In ongoing research into the Pentagon attack the following peer-reviewed paper has now been published at the Journal of 9/11 Studies:

“The Pentagon Attack: Problems with Theories Alternative to Large Plane Impact” by John D. Wyndham.
http://www.journalof911studies.com/volume/2010/Wyndham1.pdf

As stated in the abstract, this paper shows that, of all the theories about what caused the damage and debris at the Pentagon on 9/11, a large plane impacting the Pentagon is in best accord with the majority eye witness testimony and main physical evidence, and is by far the most plausible theory. The failure of the 9/11 truth movement to reach consensus on this issue after almost a decade is largely due to a failure to rigorously apply the scientific method to each proposed theory.

This work is supported by recent papers by Frank Legge and David Chandler:
http://stj911.org/legge/Legge_Chandler_NOC_Refutation.html
http://www.foreignpolicyjournal.com/2011/12/27/addendum-to-the-paper-refuting-the-pentagon-flyover-hypothesis/

David Chandler and I have now published an Addendum to our paper "The Pentagon Attack on 9/11:
A Refutation of the Pentagon Flyover Hypothesis Based on Analysis of the Flight Path"
http://stj911.org/legge/Legge_Chandler_NOC_Refutation.html

The Addendum draws on two additional pieces of evidence to revise the calculations of bank angle and wing loading which would be required if the plane followed the curved path north of the Citgo service station. This strengthens the previous conclusions set out in the original paper. Previously the failure of the many witnesses to mention a steep bank was taken as proof that the curved path did not happen, while the survival of the aircraft, if it deviated round the service station, was regarded as unlikely. With this new analysis of the witness testimony, showing the plane was flying wings level near the Naval Annex, survival of the plane is now found to be absolutely impossible. There is thus no rational explanation of the event other than that the plane flew virtually straight past the Naval Annex and the service station to the impact point.

From Kevin Ryan's Blog:

http://digwithin.net/2011/12/04/gofer-and-trout-questions-on-two-flights-out-of-andrews-afb-on-911/

Gofer and Trout: Questions on Two Flights Out of Andrews AFB on 9/11

Due to the incredible number of coincidences proposed by the official reports on the events of September 11, 2001, it makes good sense for citizens to question any improbable claims related to that day.  We have been given at least two such odd stories about flights that left Andrews Air Force Base that morning.  One represents a highly improbable flight path and the other has produced a contradiction in official accounts.

The first of these flights concerns a large military cargo plane, a C-130H, called Gofer 06.  This plane was from the 133rd airlift wing of the Minnesota Air National Guard.  The 9/11 Commission Report claims that the Gofer 06 pilot and crew were first-hand witnesses to the demise of both Flight 77 and Flight 93.

It was said that the C-130H pilot, Lt. Col Steve O’Brien, was returning from delivering supplies to the Carribean, which more specifically meant the U.S. Virgin Islands.  Air Force Magazine recently reported that seven other crew members were on board, including copilot Maj. Robert Schumacher and flight engineer MSgt Jeff Rosenthal.[i]

The official timeline of this improbable flight begins as follows:  Just after 09:30, Gofer 06 took off from Andrews AFB and Flight 77 flew “right in front of [it], a mile and a half, two miles away.”[ii]  Air traffic controllers (ATCs) from Reagan National Airport (in Arlington, VA) asked the C-130H pilot to identify and follow the “suspicious aircraft.”[iii] According to the Commission report, Gofer 06 identified the aircraft as a Boeing 757 and, seconds after impact, Lt. Col. O’Brien said — “it looks like that aircraft crashed into the Pentagon, sir.”  In the recent Air Force Magazine article, Rosenthal claims that – ”We saw it crash into the Pentagon.”

"Do the orders still stand?" -- Military aide to Vice President Navy Capt. Douglas Cochrane

Was there a stand down on 9-11? In a sense yes, but there is no evidence that a stand down order was issued. There would be no reason for VP Cheney to issue a stand down order, since he issuing a shoot down order, would have the same effect. I will proceed to show this as a fact along with the disturbing fact that the President of the United States, and the Secretary of Defense, both deserted their posts in a time of war. These two individuals who are the only ones authorized to issue shoot down orders of civilian aircraft, created the stand down, by deserting their posts, and then further disgraced themselves, and their offices, by lying to the American people.

