9-11 why did our intelligence agencies stand down
The Executive Branch
Redaction of threats from the national security brief
George Bush' behavior:
“President George W. Bush reportedly believed, upon hearing that a plane had struck one of the Twin Towers, that it was an accident. It was not terribly strange, therefore, that he decided to go ahead with the photo-op at the school in Sarasota. Word of the second strike, however, should have indicated to him and his Secret Service agents---assuming the truth of official story, according to which these strikes were unexpected---that the country was undergoing an unprecedented terrorist attack. And yet the Secret Service allowed him to remain at the school for another half hour.
“This behavior was very strange. The president’s location had been highly publicized. If the attacks were indeed unexpected, the Secret Service would have had no idea how many planes had been hijacked, and they would have had to assume that the president himself might be one of the targets: What could be more satisfying to foreign terrorists attacking high-value targets in the United States than to kill the president? For all the Secret Service would have known, a hijacked airliner might have been bearing down on the school at that very minute, ready to crash into it, killing the president and everyone else there---including the Secret Service agents themselves. It is, in any case, standard procedure for the Secret Service to rush the president to a safe location whenever there is any sign that he may be in danger. And yet these agents, besides allowing the president to remain in the classroom another 10 minutes, permitted him to speak on television, thereby announcing to the world that he was still at the school.
Dick Cheney's behavior on 9/11 according to Norm Mineta
Former Transportation Secretary Norman Mineta answered questions from members of 9/11 Truth Seattle.org about his testimony before the 9/11 Commission report.
Mineta says Vice President Cheney was "absolutely" already there when he arrived at approximately 9:25 a.m. in the PEOC (Presidential Emergency Operations Center) bunker on the morning of 9/11. Mineta seemed shocked to learn that the 9/11 Commission Report claimed Cheney had not arrived there until 9:58-- after the Pentagon had been hit, a report that Mineta definitively contradicted.
Norman Mineta revealed that Lynn Cheney was also in the PEOC bunker already at the time of his arrival, along with a number of other staff.
Donald Rumsfeld's behaviour:
I haven't yet been able to get something concise on Rumsfeld so you will have to look at this link, but his behavior was equally bizarre:
Drake sounded the alarm, continuing to push for THINTHREAD use even after all its developers left the NSA in October 2011. In his steady support for the discarded program, he found out how much actionable intelligence the NSA had legally gathered that could have thwarted the 9/11 attacks, he says.
Upon being asked to prepare a report at the request of Congress on the NSA’s knowledge of the 9/11 plot and hijackers before September 11, 2001, Drake says the agency decided to balk at taking any responsibility.
“After a couple of weeks [SIGINT chief Maureen] Baginski rejected my draft team Statement for the Record report and removed me from the task,” Drake writes. “When I asked her why, she said there was a ‘data integrity problem’ (not further explained) with my draft Statement for the Record. I had come upon additional damaging revelations. For example, NSA had the content of telephone calls between AA-77 hijacker Khalid al-Mihdhar in San Diego, CA, and the known al-Qaeda safe house switchboard in Yemen well before 9/11, and had not disseminated that information beyond NSA.”
“In short, when confronted with the prospect of fessing up, NSA chose instead to obstruct the 9/11 congressional investigation, play dumb, and keep the truth buried, including the fact that it knew about all inbound and outbound calls to the safe house switchboard in Yemen. NSA’s senior leaders took me off the task because they realized – belatedly, for some reason – that I would not take part in covering up the truth about how much NSA knew but did not share.”
From my own studies it seems they wanted an attack to go through, so they could into high gear the ideas of the "Project for a New American Century" which in 1998 called for a "New Pearl Harbor" to allow this agenda to go forward.
This is different from a conspiracy that deliberately facilitated 9-11, it was rather a relaxation of security to provoke an attack which could be used to fulfill the "neo-con" agenda, for lack of time to flesh out what this means. It is also known that Rumsfeld wanted a full attack of Iraq prior to 9-11.
Abstract: I don't know if you are aware of this, but whistle blowers up to and including former Senate Chair of the 9-11 committee Bob Graham complained all reports of middle eastern terrorism plots were ignored by the leadership of the intelligence agencies.
