If you have watched David Ray Griffin's speech on CSPAN, the first question most people ask is how could such a large conspiracy be true?

Think about these points:

Why haven't there been leaks or top leaders questioning the administrations story?
The pentagon is under military control. Easy for them to keep most of the occupants busy doing something else. Daschle and Leahy as well as some representatives were speaking out for a full investigation. Both Bush and Cheney called Daschle and told him not to persue it. Shortly after that, we had the anthrax scare with letters addressed to Daschle, Leahy, Brokaw and the NewYork Post (those that were speaking out against the administration). That investigation never went very far either. Best I can tell it was traced to a US lab and that is when investigation stopped.
http://www.fbi.gov/pressrel/pressrel01/102301.htm

There was also Dr. David Kelly, a weapons inspector in Europe that was speaking out against the WMD claim. He was heard saying if Bush attacked Iraq, he would probably be found dead in the forest somewhere. Shortly later, he went for his daily walk and "commited suicide". Judge Lord Hutton (not the medical examiner) said there was no need for an investigation into the incident.
http://news.bbc.co.uk/1/hi/in_depth/uk/2003/david_kelly_inquiry/default.stm

Bush and Cheney refused to give their story to the 9/11 commission and the report doesn't address any evidence as to who caused the 9/11 tragedy or what Bush or Cheney said. It is hard to prove someone is lying when they don't even give you one story to check.

Project for the New American Century (PNAC)
The key people in the administration (Dick Cheney, Paul Wolfowitz, Donnald Rumsfield, I. Lewis Libby, John Bolton, etc.) through a group called Project for the New American Century produced a document in the late 1990s called "Rebuilding Americas Defences". In short, this document describes their plans for Americas world domination. This document stated four major goals:

• Homeland Defense. (Homeland Security)
• Two wars at once. (We now have Afghanistan and Iraq)
• Constabulary duties (America taking on the duties of the UN and NATO)
• Transforming US Forces (permanent bases in the Middle East and development of new nuclear weapons).

One telling paragraph of the PNAC document shows the groups intentions before Bush was even elected to office (emphasis added):

"...the process of transformation, even if it brings revolutionary change, is likely to be a long one, absent some catastrophic and catalyzing event – like a new Pearl Harbor. Domestic politics and industrial policy will shape the pace and content of transformation as much as the requirements of current missions."

9/11 Report
The 9/11 commission report does not provide any evidence as to who attacked us but just assumes it was Bin Ladin and Al Queda as we were first told. The NTSB was not allowed to investigate the four airplane incidents and the crash sites were cleaned up very quickly (ntsb report site - enter 9/11/2001 for start and end dates). Notice that the number of passengers on 3 of the 4 flights were only 65 or fewer passengers (unusual for a pre-9/11 flight on a 757 or 767 to be that empty).

Blame for the 9/11 attacks and Iraq's lack of WMD on inteligence errors. Now it has been shown that John Bolton picked inteligence to support his claims and if someone disagreed or challenged him, he would fight to get that person removed (up to 5 levels below him). Now the adminstration is trying to get him appointed to the possition of ambasador to the UN (remember one of PNACs goal was to dismantle the UN?).

Summary
If you look at the administrations story of 9/11 and world politics, it looks like they are making a lot of mistakes. If you follow this theory, they haven't made any mistakes and they are still on plan.

CNNs pictures of the attack on the pentagon.

Snopes analysis of the "conspiracy theory". They try to explain many of the unanswered questions, but their analysis does not add up. There are still no pictures of wings sheered off or cracks in the building where they penetrated the exterior.

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