From the History Commons Groups blog:

A large number of entries have been added to the Complete 9/11 Timeline at History Commons. Most of these focus on the events of September 11, 2001, including the actions of White House personnel in response to the terrorist attacks that day, and a number of apparent threats to President Bush and his plane, Air Force One.

White House Officials Visited Emergency Bunker during Exercise

A new timeline entry describes a training exercise held shortly before 9/11 in which some senior White House staffers were shown to the Presidential Emergency Operations Center (PEOC), a bunker below the White House where numerous government officials went on September 11. Following the first attack on September 11, Josh Bolten, the deputy White House chief of staff, was called by a former member of the Clinton administration who wanted to check that he was aware of the PEOC.

Bolten, according to his own recollection, alerted National Security Adviser Condoleezza Rice to the second crash at the World Trade Center after seeing coverage of it on television. Later on, he headed to the PEOC where he joined Vice President Dick Cheney and other government officials.

Also early on the morning of September 11, a sheriff in Sarasota, Florida, was surprised to find that when he contacted colleagues who were with President Bush's Secret Service detail, shortly after he saw the TV reports of the first crash at the WTC, those colleagues were unaware of what had happened in New York.

From the History Commons Groups blog:

A large number of entries have been added to the Complete 9/11 Timeline at History Commons, most off which provide new details about the events of the day of September 11, 2001.

One new timeline entry describes a training exercise based on the scenario of a possible terrorist attack that was run on the morning of September 11 by the US Coast Guard in Tampa Bay, Florida, quite close to Sarasota, where the president was at the time. Another entry deals with a meeting scheduled to take place at the Pentagon that morning, regarding a planned "disaster exercise" at the nearby Navy Annex building.

An entry reveals that a number of FBI agents had, for reasons that are unknown, already arrived at the Navy Annex when the Pentagon was hit. Later on, the Navy set up a new command center at the Navy Annex, after its original command center was destroyed in the Pentagon attack.

Several entries describe the futile attempts of intelligence officers at NORAD's Northeast Air Defense Sector (NEADS) to obtain information about the first hijacking. After learning of the hijacking, a NEADS intelligence officer called the FBI's Strategic Information and Operations Center and the National Military Joint Intelligence Center at the Pentagon, but neither of them could provide any information. Searches on the SIPRNET--the US military Internet system--also revealed nothing. Furthermore, the threat briefing at NEADS that morning had included no indication of an increase in the terrorist threat level.

Some NEADS personnel have said they were monitoring Flight 93 long before the time at which the 9/11 Commission concluded the military was first alerted to this hijacked aircraft. Also, a commander at NEADS complained that an officer from the NEADS battle cab had come down to the operations floor, where he had been "circumventing my system." What is more, NEADS personnel only learned that the president's plane, Air Force One, was airborne about half an hour after it took off from Sarasota.

The only thing I have read about this strange event that asked the right question was on wsws.org, one of my favorite sites. Alex Lantier wrote on April 29:

How could one of two specially-designed presidential jets be requisitioned for a flight over New York City, where nearly 3,000 were killed in the 9/11 attacks, without the knowledge of the president, the mayor or high-ranking US military officials such as the defense secretary and the joint chiefs of staff? If the official story is indeed true, it raises the question of who is in control of the US military.

The White House internal review published a week later, I think, answers the question: the US military is in control of the US military.

...Read more at http://www.mdmorrissey.info/flyover

The Associated Press reports that a White House internal investigation has released the findings of an internal investigation into the recent incident involving a low-flying Air Force One over New York City; and that, in consequence of the 'embarassing incident,' Louis Caldera of the White House Military Office has submitted his resignation, effectively accepting the blame:

------------------------------------------
(Excerpts)

WASHINGTON – The White House official who authorized a $328,835 photo-op of Air Force One soaring above New York City resigned under fire Friday as the administration tried to move past the embarrassing incident that sent panicked workers rushing into the streets amid flashbacks of Sept. 11.

As former Army Secretary Louis Caldera took the fall for the flyover, the White House released the findings of an internal investigation that portrayed him as out of the loop in a cycle of missed messages and questionable judgments as plans for the photo shoot proceeded.

http://www.wsws.org/articles/2009/apr2009/over-a29.shtml
From wsws.org, by Alex Lantier
29 April 2009

On the morning of April 27, one of two Boeing 747 jetliners used by the US president flew at low altitude over downtown New York, escorted by fighter jets. The official explanations and media commentaries concerning this extraordinary event raise more questions than they answer.

For half an hour the planes banked over the city, passing the Statue of Liberty, Lower Manhattan and the former site of the World Trade Center, where two jetliners crashed into the Twin Towers on September 11, 2001. CNN and YouTube videos show the planes passing only a few hundred feet above the New York skyline.

President Barack Obama was not on board the 747.

Residents and passers-by ran for cover, fearing that another terrorist attack might be in progress.

According to unnamed military and administration sources cited in the Wall Street Journal, the flight was a “secret” photo-op, of which only select officials at the Federal Aviation Administration (FAA), the White House, the New York Police Department and New York City Hall had advance knowledge.

From Slashdot:

"A Boeing 747 that serves as an Air Force One backup and two F-16 fighters escorting it caused a brief panic among office workers at the World Financial Center in lower Manhattan this morning, as large numbers evacuated the buildings. The incident was also spurred evacuations in Jersey City across the Hudson River from Manhattan."

Two F-16 fighters seems incorrect: the photos and the reports indicate only one. However, who ever thought this "photo op" was a good idea? I can't possibly imagine that the ensuing panic and bad press was unforeseeable. Is this just a cock-up? If it is, it's a real bad one.

Some pictures: (for the bottom one, ripped the link from the WSJ Flash slideshow for your convenience)

Today's conspiracies were yesterday's facts on the ground
Part III
William Safire hinted White House “mole” may have aided 9-11 terrorists

By Peter Duveen

PETER'S NEW YORK, Jan. 5, 2009—The discovery in my personal archives of issues of The New York Times and the New York Post from the days immediately following September 11, 2001 has become the basis for a several-part series on early reportage of the events of that day. The use of the original issues as opposed to electronic media has the advantage of easy reference, and absolute reliability regarding the source. This third essay will explore the remarkable drama surrounding the activities of President George W. Bush on that fateful day. We find that once New York Times columnist William Safire came into possession of the facts related to Bush’s 10-hour absence from Washington, he concluded that a “mole” in the White House may have cooperated with the 9-11 terrorists. He is thus joined at the hip with Robert Novak, who came to a similar conclusion in his column of the same day.

The Three Amigos on 9/11
New examination of Bush, Cheney, Rumsfeld whereabouts on 9/11 turns up many troubling questions

James Corbett
The Corbett Report
5 June, 2008

The Corbett Report has just released the final installment in a three-part YouTube documentary series seeking to highlight some of the bizarre facts surrounding the movements and whereabouts of President Bush, Vice President Cheney and Secretary of Defense Rumsfeld on the day of 9/11. The three videos can be watched in the players below.

Where Was Rumsfeld on 9/11?