The plan was coordinated and executed within the US government, but this doesn't mean "the government" was behind it. It was almost surely not an official government plan. Bush almost certainly knew nothing about the plan, let alone authorize it. No documents detailing the plan were debated or discussed internally within the administration, it came as a surprise to everyone. Everyone, that is, except one person, the person who was behind the simulation drills coincident with the attacks. It is only by manipulating the details of such drills that you can pull off an attack such as this from the inside.
It is impossible to make a large nefarious conspiracy within the government, you can hardly expect to persuade hundreds of top official people to go along with treason and murder. But you can make the event happen all by yourself, under two conditions.
Under these circumstances, to make a fake terrorist attack, all you have to do is pull a little switcheroo on the day of the drill, something one well placed person can easily manage.
On the day of 9/11, there were a massive number of coordinated military drills, which simulated many aspects of the actual plot, and overlapped in time. This was noted by Bush, who called this an uncanny coincidence. It is uncanny, but it's not a coincidence.
One of the drills of 9/11 involved a hijacking scenario, where planes were supposed to be hijacked and flown somewhere else. Someone designed computer equipment to muck around with air-traffic control for the purpose of this drill, to test how they would respond to bad blips, stuff going wrong.
There was another drill which sent military planes to ward off an imaginary Russian attack, leaving American airspace vulnerable, and another drill involving the agency that is responsible for space imaging, which sent them out of the building during the hours of the attack. There were about 46 separate drills on that day, more than any other day in American history. The most interesting and relevant drill in the attack was a flight simulation designed to see if airplanes can be piloted into the pentagon or world trade center. News of this drill leaked in 2002, much to the consternation of senior folks in the Bush administration.
Putting the drills together, with the proper authority, it is a cinch to pull of 9/11. You simply give the fighters, who are supposed to be shooting drones out of the sky, the coordinates of real civilian aircraft instead, and have them shoot the civilian aircraft down unwittingly, using long-range missiles. They would never know what they did. Then you morph the path of these downed aircraft into the path of the drones, either by placing the drones near to where the airliners were shot down, and switching their identifying signals, or else by manipulating the air-traffic control radar, which was rigged for a hijacking drill on 9/11.
Instead of running a flight simulation for planes crashing into the world trade center, you have the pilots in the simulation pilot the remaining drones into the real world trade center. You can justify the drones resembling civilian aircraft, because the drill is after all simulating civilian aircraft getting hijacked and flown into buildings. They won't be spot on, however, and witness testimony and photographs of that day are more consistent with a drone than with a civilian aircraft. Besides, no pilot in their right mind, including Al-Qaida jihadists, would pilot an airplane into an occupied building. That's the kind of comic-book villainy only novelists and military planners image. Real suicide bombers always come in groups of one, a suicide pact of 19 or 20 people is kind of a big conspiracy for people who are committing suicide, one of them might decide they don't want to die.
The result is that you have pulled off an attack with no explicit co-conspirators necessary, and after the attack, the only people who suspect that they are responsible for something terrible are the few pilots who were involved in the simulation, who would surely realize that they were piloting the planes into the World Trade Center. Considering their terrible guilt and horror, you can blackmail them, or have them killed using your security clearance to fabricate secret evidence against them. Or you could use co-conspirators, if you have them.
(see minute 23 of this video for plausible but uncorroborated testimony)
It would be a violation of security clearance to come forward with any information, so people who participate in the drills more peripherally, and have suspicions, would need to risk their jobs and jail time in order to testify. They would not be absolutely certain that the attack didn't happen as the government said, and these doubts would make coming forward difficult, considering the consequences.
One requirement of this plan is that the evidence of the planes, that they are drones, be destroyed in the attack. This does not mean that we don't have plenty of witness evidence:
But it means that any part of the World Trade Center which contains parts of the aircraft inside must be demolished as part of the attack. You can do this by contacting the owner and requesting permission for emergency demolition charges to be placed in the building. You don't need the building owner to be a co-conspirator for this, it makes sense to have the power to demolish tall buildings in case of emergency, to prevent property damage to other buildings in the dense area, from falling towers. It also makes sense to keep it secret, because, who the heck would rent space in a building that's rigged to go down? Such a system would also make the building a more attractive target for any actual terrorists, who would be guaranteed a spectacular result if the attack succeeds.
Further, since no one knows about it, even if the owner were to say "Yes, there were charges in the building, it was demolished", he would be liable for wrongful death lawsuits totalling billions of dollars, for neglecting to disclose it to his tenants. So he keeps his mouth shut.
(see the beginning of this video for more sincere sounding testimony)
The owner doesn't need to know about the full plot, the point is that nobody really needs to know about the full plot, except for the person coordinating it. But there will be suspicious people. If the drill involved contacting American Airlines, for instance, and suggesting that there would be a simulated hijacking on this airlines, people would figure "hey, either they have intelligence about this, or else people won't want to fly American, because of association with terrorism", and you could get a person placing put options on American, and their friends, and their friend's friends. The high volume of hedged short-selling on the Airlines does not necessarily indicate an enormous conspiracy of fully clued in conspirators, although it doesn't rule it out either of course. The illicit trading discovered on WTC computers might have all been done in the last few minutes, on lower floors, as people evacuated, betting that the building would be going down. It is not necessarily indicative of a huge conspiracy (although it's consistent with a large conspiracy).
The fact that a simulation nearly exactly mirroring the events of 9/11 were being carried out as an exercise at the same time as the attacks occurred, is not just an implausibility, it is statistically impossible in the common meaning of the word (not in the scientific meaning, however, that requires more evidence). To match the year, day, time, and targets of a unique attack is a one-in-a-thousand coincidence, even assuming there were terrorists around interested in carrying out such a plot, which there weren't. So, given knowledge of the drills of 9/11, your prior confidence in the government being involved should be 999/1000.
A statistical prior can modified with new information, if some group would have taken some responsibility, for example. But Al Qaida condemned the attacks, and claimed they had nothing to do with it. No other group claimed responsibility. The leadership of Al Qaida has never been tied to 9/11, except through alleged information acquired under torture, behind closed doors, and leaked to the press by people selected for their deference to authority.
The Clinton administration also has a terrorist attack which matched and coincided with a drill, the first such event in my memory, which is the Oklahoma City bombing, which coincided with a planned drill as well. So Bush administration officials who knew, or figured it out, could blackmail Clinton officials with complicity in terrorism, preventing Democrats from exposing the plot. For political support, any Democratic insider would have a difficult time trying to tell the truth, since it would open a can of worms which would engulf both parties. Really, the whole thing tarnishes both parties so terribly, that it would be a miracle if they can survive.
What is required is legislation making it illegal, attempted murder really, to have any sort of anti-terrorism drill that involves a simulation of an attack. Israel has never held such a drill, they have more attacks than any other country. These drills are counterproductive, since the events they imagine never turn real. Except, of course, when they do. This is in the case of Oklahoma City, 9/11, The London Bombings of 2005, The Madrid bombings of 2004, the Oslo attacks, the Boston Marathon bombing, and essentially every terror attack in the last 19 years. When attacks coincide with drills, the drills aren't drills at all, but covers for the attacks. In this case, the coordinators of the drills should not be commended for their foresight in anticipating the exact time place and form of the attack, they should be tried for murder.
Pretty sure if you shot a plane down it would splat all over where it crashed and not disappear. I remember a chinese 747 got shot down and soon everyone knew about it. Also, if that was the case what about the 757 parts at the WTC?