Answer that and you are on the trail to answering the rest.