According to the official account of 9/11, American Airlines Flight 77--which supposedly crashed into the Pentagon--was hijacked shortly after 8:51 a.m. on September 11, 2001. This claim is so central to the U.S. government's story that we would reasonably expect it to have been proven. Yet a closer analysis of the evidence shows that, in fact, it appears preposterous.
THE TOUGH PILOT
On September 11, 2001, NBC News Pentagon correspondent Jim Miklaszewski was the first reporter at the scene to relay that the Pentagon had been attacked. In a 9:39 a.m. report, he said, "[J]ust a few moments ago ... there was an explosion of some kind here at the Pentagon." After describing what he was seeing and hearing around him, Miklaszewski added: "[I]nterestingly enough, one intelligence official here in the building said [that] when he saw what appeared to be the coordinated attack on the World Trade Center, his advice was to stay away from the outside of the building today, just in case." 
Miklaszewski later described this incident again for a book. He recalled that, while heading down the hallway at the Pentagon, he'd "ran into a Defense official who said he didn't know anything specific about the attack yet. But it was so coordinated, he said, 'If I were you I would stay off the E-ring today, because we're next.'" According to Miklaszewski, this official "had no specific information; that was just his gut instinct." 
As the two entries from the Complete 9/11 Timeline copied below show, several witnesses have recalled seeing large fireballs coming from the bases of each of the Twin Towers when they collapsed on September 11, 2001. From their descriptions, it seems the fireballs erupted at the time the collapses began, or just before.
These accounts are important evidence, strongly refuting official explanations of why the World Trade Center fell. In its final report on the collapses of the Twin Towers, the National Institute of Standards and Technology (NIST) claimed the collapses "initiated at the fire and impact floors," and "progressed from the initiating floors downward." This would mean the collapse began, in the case of the South Tower, around the 78th to 84th floors, and for the North Tower, around the 93rd to 98th floors.
How did President Bush feel about the September 11 attacks? In the following hours, weeks, and months, he repeatedly used one word. While most people no doubt felt that it was an absolute catastrophe, George W. Bush described 9/11--or at least the political climate it had engendered--as an "opportunity." He said this again and again:
September 11, 2001
Hours after the attacks, during a 9:30 p.m. meeting with his key advisers, Bush declared: "This is a great opportunity. We have to think of this as an opportunity." 
Later that evening, he dictated for his diary: "My hope is that this will provide an opportunity for us to rally the world against terrorism." 
September 13, 2001
During an appearance in the White House Oval Office, Bush said: "You know, through the tears of sadness I see an opportunity. ... And now is an opportunity to do generations a favor, by coming together and whipping terrorism." 
During the National Security Council meeting later that day, he said: "This is a new world. ... Start the clock. This is an opportunity. ... I want Afghan options ... I want decisions quick." 
A key element of the official 9/11 story is the phone call Todd Beamer made from United Airlines Flight 93 shortly before it supposedly crashed in rural Pennsylvania. It was at the end of this call that Beamer was heard declaring: "Let's roll," before joining a passenger revolt against the terrorists. Without this now-famous call to battle, 9/11 would arguably have been less effective in motivating the public to get behind the war on terror. By May 2002, the Washington Post reported, Beamer's phrase "Let's roll" had been "Embraced and promoted by President Bush as a patriotic battle cry," and was "now emblazoned on Air Force fighter planes, city firetrucks, school athletic jerseys, and countless T-shirts, baseball caps and souvenir buttons.
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After September 11, 2001: Unlike Previous Incidents, NTSB Does Not Investigate 9/11 Plane Crashes
On September 12, 2001, the commander in chief of the Russian air force, General Anatoly Kornukov, offered his thoughts on the previous day's events: "Generally it is impossible to carry out an act of terror on the scenario which was used in the USA yesterday. ... The notification and control system for the air transport in Russia does not allow uncontrolled flights and leads to immediate reaction of the anti-missile defense. As soon as something like that happens here, I am reported about that right away and in a minute we are all up."  One would assume the defenses of the United States should have been more effective than those of Russia. Yet the 9/11 attacks seem to have proceeded with ease, and America's air defenses appear to have been almost non-existent at the time they were most needed.
