Much thanks for answering my question. However, your answer seems to indicate that until all top secret operations are exposed, you still hold out some sort of moderate possibility of government manipulation. In that case...how long is this research phase anyway? It looks like you might be speaking in speculation for...all time?
Disproving such a notion will be harder. We know there are groups within government agencies tasked with secret operations. Our hope is that those "operations" are never such things as a "9/11 LIHOP," but the skeptical conspiracist knows many such operations skirt the law or worse.
Sure, these operations will skirt the law and are declared top secret, but the detractions of such a conspiracy are visible as well.
First, if the entire operation is as big as enabling something like 9/11 across several intelligence agencies, then a good deal of people would have to be involved and/or see lots of evidence that something extremely dangerous was going on. The fact that out of this potential sea of people you can only draw one prominent, yet undeniably shaky, witness seems contrary to the grand magnitude of the effort.
Second, Osama bin Laden has been a notoriously hard man to track down for several years. It seems unlikely that if a group of government elite could plot his moves well enough to tell what was going to happen well in advance (which they would need to in order to enable him as you are suggesting), they somehow would be unable to get him into custody when he was needed most as a tangible scapegoat. Instead, he's been embarrassing us.
Third, there have been so many botched "top secret" operations and directives in the Bush Administration, most of them relatively important revelations, that it seems even more unlikely that for some reason they'd be able to hold onto the biggest, most slippery fish (covering up 9/11 involvement) while losing all the other ones. Take, for example, the outing of CIA secret prisons in Europe, or the oft-cited domestic wiretapping program that has recently been a subject of extreme debate. These are NOT minor operations - the government had a vested interest in keeping each of them as quiet as possible. When one considers the sheer scope of a coverup over 9/11, it's rational to believe that if such a huge campaign did exist, there would be at least as many whistleblowers as surfaced for the CIA secret prisons.
Plus, the mainstream media (NYT, W. Post, etc.) would be all over it. Yet none of the witnesses brought forward have been credible enough to spark a newspaper firestorm.
Fourth, the difficulties in operation and intelligence sharing that have already been chronicled in the 9/11 Commission Report and several other print sources seem viable enough to explain the colossal failure of our national security system without invoking shadowy government meddlers. We've got 20 (more or less) intelligence agencies that were all split before 9/11. Add the reported rampant territoriality to the mix, and it's easy to see how we were caught off guard. Nobody put the pieces together.
There's more. But to me, the all-powerful state apparatus and sheer volume of coincidences/fortunate happenings necessary to make this work go beyond the pale.
-Sporanox
(and the sense of humour)