From the History Commons Groups blog:
A large number of new entries have been added to the Complete 9/11 Timeline at History Commons. Most of these describe events from the day of 9/11 itself, although a few entries look at pre-9/11 and post-9/11 events.
One new entry reveals that in April 2001, CIA counterterrorism chief Cofer Black warned that "something big [is] coming and that it very likely could be in the US." Then, about a month before 9/11, White House counterterrorism chief Richard Clarke visited Wall Street, to investigate the security precautions there.
"There were a number of false reports out there. What
was valid? What was a guess? We just didn't know."
- Colonel Robert Marr, battle commander at
NORAD's Northeast Air Defense Sector on 9/11
Although it has been widely reported that four commercial aircraft were hijacked over the United States on September 11, 2001, what is less well known is that while the terrorist attacks were taking place and for many hours after, numerous additional aircraft gave indications that they had been hijacked or, for other reasons, were singled out as potential emergencies. More than 20 aircraft were identified as possible hijackings, according to some accounts, and other aircraft displayed signs of emergencies, such as losing radio communication with air traffic controllers or transmitting a distress signal.
Reports about these false alarms have revealed extraordinary circumstances around some of the incidents and bizarre explanations for how they arose. For example, it has been claimed that the pilots of one foreign aircraft approaching the U.S. set their plane's transponder to transmit a code signaling they had been hijacked simply to show authorities that they were aware of what had been taking place in America that morning.  Another aircraft reported as transmitting a distress signal while approaching the U.S. was subsequently found to have been canceled, and still at the airport. 
There may be innocent explanations for some of the less serious false alarms, such as those simply involving the temporary loss of radio communication with the plane, which is a common occurrence and happens on a daily basis.  But, viewed in its entirety, the evidence appears highly suspicious and raises serious questions. Why, for example, were there so many false alarms on September 11? Why did so many of them involve false reports of hijackings or aircraft falsely signaling that they had been hijacked? The details of specific incidents that have been reported, which I describe below, show that these false alarms must have been something more than just the results of confusion caused by the terrorist attacks.
Army Command Center at the Pentagon Planned to Hold Exercise in Week After 9/11 Based on a Plane Hitting the WTC
Army officers at the Pentagon were planning a training exercise that would take place less than a week after 9/11 and that would, extraordinarily, be based around the scenario of a plane crashing into the World Trade Center. Preparations for the exercise were being made about a week before September 11.
The existence of the planned exercise was revealed by Major General Peter Chiarelli, who on September 11, 2001, was the Army's director of operations, readiness, and mobilization. In that position, which he had moved into about a month before 9/11, Chiarelli was in charge of current operations in the Army Operations Center (AOC) at the Pentagon.
Backup Communications System Was 'Miraculously' Switched on for 'Exercise Mode' and Ready for Use on 9/11
A special backup network that allows communications between government and military agencies to continue during emergencies was "miraculously" switched on the day before 9/11, and so was already operational when the terrorist attacks in New York and at the Pentagon took place. The Special Routing Arrangement Service (SRAS) was, for reasons unknown, turned on for "exercise mode" on September 10, 2001, and was therefore ready to be utilized the following day, when there was a national emergency like that for which it was intended.
The SRAS is the responsibility of a little-known government agency called the National Communications System (NCS), which works to keep critical telecommunications functioning during emergencies and played a crucial role in the government's response to the 9/11 attacks, helping to maintain and restore communications networks. Furthermore, the SRAS is related to "Continuity of Government"--a plan that was activated for the first time during the attacks.
Here is another oddity surrounding the 9/11 attacks. Two new entries in the Complete 9/11 Timeline reveal that a New York air traffic controller mistakenly reported over an FAA teleconference that the first aircraft to crash into the World Trade Center on September 11, 2001 was a helicopter, and this hit the north WTC tower at 8:27 a.m., almost 20 minutes before the attack there actually occurred.
The National Military Command Center (NMCC) is the most secure part of the Pentagon and, at the time of the 9/11 attacks, was "the focal point within [the] Department of Defense for providing assistance" to law enforcement efforts in response to aircraft hijackings in U.S. airspace, according to military instructions.  In response to the attacks on New York and Washington, the job of the NMCC, according to the 9/11 Commission, was "to gather the relevant parties and establish the chain of command between the National Command Authority--the president and the secretary of defense--and those who need to carry out their orders." 
Check out this curious incident relating to the 9/11 attacks. According to a new entry in the Complete 9/11 Timeline, at around 9 p.m. on the evening before 9/11--less than 12 hours before the attacks began--the U.S. military lowered its "Infocon" threat level to the lowest possible level, supposedly because of "reduced fears of attacks on computer networks."
The Infocon system is intended as "a structured, coordinated approach to defend against and react to attacks on Defense Department systems and networks." General Ralph Eberhart, the commander of NORAD, was responsible for issuing Infocons to the US military, and so he was presumably responsible for lowering the Infocon level on September 10. (See my previous blog entry for details of Eberhart's suspicious actions on the day of 9/11 itself.)
The Infocon level was raised again after the second plane hit the World Trade Center on 9/11.
Yet another strange "coincidence."
