I'm not saying you didn't see what you think you saw, but I still think this whole "Govt conspiracy" thing is a load of crap.
If for no other reason than the sheer complexity of the operation.
Even as a terrorist plot only 19 of 20 participants managed to make their appointed connections, that's a 5% failure rate. Out of 4 planes, only 3 managed to engage their targets, that's a 25% failure rate. That assumes a terrorist operation, these people are not stupid, attention grabbing, mass casualty attacks are what they do, what they train for. And the idea of using manned aircraft as missiles dates back to at least the 1940's.
Things like using a cruise missile, then faking video of an air craft adds levels of complexity that guarantee failure, and take the operation out of the realm of believability.
My own belief is that you have watched a couple to many episodes of "X Files", or "Mission Impossible".