Following months of denials, the FBI is now promising a “comprehensive review of all training and reference materials” after Danger Room revealed a series of Bureau presentations that tarred average Muslims as “radical” and “violent.”

But untangling the Islamophobic thread woven into the FBI’s counterterrorism training culture won’t be easy. In addition to inflammatory seminars which likened Islam to the Death Star and Mohammed to a “cult leader,” Danger Room has obtained more material showing just how wide the anti-Islam meme has spread throughout the Bureau.

The FBI library at Quantico currently stacks books from authors who claim that “Islam and democracy are totally incompatible.” The Bureau’s private intranet recently featured presentations that claimed to demonstrate the “inherently violent nature of Islam,” according to multiple sources. Earlier this year, the Bureau’s Washington Field Office welcomed a speaker who claimed Islamic law prevents Muslims from being truly loyal Americans. And as recently as last week, the online orientation material for the FBI’s Joint Terrorism Task Forces included claims that Sunni Islam seeks “domination of the world,” according to a law enforcement source.

“I don’t think anyone with half a brain would paint 1.2 billion people of any ethnic or religious persuasion with a single brushstroke,” Mike Rolince, an FBI counterterrorism veteran who started Boston’s JTTF, tells Danger Room. “Who did they run that curriculum by — either an internal or outside expert — to get some balance?”

The FBI declined to respond directly to such questions from Danger Room. But what’s clear is that the anti-Islam sentiment in the FBI’s training and orientation isn’t the marginal problem that the Bureau portrayed in its previous public statements and press releases. It’s not a historical problem, it’s ongoing. And it will require substantial effort to root out. Not even a July warning from the office of a powerful senator was able to spur the Bureau to purge itself of its anti-Islam material.

One example is found in the mandatory orientation material for the FBI’s Joint Terrorism Task Forces, or JTTFs. Those task forces are a nationwide partnership between the FBI, intelligence analysts and state and local police. As of late last week, according to a law enforcement source familiar with the program, new members or those needing a belated orientation saw this description of Sunnism — the largest branch of Islam — as part of their online training course:

Sunni Muslims have been prolific in spawning numerous and varied fundamentalist extremist terrorist organizations. Sunni core doctrine and end state have remained the same and they continue to strive for Sunni Islamic domination of the world to prove a key Quranic assertion that no system of government or religion on earth can match the Quran’s purity and effectiveness for paving the road to God.

That paragraph is contained in orientation material, known as the Joint Terrorism Task Force Orientation v2 course, distributed online through a secure intranet for every member of the JTTFs. That’s approximately 4,400 officials, according to FBI figures, all charged with stopping terrorism. The orientation course is mandatory for every member of the task force.

The passage is especially odd because most of the orientation consists of practical, mundane information, such as the proper forms to fill out during an inquiry or FBI standards for investigations, according to the source. It consists of five sections, one of which is about Islam, Muslims and Arab culture. The supervisor of each JTTF has to certify that all his or her personnel have completed the online orientation course, and then must pass that certification up to FBI Headquarters’ Counterterrorism Division.

The FBI would neither confirm nor deny the existence of the JTTF orientation material.

The excerpt from the JTTF orientation material was provided to Danger Room by a concerned law enforcement official, who says the material contains 20 paragraphs about Islam in a similar vein. Several Bureau and law enforcement officials who spoke to Danger Room on condition of anonymity believe that such instructions are detrimental to uncovering and thwarting terrorist plots, and that the FBI continues to be less than forthright with the press and the public about the extent of its teaching that Islam is at the root of the menace of terrorism. Evidence for this continuing belief can be found in Quantico, Virginia, at the FBI’s elite training academy.

Within the sprawling campus of that academy, Quantico maintains a library befitting the FBI’s status as America’s most important law enforcement agency. It stacks thousands of books, from heavy tomes containing the U.S. criminal code to forensics reference material that could be out of CSI, across three unclassified floors. The library is open to all FBI agents, plus intelligence officials and police from across the country, for a single purpose: to provide background material for cases, guidance material for intelligence analysis and other tools meant directly to aid law enforcement. In other words, it’s not your public library.