THE CIA and DoD
Update: Richard Clarke, who was the White House counterterrorism czar beginning in 1998 and through 9/11, told ProPublica that the NSA had both the ability and legal authority to trace calls from Mihdhar to Yemen in 2000.
“Justice could have asked the FISA Court for a warrant to all phone companies to show all calls from the U.S. which went to the Yemen number. As far as I know, they did not do so. They could have,” Clarke wrote in an email. “My understanding is that they did not need the current All Calls Data Base FISA warrant to get the information they needed. Since they had one end of the calls (the Yemen number), all they had to do was ask for any call connecting to it.”
"Set up" to fail
The two co-chairs of the Commission, Thomas Kean and Lee Hamilton, believe that the government established the Commission in a way that ensured that it would fail. In their book Without Precedent: The Inside Story of the 9/11 Commission describing their experience serving, Hamilton listed a number of reasons for reaching this conclusion, including: the late establishment of the Commission and the very short deadline imposed on its work; the insufficient funds (3 million dollars), initially allocated for conducting such an extensive investigation (later the Commission requested additional funds but received only a fraction of the funds requested and the chairs still felt hamstrung); the many politicians who opposed the establishment of the Commission; the continuing resistance and opposition to the work of the Commission by many politicians, particularly those who did not wish to be blamed for any of what happened; the deception of the Commission by various key government agencies, including the Department of Defense, NORAD and the FAA; and, the denial of access by various agencies to documents and witnesses. "So there were all kinds of reasons we thought we were set up to fail."
On Drills occurring on 9/11 -
Prosecuting whistleblowers under the espionage act:
Espionage is very narrowly defined. To perform espionage their are two criteria:
1. You must be an agent of a foreign power.
2. Failing that, you must be seeking financial gain. (Selling state secrets).
If a person reveals classified information, but is not an agent of a foreign power, nor is seeking to profit from the sale of state secrets, the word espionage cannot be applied. They could be charged with other offenses, but not espionage, and the espionage act states as much. Read the language of the espionage act, and the definition of espionage, and see that this statute is being misapplied.
After the September 11, 2001, attacks, Rowley wrote a paper for FBI Director Robert Mueller documenting how FBI HQ personnel in Washington, D.C., had mishandled and failed to take action on information provided by the Minneapolis, MinnesotaField Office regarding its investigation of suspected terrorist Zacarias Moussaoui. Moussaoui had been suspected of being involved in preparations for a suicide-hijacking similar to the December 1994 "Eiffel Tower" hijacking of Air France 8969. Failures identified by Rowley may have left the U.S. vulnerable to the September 11, 2001, attacks. Rowley was one of many agents frustrated by the events that led up to the attacks, writing:
During the early aftermath of September 11th, when I happened to be recounting the pre–September 11th events concerning the Moussaoui investigation to other FBI personnel in other divisions or in FBIHQ, almost everyone's first question was "Why?--Why would an FBI agent(s) deliberately sabotage a case? (I know I shouldn't be flippant about this, but jokes were actually made that the key FBI HQ personnel had to be spies or moles, like (Robert Hanssen), who were actually working for Osama Bin Laden to have so undercut Minneapolis's effort.) 
"On 1 February 2011, Edmonds published a story on her own website, adding details of events she described as taking place in April 2001. The account centered around her post-9/11 role as translator of a pre-9/11 interview during which an informant had told the FBI agents:
Bin Laden’s group is planning a massive terrorist attack in the United States. The order has been issued. They are targeting major cities, big metropolitan cities; they think four or five cities; New York City, Chicago, Washington DC, and San Francisco; possibly Los Angeles or Las Vegas. They will use airplanes to carry out the attacks. They said that some of the individuals involved in carrying this out are already in the United States. They are here in the U.S.; living among us, and I believe some in US government already know about all of this.
The agents, along with Edmonds, reported this information internally at the FBI but, according to Edmonds, no one at the bureau ever asked for follow-ups or further information prior to 9/11."
From: 5:10 in http://www.youtube.com/watch?v=7pTBJmWVXhA interview with Abby Martin:
Q. [Abby Martin] Do you think the government purposefully ignored intelligence because they wanted 9-11 to happen?
A. [Sybel Edmonds] "Absolutely. Certain elements within our Government absolutely intentionally purposefully ignored and let it happen"
Senator Bob Graham