I read a theory (didn't save, sorry) in which the planes that hit WTC were unmarked remote-controlled planes, with the actual flights being re-routed to another airport, passengers disembarked to a holding hangar where some were allowed to make phone calls for controlled use in the narrative before they were re-boarded onto another flight directly to the Atlantic. It gave a minute-by-minute timeline with plausible explanations on all fronts, including how that jives with radar and squawking. Lots of possibilities, but none will explain everything beyond doubt until more hard evidence is available.