At the Bureau’s training ground in Quantico, Virginia, agents are shown a chart contending that the more “devout” a Muslim, the more likely he is to be “violent.” Those destructive tendencies cannot be reversed, an FBI instructional presentation adds: “Any war against non-believers is justified” under Muslim law; a “moderating process cannot happen if the Koran continues to be regarded as the unalterable word of Allah.”

These are excerpts from dozens of pages of recent FBI training material on Islam that Danger Room has acquired. In them, the Constitutionally protected religious faith of millions of Americans is portrayed as an indicator of terrorist activity.

“There may not be a ‘radical’ threat as much as it is simply a normal assertion of the orthodox ideology,” one FBI presentation notes. “The strategic themes animating these Islamic values are not fringe; they are main stream.”

The FBI isn’t just treading on thin legal ice by portraying ordinary, observant Americans as terrorists-in-waiting, former counterterrorism agents say. It’s also playing into al-Qaida’s hands.

Focusing on the religious behavior of American citizens instead of proven indicators of criminal activity like stockpiling guns or using shady financing makes it more likely that the FBI will miss the real warning signs of terrorism. And depicting Islam as inseparable from political violence is exactly the narrative al-Qaida spins — as is the related idea that America and Islam are necessarily in conflict. That’s why FBI whistleblowers provided Danger Room with these materials.

Over the past few years, American Muslim civil rights groups have raised alarm about increased FBI and police presence in Islamic community centers and mosques, fearing that their lawful behavior is being targeted under the broad brush of counterterrorism. The documents may help explain the heavy scrutiny.

They certainly aren’t the first time the FBI has portrayed Muslims in a negative light during Bureau training sessions. As Danger Room reported in July, the FBI’s Training Division has included anti-Islam books, and materials that claim Islam “transforms [a] country’s culture into 7th-century Arabian ways.” When Danger Room confronted the FBI with that material, an official statement issued to us claimed, “The presentation in question was a rudimentary version used for a limited time that has since been replaced.”

But these documents aren’t relics from an earlier era. One of these briefings, titled “Strategic Themes and Drivers in Islamic Law,” took place on March 21.

The Islam briefings are elective, not mandatory. “A disclaimer accompanied the presentation stating that the views expressed are those of the author and do not necessarily reflect the views of the U.S. government,” FBI spokesman Christopher Allen tells Danger Room.

“The training materials in question were delivered as Stage Two training to counterterrorism-designated agents,” Allen adds. “This training was largely derived from a variety of open source publications and includes the opinion of the analyst that developed the lesson block.”

Not all counterterrorism veterans consider the briefings so benign. “Teaching counterterrorism operatives about obscure aspects of Islam,” says Robert McFadden, who recently retired as one of the Navy Criminal Investigative Service’s al-Qaida-hunters, “without context, without objectivity, and without covering other non-religious drivers of dangerous behavior is no way to stop actual terrorists.”

Still, at Quantico, the alleged connection between Islam and violence isn’t just stipulated. It’s literally graphed.

What’s more, the Islamic “insurgency” is all-encompassing and insidious. In addition to outright combat, its “techniques” include “immigration” and “law suits.” So if a Muslim wishes to become an American or sues the FBI for harassment, it’s all just part of the jihad.

On Tuesday, the leaders of the Senate Committee on Homeland Security, Joe Lieberman (I-Connecticut) and Susan Collins (R-Maine), warned that law enforcement lacks “meaningful standards” to prevent anti-Islam material from seeping into counterterrorism training. Some FBI veterans suspect the increased pressure on American Muslims has a lot to do with the kind of training that Quantico offers.

“Seeing the materials FBI agents are being trained with certainly helps explain why we’ve seen so many inappropriate FBI surveillance operations broadly targeting the Muslim-American community, from infiltrating mosques with agents provocateur to racial- and ethnic-mapping programs,” Mike German, a former FBI agent now with the American Civil Liberties Union, tells Danger Room after being shown the documents. ”Biased police training can only result in biased policing.” (Full disclosure: This reporter’s wife works for the ACLU.)

The chief of the Training Division, Assistant FBI Director Thomas Browne, came into his current job in January. His official biography lists no terrorism expertise beyond serving as a coordinator for a bureau “Domestic Terrorism Program” in Tennessee sometime in the last decade.

It is unclear what vetting process the FBI used to approve these briefings; if any Muslim scholars contributed to them; and what criteria Quantico uses to determine Islamic expertise. “The development of effective training is a constantly evolving process,” says FBI spokesman Allen. “Sometimes the training is adapted for long-term use. This particular training segment was delivered a single time and not used since.”