There’s a section on religion — in which Islam, perhaps understandably, predominates. A law enforcement source provided Danger Room with a photographic catalog, compiled in late August, of approximately 100 books on Islam out of around 150 stacked at Quantico. Many of them are innocuous or contain unquestioned scholarship, ranging from authors like Fawaz Gerges of the London School of Economics, Juan Cole of the University of Michigan and Thomas Hegghammer, a terrorism expert at the Norwegian Defence Research Establishment.

But, significantly, the library also contains books by anti-Islam authors that portray the religion as devoted to murder and world domination.

There’s Militant Islam Reaches America by Daniel Pipes, who claims to have “confirmed” that President Obama was once a practicing Muslim, and whose book asks, “Why would terrorists oppress women if this did not have something to do with their Islamic outlook?” A book called Islamikaze: Manifestations of Islamic Martyrology ties “normative Islam” to “horrendous cruelty and inhumanity.” The editor of the anthology Muhammad’s Monsters has previously written that “Islam and democracy are totally incompatible, and are mutually inconclusive. The same applies to Modernity, which is perceived as a threat to Islamic civilization.”

And there is also Onward Muslim Soldiers by Robert Spencer. Spencer is one of the U.S.’ leading opponents of Islam. Along with the blogger Pamela Geller, Spencer leads a group called Stop Islamicization of America, which “promotes a conspiratorial anti-Muslim agenda under the guise of fighting radical Islam,” according to the Anti-Defamation League. Spencer’s work was cited 64 times in the political manifesto of Anders Behring Breivik, the Oslo terrorist who killed 69 people earlier this year.

When Danger Room presented the FBI in July with recently declassified material showing that its Law Enforcement Training Unit recommended one of Spencer’s other books to agents, its response was unequivocal: “The presentation in question was a rudimentary version used for a limited time that has since been replaced.” Onward Muslim Soldiers was available for checkout in the Quantico library as recently as late August.

The FBI’s dalliance with Robert Spencer is not limited to the stacks of Quantico. In July 2010, Spencer presented what he described as “two two-hour seminars on the belief-system of Islamic jihadists” to the JTTF in Tidewater, Virginia. He presented a similar lecture to the U.S. Attorney’s Anti-Terrorism Advisory Council, which is co-hosted by the FBI’s Norfolk Field Office. When a coalition of civil rights groups sent a letter protesting the FBI’s embrace of Spencer, the Special Agent in Charge of the Norfolk FBI, Alex J. Turner, replied, “Seeking broad knowledge on a wide range of topics is essential in understanding today’s terrorist environment, and helps us to defeat ignorance and strengthen relationships with the diverse communities we serve.”

Spencer was only one of an array of self-anointed experts delivering similar messages about Islam to Bureau audiences.

On January 11, the FBI’s Washington, D.C. Field Office held a seminar on Islamic extremism. In the conference room of its Judiciary Square offices, about 60 of the Field Office’s agents and intelligence analysts spent the morning hearing two presentations — one from terrorism expert Sebastian Gorka, a fellow with the Foundation for the Defense of Democracies, and another from a self-identified expert on Islamic law, Stephen Coughlin, a former consultant to the military’s Joint Staff. The takeaway of Coughlin’s presentation, according to an attendee: Islam is out to take over the world and there is no such thing as a loyal American Muslim.

Coughlin was described to Danger Room as presenting a far more extreme take on Islam than Gorka, who spoke separately on the subject of “Core Texts of Salafi Jihad.” But Coughlin allegedly told the agents that Muslims believe Islamic law to be all-encompassing, preventing an either/or choice to U.S. Muslims: either reject the U.S. Constitution or fall into apostasy. Sharia law, Coughlin instructed in the tone of a neutral reporter, was a threat to the agents in the room. He explored an obscure Islamic concept known as “abrogation,” the supposition that some Koranic verses supersede others, to argue that the Koran’s non-violent passages are overtaken in Muslim eyes by commands to wage war against “non-believers.”

