Conspiracy theories often engender two pathologies. One is that of the deferential who accepts the official version of everything from 9/11 to the deaths of Dinah and Dr Kelly; the other is perennial paranoiac who never fails to sees the hand of omnipotent shadowy agents pulling the strings behind courts, the media and so on. (In fact the paranoia narrative is most common in the most deferential of countries the US where a regular film scenario is of trusting patriotic Joe stumbling on a web of government mis-doings and then being called on to put matters to right).
There are times when the conspiracy theorists are absolutely right (e.g. the Zinoviev Letter, 1924) but more often the unexplained and unexplainable would, if explained, show hitherto unknown details which at best would add a new dimension to the accepted master explanation. And I believe that is probably the case with the 9/11 events.
Every political event has unknown aspects and these unknown aspects throw up ‘clues’ which cannot be readily explained. It is job of historians and political scientists to probe, seek the facts and provide the best possible explanations.