Several of these briefings were the work of a single author: an FBI intelligence analyst named William Gawthrop. In 2006, before he joined the Bureau, he gave an interview to the website WorldNetDaily, and discussed some of the themes that made it into his briefings, years later. The Prophet “Muhammad’s mindset is a source for terrorism,” Gawthrop told the website, which would later distinguish itself as a leader of the “birther” movement, a conspiracy theory that denies President Obama’s American citizenship.

At the time, Gawthrop’s major suggestion for waging the war on terrorism was to attack what he called “soft spots” in Islamic faith that might “induce a deteriorating cascade effect upon the target.” That is, to discredit Islam itself and cause Muslims to abandon their religion. “Critical vulnerabilities of the Koran, for example, are that it was uttered by a mortal,” he said. Alas, he lamented, he faced the bureaucratic obstacle of official Washington’s “political taboo of linking Islamic violence to the religion of Islam,” according to the website.

Back then, however, Gawthrop didn’t work for the FBI. He had recently stepped down from a position with the Defense Department’s Counterintelligence Field Activity. That agency came under withering criticism during the Bush administration for keeping a database about threats to military bases that included reports on peaceful antiwar protesters and dovish Church groups. It is unclear how Gawthrop came to work for the FBI.

Through an intermediary, Gawthrop told Danger Room that he was unavailable for comment before our deadline.

The FBI didn’t always conflate terrorism with Islam. “I never saw that,” says Ali Soufan, one of the FBI’s most distinguished counterterrorism agents and author of the new memoir The Black Banners, who retired from the bureau in 2005. “Sometimes, toward the end of my time, I started noticing it with different entities outside the FBI. You started feeling like they had a problem with Islam-as-Islam, because of the media. But that was a few people, and was usually hidden behind closed doors.”

Soufan, a Muslim, has interrogated members of al-Qaida and contributed to rolling up one of its cells in Yemen after 9/11. But by the logic of the FBI’s training materials, Soufan’s religious practices make him a potential terrorist.

McFadden, the former NCIS counterterrorist, has a lot of respect for his FBI colleagues, who he believes are ill-served by these Islam briefings. “These are earnest special agents and police officers who want to know how do their job better,” McFadden says.

Too often, McFadden says, counterterrorism training becomes simultaneously over-broad and ignorant. “Instead of looking for indicators of nefarious behavior, you have a sweeping generalization of things like, for instance, the Hawala system,” McFadden explains. “It’s a system that most of the developing world and expatriates from it use to move money around, including terrorists. But you can’t say the whole hawala system is about terrorism, just like you can’t say that Islam as a whole has anything to do with bad behavior.”

McFadden, a Catholic, believes that obsessing over obscure Koranic verses is as useful a guide to terrorist behavior as “diving into the rite of exorcism” is to understanding Catholicism.

On April 6, barely two weeks after the “Islamic Motivations for ‘Suicide’ Bombers” briefing at Quantico, FBI Director Robert Mueller defended the bureau’s budget before a congressional committee. Among his major points: the FBI needs cooperation from American Muslims to stop the next terrorist attack.

“Since September 11th, every one of our 56 field offices and the leadership of those offices have had outreach to the Muslim community,” Mueller said. “We need the support of that community … our business is basically relationships.” That is exactly the opposite message sent in the training rooms of Quantico, where the next generation of FBI counterterrorism is shaped.

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Like FBI agent Ali Soufan and Lt. Col. Anthony Shaffer before them, the podcast team, including John Duffy and Ray Nowosielski, are being subjected to intimidation and censorship by government officials over blowing the whistle on the true story surrounding two alleged 9/11 hijackers, Nawaf al-Hazmi and Khalid al-Mihdhar.

The podcast originally scheduled for September 11th release presents a narrative of how three CIA analysts working under Richard Blee, the long unknown former head of CIA’s Bin Laden Station, deliberately misled their colleagues and withheld key intelligence from FBI and the White House regarding the presence of two known Al-Qaeda operatives in the U.S.

Four government investigations into CIA handling of pre-911 intelligence included personal details of the two CIA analysts and their actions. Nowosielski and Duffy deduced the identities of the two as yet unnamed CIA employees from internet research based on details provided from these and other open sources. When the producers used their full names in interviews, interviewees offered no correction. The CIA response provided the final confirmation.

In project updates posted at SecrecyKills.com the producers announced the delay of the podcast and posted background of a complicated case that involves dozens of violations of protocol, intimidation, and incidents of obstruction by the CIA, with the two yet named CIA analysts at the center of many of them.

Author and expert on the subject, Kevin Fenton, documents 35 such incidents between January 2000 and September 11th in his book, Disconnecting the Dots: How 9/11 Was Allowed to Happen.