It has been established that at the time the 9/11 attacks began, the United States Strategic Command (Stratcom) was in the middle of a major annual training exercise called Global Guardian. Stratcom is responsible for the readiness of America's nuclear forces, and the exercise aimed to test its ability to fight a nuclear war, being described as "one of many practice Armageddons" that the U.S. military routinely conducts. 
Questions arise over whether this exercise impeded the military--particularly the staff at Offutt Air Force Base near Omaha, Nebraska, where Stratcom is headquartered--in its ability to respond to the crisis. Global Guardian was not canceled until after 9:03, when the second WTC tower was hit.  In fact, some accounts suggest it did not end until after 9:37, when the Pentagon was struck.  So could military personnel have mistaken reports of the real attacks for part of the exercise? And might vital resources that could have helped stop the attacks have been unavailable, being used instead for the exercise?
Activists and researchers have long tried to understand how the highly sophisticated U.S. military could have failed so completely to stop the attacks that took place on September 11, 2001. Statements made by several U.S. military personnel who were deeply involved in the crisis response that morning suggest an alarming method that may have been used to sabotage normal defenses. Revealed here for the first time, this is one possible reason that the military was in such a state of paralysis until it was too late to make a difference.
NORAD AND THE NMCC
According to the 9/11 Commission Report, "On 9/11, the defense of U.S. airspace depended on close interaction between two federal agencies: the FAA [Federal Aviation Administration] and the North American Aerospace Defense Command (NORAD)." NORAD in particular is tasked with defending the airspace over North America and protecting the continent. The attacks on 9/11 all took place within its Northeast Air Defense Sector (NEADS), which, according to the 9/11 Commission, was able to call upon two 'alert' military sites for assistance: Otis Air National Guard Base in Cape Cod, Massachusetts and Langley Air Force Base in Hampton, Virginia. Each of these had just one pair of fighter jets at the ready. "Other facilities, not on 'alert,' would need time to arm the fighters and organize crews." 
It is well known within the 9/11 truth community that, on September 11, 2001, the North American Aerospace Defense Command (NORAD) failed appallingly to protect the United States from the attacking aircraft, in the way we would have expected it to. But evidence indicates there were other military departments that could also have played a significant role in stopping the attacks. Yet, like NORAD, these appear to have been in a state of paralysis that morning. They only seem to have become properly active, and able to effectively perform their usual role, when it was too late for them to have made a difference.
Dawdler in chief: The suspicious behavior of George W. Bush during the 9/11 attacks
By Matthew Everett
Online Journal Contributing Writer
Sep 11, 2007
"Sandy Kress, Bush's unpaid education advisor, was puzzled. Bush was always on time. But on the morning of Tuesday, September 11, he seemed to want to linger, talking about politics and mutual friends in Texas."  So wrote Ronald Kessler in his account of the Bush presidency, A Matter of Character. The time in question was around 8:30 a.m., a quarter of an hour after American Airlines Flight 11 had broken communication with air traffic controllers. The 9/11 attacks were now underway. While many odd things took place that morning, Kress's observation highlights another curious detail: On September 11, 2001, President Bush was running late.
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Right after the first World Trade Center tower collapsed, at 9:59 a.m. on September 11, 2001, Father John Delendick--one of New York Fire Department's chaplains--ran down a ramp to below the nearby World Financial Center, so as to escape the dust cloud. There he met with Deputy Chief Ray Downey, the head of the FDNY's Special Operations Command. Delendick asked Downey if the jet fuel from the plane had blown up, thus causing the South Tower to collapse. According to Delendick, Downey "said at that point he thought there were bombs up there because it was too even."