"On September the 11th, enemies of freedom committed an act of war against our country." - Pres G Bush
http://www.americanrhetoric.com/speeches/gwbush911jointsessionspeech.htm

First - the players involved:

Condoleezza Rice -- National Security Adviser
Dick Cheney -- Vice President of the United States
Donald Rumsfeld - Secretary of Defense
George W Bush - President of the United States

The 2nd U.S. Circuit Court of Appeals imposed sanctions and penalties against attorneys involved in bringing forward a 9/11 Truther lawsuit, specifically for frivolous and vexatious appeals and motions. The suit, originally filed by a survivor of the Pentagon attack, accuses various U.S. leaders of conspiring to arrange the September 11 attacks. In addition to learning how hard it can be to convince a court of controversial subject matter, the lawyers discovered something more fundamental: If you’re upset that the judges on a federal circuit panel aren’t buying into your conspiracy theories, it might be wise to refrain from making bold accusations regarding their professionalism in your subsequent submissions—as it turns out, judges do read them and can be rather unamused.

http://cryptome.org/info/fbi-pentagon/fbi-pentagon.htm

Also, http://911datasets.org/index.php/PENTAGON_FBI_FOIPA_1141552 has images and video that the FBI released.

.
The Pentagon Attack on 9/11: A Refutation of the Pentagon Flyover Hypothesis Based on Analysis of the Flight Path

Frank Legge
(B.Sc., Ph.D., Chemistry)
and
David Chandler
(B.S. Physics, M.S.,Mathematics)

September 2011

Introduction

The legal and political implications of 9/11 have turned scientific research in this area into a high stakes competition for the minds of the public. Pertinent information has been kept secret, the corporate media has systematically kept "damaging" information (such as video images of the World Trade Center Building 7) out of public view, 9/11 research has been marginalized, and the official investigations have failed to answer, or in many cases even address, the most troubling questions. One development that appears to be a tactic in the ongoing cover-up is the high profile promotion of transparently false theories, "straw men," the only purpose of which appears to be to allow the 9/11 Truth Movement to be ridiculed.

Your support is needed for our appeal of a recent ruling by the U.S. District Court of Nevada which erroneously blocked access to responsive records from the FBI regarding the Pentagon attack and the cockpit voice recording from United Airlines flight 93. An attorney specializing in the Freedom of Information Act (FOIA) is representing the plaintiff in this case at a reduced public interest rate. Funds will be applied to appeal court filing fees, the creation of required appeal briefs, and attorney travel expenses to the hearing to provide in-person oral arguments before the U.S. 9th Circuit Court of Appeals in San Francisco, California in this matter.

Unfortunately, the legal services being provided cannot continue beyond what can be paid for. Please donate today so that this extensive effort to obtain long awaited 9/11 information can be completed.

Washington's Blog

A whistleblower using the alias "Iron Man" was the head of a special joint military-intelligence operation called DO5, a branch of the Joint Forces Intelligence Command, alleges that his team knew that the World Trade Centers and Pentagon were likely targets of Al Qaeda, and that he ran this information up the chain of command.

As Truth-out reports:

"I kept the original classifications on the slides, as historical documents, although the fact that al-Qa'ida was likely to attack the World Trade Center and the Pentagon was clearly no longer classified" ...

Iron Man further elaborated on this point by stating that high-level DoD officials held discussions about DO5's intelligence activities between the summer of 2000 and June 2001 revolving around al-Qaeda's interest in striking the Pentagon, the World Trade Center (WTC), and other targets.

In other words, the Bush administration was fully aware the terrorist organization had set its sights on those structures prior to 9/11 and, apparently, government officials failed to act on those warnings.

A mysterious helicopter was seen flying near the Pentagon in the minutes before the attack there on September 11, 2001. Several witnesses have described seeing the helicopter, which circled the Pentagon and then apparently landed for a brief period on the helipad, near where the building was subsequently hit. It then flew off very shortly before the attack took place. And yet there has never been any public acknowledgement of this incident, or any official explanation of what the helicopter was doing at the Pentagon at that time.