Pulitzer-prize winner Lawrence Wright, interviewed for the podcast, told producers the actions of one of the unnamed CIA analysts still employed at CIA amounts to obstruction of justice in the FBI’s criminal investigation of the deaths of 17 seaman aboard the USS Cole.

The producers are not the first subject to government censorship over this case. Last month The New York Times reported on CIA efforts to censor an autobiography by Ali Soufan, a front-line FBI counter-terrorism special agent. Prior to 9/11, Soufan was interested in Mihdhar and Hazmi because of links to the bombing of the USS Cole in Yemen. The CIA censored references to a passport photo of Mihdhar the CIA had withheld from Soufan, despite three written requests.

Scott Shane of the New York Times reports today that, “Mr. Soufan accuses C.I.A. officials of deliberately withholding crucial documents and photographs of Qaeda operatives from the F.B.I. before Sept. 11, 2001, despite three written requests, and then later lying about it to the 9/11 Commission.”

Lt. Colonel Anthony Shaffer, interviewed for the podcast, was himself intimidated, demoted and smeared by the Pentagon after he came forward to the 9/11 Commission with details of how, on three occasions, unnamed DoD officials prevented his Able Danger operation from meeting with the FBI prior the attacks.

In 2000 the Able Danger data-mining program placed Mohammed Atta in a Brooklyn terrorist cell but had also placed Hazmi and Mihdhar in a San Diego cell, the epicenter of intrigue around Alec Station’s Rich Blee, Tom Wilshere and the two as yet unnamed subordinates who themselves repeatedly withheld intelligence from the FBI. Though Shaffer was interviewed by 9/11 Commission’s Director Philip Zelikow and staffer Dieter Snell, the Commission left any mention of Able Danger from its final report.

In the planned podcast, 9/11 Commission Chair Tom Kean is asked about a scant footnote to Chapter 6 of the 9/11 Report referring to an intelligence cable, seen by 50 at the CIA, but prevented from reaching the FBI. For Kean the incident was not a case of bungling or intel ‘stovepiping’: “Oh, it wasn’t careless oversight. It was purposeful. No question about that in mind. It was purposeful.”

Whereas Kean explains it as a penchant for secrecy, Richard Clarke, the former head of counter-terrorism at the Bush White House, goes farther suggesting malfeasance and the possibility of illegal CIA-led domestic spying activity. Comments by Clarke released in a video in August led to a formal statement from George Tenet, Cofer Black and Richard Blee, and a response from the producers.

“This was perhaps the closest U.S. intelligence got to foiling the 9/11 plot,” explains Nowosielski, “but instead of stopping the attack, the CIA stopped intel on two high-value targets from getting to the right people, repeatedly. And still the CIA protects the individuals responsible by intimidating those who simply want to know the truth behind a shocking and possibly criminal pattern of obstruction”

In an email Thursday the CIA warned Nowosielski he could be subject to prosecution under the Intelligence Identities Protection Act, a law intended to apply to government employees who violate their security clearance and never used to convict journalists.

The producer’s online response: “The Society of Professional Journalists’ code of ethics states that ‘journalists should be free of obligation to any interest other than the public’s right to know’ and should ‘be vigilant and courageous about holding those with power accountable.’ The day that journalists’ exposés of wrongdoing within government agencies require the approval of those government agencies before release, that is the day that transparency and accountability are lost.”

John Duffy and Ray Nowosielski, both graduates of Chicago’s Columbia College Film School, produced the critically acclaimed 2006 documentary “9/11: Press for Truth.”

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Ali H. Soufan, left, who as an F.B.I. agent spent years near the center of battle with Al Qaeda.

The agent, Ali H. Soufan, argues in the book that the C.I.A. missed a chance to derail the 2001 plot by withholding from the F.B.I. information about two future 9/11 hijackers living in San Diego, according to several people who have read the manuscript. And he gives a detailed, firsthand account of the C.I.A.’s move toward brutal treatment in its interrogations, saying the harsh methods used on the agency’s first important captive, Abu Zubaydah, were unnecessary and counterproductive.

Neither critique of the C.I.A. is new. In fact, some of the information that the agency argues is classified, according to two people who have seen the correspondence between the F.B.I. and C.I.A., has previously been disclosed in open Congressional hearings, the report of the national commission on 9/11 and even the 2007 memoir of George J. Tenet, the former C.I.A. director.

Mr. Soufan, an Arabic-speaking counterterrorism agent who played a central role in most major terrorism investigations between 1997 and 2005, has told colleagues he believes the cuts are intended not to protect national security but to prevent him from recounting episodes that in his view reflect badly on the C.I.A.

