What if the planes were shot down in midair and replaced with drones that continued to their 9/11 targets? One question that then suggests itself is what happened to the debris from the original planes. I think I have an answer: They were shot down by means of a minigun, which completely shreds its target since it is capable of firing 4,000 rounds per minute. Miniguns, essentially electrically-driven Gatling guns, were first put into service in the 1960s. A barrage from such a gun could conceivably reduce an aircraft to such small pieces that what ends up on the ground is hardly noticeable. Also, if the planes were shot down from a fairly high altitude, which is likely, the debris would have spread over a very large area, making detection doubly difficult. If the engagements took place over sparsely populated territory, there wouldn't have been any noise witnesses when the guns were fired. The guns could have been fired from the drones or from additional planes utilized by the perpetrators. The drones presumably were specially hardened so that they could penetrate the target buildings where ordinary craft would have crumpled on impact.
I'm not saying this is what happened, just that the story holds together.