While interviewing one of the witnesses to the incident, however, a Navy historian revealed that the helicopter belonged to the United States Park Police, and, the historian said, had been instructed to intercept the aircraft that was on a crash-course for the Pentagon.

As the aircraft attacks of September 11, 2001 unfolded at the World Trade Center (WTC) and Pentagon buildings, maximum and near maximum augmented GPS positioning quality for the entire daylight period was provided to the geographic coordinates for the World Trade Center in New York City and the Pentagon in Arlington, VA. Based on output graphs generated by Trimble’s free and highly regarded downloadable GPS planning software [1], which utilizes GPS “almanac” data transmitted by the GPS constellation on September 11, 2001 and now archived at the website for the United States Coast Guard [2], conditions such as GPS satellite visibility and geometric “dilution of precision” are both shown to be at maximum or within minutes of maximum during the aircraft impacts at the World Trade Center and Pentagon. Such augmented GPS service is now in routine use by the U.S. commercial aviation industry to allow aircraft flight management computers to utilize precise aircraft positional information, accurate to within just several meters. This GPS service was activated on a conditional basis by the FAA just one year before the September 11, 2001 attacks [3]. This service provided virtual aerial guidance corridors only 243 feet wide and a 95% confidence that an aircraft's true position will fall within any such designed corridor. The augmented GPS service was also utilized to precisely survey the Ground Zero site immediately after September 11, 2001. [4] Such corridors can be navigated entirely by autopilot and flight management systems scheduled in 1996 and 1998 to be contained by United and American airlines Boeing 757 and 767 aircraft like those used during the terrorist attacks of September 11, 2001.

Real-Time Raid Hoax Exposed As Photo Op
http://wearechangenewjersey.com/?p=1426

http://content.usatoday.com/communities/ondeadline/post/2011/05/panetta-obama-did-not-see-bin-laden-being-killed/1
Panetta: Obama did not see bin Laden being killed
May 03, 2011
By Michael Winter

In an interview with the PBS NewsHour, CIA Director Leon Panetta said that although President Obama was watching some "real-time aspects" of the raid on Osama bin Laden's compound, he did not see the al-Qaeda leader being killed.

Here's part of the exchange with Jim Lehrer:

JIM LEHRER: Did you have access to video of what was actually happening in the compound, etc.?

LEON PANETTA: We had live-time intelligence information that we were dealing with during the operation itself.

JIM LEHRER: Did you actually see - or did you actually see Osama bin Laden get shot?

http://wearechangenewjersey.com/?p=1409

http://www.ibtimes.com/articles/140099/20110502/osama-bin-laden-never-charged-for-911-inside-job-likely-wtc7.htm
Osama Bin Laden never charged for 911 – Inside Job likely
May 2, 2011

Osama Bin Laden’s death is being celebrated, and everyone seems to repeat the old conspiracy theory that he was indeed the mastermind behind the terror attacks of 9/11. But that was never proven, and there is not even evidence hinting at such a connection according to the FBI. It is very well possible that completely different organizations than al-Qaeda were responsible for the planning and execution of 9/11, and that the latter was merely one of the involved parties.

Another in a series of warships "honoring" 9/11 is christened into action.

From the Mississippi Sun Herald:

The third in a series of U.S. Navy amphibious assault vessels named in honor of the victims of the 9/11 terrorist attacks [was] christened Saturday, and a key responder at the Pentagon nearly a decade ago is bringing the heroics of his fellow emergency workers with him.

The future USS Arlington is being built at the Northrop Grumman Corp. shipyard in Pascagoula. It's named in honor of Arlington County, Va., where American Airlines Flight 77 crashed into the Pentagon on Sept. 11, 2001, killing 184 people, after being hijacked en route from Washington-Dulles International Airport to Los Angeles.

The ship's sponsor is Joyce Rumsfeld, wife of former Secretary of Defense Donald Rumsfeld, who was in the Pentagon on the day of the attack.

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.