Some of the scores of cuts demanded by the C.I.A. from Mr. Soufan’s book, “The Black Banners: The Inside Story of 9/11 and the War Against Al Qaeda,” seem hard to explain on security grounds.

Among them, according to the people who have seen the correspondence, is a phrase from Mr. Soufan’s 2009 testimony at a Senate hearing, freely available both as video and transcript on the Web. Also chopped are references to the word “station” to describe the C.I.A.’s overseas offices, common parlance for decades.

The agency removed the pronouns “I” and “me” from a chapter in which Mr. Soufan describes his widely reported role in the interrogation of Abu Zubaydah, an important terrorist facilitator and training camp boss. And agency officials took out references to the fact that a passport photo of one of the 9/11 hijackers who later lived in San Diego, Khalid al-Midhar, had been sent to the C.I.A. in January 2000 — an episode described both in the 9/11 commission report and Mr. Tenet’s book.

In a letter sent Aug. 19 to the F.B.I.’s general counsel, Valerie E. Caproni, a lawyer for Mr. Soufan, David N. Kelley, wrote that “credible sources have told Mr. Soufan that the agency has made a decision that this book should not be published because it will prove embarrassing to the agency.”

In a statement, Mr. Soufan called the C.I.A’s redactions to his book “ridiculous” but said he thought he would prevail in getting them restored for a later edition.

He said he believed that counterterrorism officers have an obligation to face squarely “where we made mistakes and let the American people down.” He added: “It saddens me that some are refusing to address past mistakes.”

A spokeswoman for the C.I.A., Jennifer Youngblood, said, “The suggestion that the Central Intelligence Agency has requested redactions on this publication because it doesn’t like the content is ridiculous. The C.I.A.’s pre-publication review process looks solely at the issue of whether information is classified.”

She noted that under the law, “Just because something is in the public domain doesn’t mean it’s been officially released or declassified by the U.S. government.”

A spokesman for the F.B.I., Michael P. Kortan, declined to comment.

The book, written with the assistance of Daniel Freedman, a colleague at Mr. Soufan’s New York security company, is scheduled to go on sale Sept. 12. Facing a deadline this week, the publisher, W. W. Norton and Company, decided to proceed with a first printing incorporating all the C.I.A.’s cuts.

If Mr. Soufan ultimately prevails in negotiations or a legal fight to get the excised material restored, Norton will print the unredacted version, said Drake McFeely, Norton’s president. “The C.I.A.’s redactions seem outrageous to me,” Mr. McFeely said. But he noted that they are concentrated in certain chapters and said “the book’s argument comes across clearly despite them.”

The regular appearance of memoirs by Bush administration officials has continued a debate over the facts surrounding the failure to prevent 9/11 and the tactics against terrorism that followed. In former Vice President Dick Cheney’s memoir, set for publication next week, he writes of the harsh interrogations that “the techniques worked.”

A book scheduled for publication next May by José A. Rodriguez Jr., a former senior C.I.A. official, is expected to give a far more laudatory account of the agency’s harsh interrogations than that of Mr. Soufan, as is evident from its tentative title: “Hard Measures: How Aggressive C.I.A. Actions After 9/11 Saved American Lives.”

Government employees who hold security clearances are required to have their books vetted for classified information before publication. But because decisions on what should be classified can be highly subjective, the prepublication review process often becomes a battle. Several former spies have gone to court to fight redactions to their books, and the Defense Department spent nearly $50,000 last year to buy and destroy the entire first printing of an intelligence officer’s book, which it said contained secrets.

The C.I.A. interrogation program sharply divided the C.I.A. and the F.B.I., whose director, Robert S. Mueller III, ordered agents to stop participating in the program after Mr. Soufan and other agents objected to the use of physical coercion. But some C.I.A. officers, too, opposed the brutal methods, including waterboarding, and it was their complaint to the C.I.A.’s inspector general that eventually led to the suspension of the program.

“The Black Banners” traces the origins and growth of Al Qaeda and describes the role of Mr. Soufan, 40, a Lebanese-American, in the investigations of the East African embassy bombings of 1998, the attack on the American destroyer Cole in 2000, 9/11 and the continuing campaign against terrorism.

Starting in May, F.B.I. officials reviewed Mr. Soufan’s 600-page manuscript, asking the author for evidence that dozens of names and facts were not classified. Mr. Soufan and Mr. Freedman agreed to change wording or substitute aliases for some names, and on July 12 the bureau told Mr. Soufan its review was complete.

In the meantime, however, the bureau had given the book to the C.I.A. Its reviewers responded this month with 78-page and 103-page faxes listing their cuts.

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