The 9/11 Time Discrepancy Oddity: Distress Signals Indicated Planes Crashed Minutes BEFORE Flights 11 and 175 Hit the WTC
Radio transmitters that are carried aboard aircraft and that are supposed to activate only in the event of the aircraft crashing went off in the New York area several minutes before the two planes hit the World Trade Center on September 11, 2001. In events that, according to the official account of 9/11, should have been impossible, emergency locator transmitters (ELTs), which are intended to help locate crashed aircraft by broadcasting a distinctive signal, were activated over two minutes before American Airlines Flight 11 hit the north WTC tower and over four minutes before United Airlines Flight 175 hit the South Tower. And yet no ELTs went off at the times these planes hit the towers, when we might have expected them to have been activated.
EMERGENCY TRANSMITTER WENT OFF OVER TWO MINUTES BEFORE FLIGHT 11 CRASHED
'Let's Get Rid of This Goddamn Sim': How NORAD Radar Screens Displayed False Tracks All Through the 9/11 Attacks
Military personnel responsible for defending U.S. airspace had false tracks displayed on their radar screens throughout the entire duration of the 9/11 attacks, as part of the simulation for a training exercise being conducted that day. Technicians at NORAD's Northeast Air Defense Sector (NEADS) were still receiving the simulated radar information around the time the third attack, on the Pentagon, took place. Those at NORAD's operations center in Cheyenne Mountain, Colorado, were still receiving it several minutes after United Airlines Flight 93 apparently crashed in rural Pennsylvania.
No one has investigated why false tracks continued being injected onto NORAD radar screens long after the U.S. military was alerted to the real-world crisis taking place that morning. And yet we surely need to know more about these simulated "inputs" and what effect they had on the military's ability to respond to the 9/11 attacks.
NEADS TECHNICIANS TOLD TO TURN OFF 'SIM SWITCHES'
NORAD Exercise a Year Before 9/11 Simulated a Pilot Trying to Crash a Plane into a New York Skyscraper--The UN Headquarters
The North American Aerospace Defense Command (NORAD) held a major training exercise in October 2000 that included the scenario of a person stealing a large jet plane, which they planned to crash into the United Nations headquarters building--a 39-story high-rise in New York, just a few miles away from the World Trade Center. Furthermore, a NORAD exercise in June that year included one scenario in which a plane was hijacked with the intention of crashing it into the White House, and another in which a transcontinental flight was hijacked with the intention of crashing the plane into the Statue of Liberty, only a short distance from where the WTC stood.
The existence of these exercise scenarios was revealed in August 2004 by General Richard Myers, at that time the chairman of the Joint Chiefs of Staff, during a hearing of the Senate Armed Services Committee. Senator Mark Dayton (D-MN) asked, "Did NORAD"-- the military organization responsible for defending U.S. airspace--"conduct exercises or develop scenarios, prior to September 11, 2001, to test a military reaction to an aircraft hijacking which appeared destined to result in a suicide crash into a high-value target?" In response, Myers outlined "five exercise hijack events" that NORAD had practiced for between November 1999 and October 2000, which all "included a suicide crash into a high-value target."  Yet the details of these chilling scenarios, which were like premonitions of the attacks on New York and Washington that lay ahead, failed to receive the public attention they deserved.
Check out this excellent recent documentary, which has just been posted on the Internet, about Nato's secret armies that were set up across Western Europe after the Second World War. While these "stay-behind" armies were supposedly intended to help put together a resistance if the Soviet Union invaded their countries, they went on to commit terrorist attacks against their own populations, so as to influence domestic politics.
"During those entire 109 minutes ... this country
and its citizens were completely undefended."
- Senator Mark Dayton
The WTC Leaseholder and His Associates That Cheated Death on 9/11: Was it Coincidence or Foreknowledge?
New York real estate developer Larry Silverstein and several key individuals associated with his firm, Silverstein Properties, appear to have had remarkable luck on September 11, 2001, when changes in their schedule or coincidental circumstances saved them from being high up in the World Trade Center when it was attacked.
Several hours after the 9/11 attacks in New York and Washington occurred, a passenger aircraft heading to the U.S. from Seoul, South Korea, was mistakenly considered hijacked. In a little-reported series of events, the pilots of Korean Airlines Flight 85 gave numerous indications that their plane had been taken over by hijackers, even though it had not. KAL 85, a Boeing 747 that had been due to land in Anchorage, Alaska, for a refueling stop, was consequently diverted to an airport in Canada. The military launched fighter jets to tail it and, with authorization from the Canadian prime minister, threatened to shoot the plane down if it refused to change course. Only after KAL 85 landed were officials able to confirm that no hijacking had taken place.
While a person might suggest this crisis was just the result of confusion due to the unprecedented events earlier that day, the number of indications the pilots gave that their plane was hijacked, and their repeated failure to confirm that this was not the case, raises another possibility: Could KAL 85 have been playing the part of a hijacked aircraft in a military training exercise?
On September 11, 2001, Richard Clarke served in the crucial position of national coordinator for security and counterterrorism, and he ran the U.S. government's response to the terrorist attacks from the White House Situation Room. It was not until March 2004, though, that Clarke came to wider attention, when he went public with his complaints about members of the Bush administration, who, he said, ignored the threat posed by al-Qaeda before September 11, despite his attempts at alerting them to it.  Clarke received praise from some quarters for his various criticisms of then-President Bush.
What is little known, however, is that in 1994 Richard Clarke was one of the key individuals responsible for the lack of international response to the genocide in the small African nation of Rwanda, where an estimated 800,000 Rwandans were killed in just 100 days. At the time of the genocide, Clarke was head of the office of global issues and multilateral affairs on the National Security Council, and was therefore in charge of the White House response to Rwanda issues.
CLARKE CLAIMS U.S. 'DID THE RIGHT THING' OVER RWANDA