It’s a line Coughlin has long pushed. During a presentation at the Conservative Political Action Conference in 2010 — in which he shared a stage with Spencer and Geller — Coughlin asserted that the Organization of the Islamic Conference, the geopolitical organization of Muslim nations, has a “ten-year plan” to make “defamation of Islam a crime” worldwide. One of his briefing slides read, “The SILENCE in the mainstream media on this DIRECT ASSAULT is DEAFENING! — not just on speech — but on thought itself!!” Coughlin’s 2007 master’s thesis at the National Defense Intelligence College claimed that President George W. Bush’s reassurance that the U.S. was not at war with Islam had a “a chilling effect on those tasked to define the enemy’s doctrine by effectively placing a policy bar on the unconstrained analysis of Islamic doctrine as a basis for this threat.” (.pdf) In 2008, his Joint Staff contract wasn’t renewed after a staffer for Gordon England, then the deputy secretary of defense, raised concerns about his work. (Through a spokesman, England declined to comment.)

Coughlin did not respond to requests for comment.

The presentation to the Washington Field Office wasn’t mandated by FBI Headquarters. It was set up on the initiative of a well-intentioned agent. But not everyone was comfortable with the presentation. Some walked out in boredom or disgust, according to the source. Others made fun of it.

But some voiced worries that the presentation sent an implicit message to agents that they should be targeting Muslims in the name of stopping terrorism. And in the past few years, the FBI has accelerated its monitoring of mosques, community centers, businesses and other organizations run by Muslims. Several observers suspect that the persistence of training materials that casts Islam in a threatening light helps explain the increased surveillance. Others — including many counterterrorism professionals within the FBI who say they are disgusted by the bigoted material they’ve received — fear that the presentations will drive a wedge between the Bureau and the U.S. Muslim communities whose assistance it needs to prevent terrorism.

“Inappropriately enlarging the characterization of the threat to include all of Islam,” says Rick “Ozzie” Nelson, a former official with the National Counterterrorism Center, “may inadvertently increase al Qaida’s ideological resonance and could facilitate recruitment of would-be terrorists.”

Books in a library and presentations in a field office will only reach the agents who visit the library or work in the field office. A Joint Terrorism Task Force orientation will only reach JTTF members. But every FBI agent can access the bureau’s intranet. And until Danger Room’s expose, that network hosted material purporting to demonstrate “the inherently violent nature of Islam.”

Two law enforcement sources with access to the intranet — sections of which are classified — described to Danger Room its page on “Islamic Law.” FBI intranet users type in “Islamic Law” or “Islam” into a Google-like search function. Up pops what’s called a Subject Matter Expert page, or SME, pronounced “Smee.” Usually, an agent seeking a SME will be searching for material directly relevant to an ongoing investigation or a timely intelligence product. But the SME for “Islamic Law” recently featured uploaded documents stretching all the way back to the 19th century, with titles like “The Personal Law of The Mahommedans.”

One such document is a text from 1915, titled “Mohammed Or Christ: An Account Of The Rapid Spread of Islam In All Parts of The Globe, The Methods Employed to Obtain Proselytes, Its Immense Press, Its Strongholds, & Suggested Means to be Adopted to Counteract the Evil.” That explicitly religious and archaic tome instructs that its purpose is “to set forth the appeal of that [Muslim] world for the Gospel. It is a decisive hour!”

Another is a Regent University master’s thesis called “Devoutly Violent or Nominally Peaceful? The Justification for Violence in Islam.” It asks: “[S]eeing as the foremost goal of Islam (which literally means ‘submission’) is to subject the entire world to Shari’a law and Allah’s guidance, can a devout Muslim who witnesses to a Christian (who rejects his invitation to Islam) really not become violent? … In conclusion, this thesis demonstrates the inherently violent nature of Islam.”

In the image above, formerly available on the FBI’s “Islamic Law” SME, a thermometer represents a correlation between the Muslim population of a country and its “violence level.” As Muslims accumulate in a given place, they incline toward “grievance fabrication,” then “chronic terror attacks,” and even “state-run ethnic cleansing.” The final stage is “peace” — in an all-Muslim state.

Two law enforcement sources told Danger Room that after our coverage of the FBI’s training materials ran, the “Islamic Law” SME and similar FBI intranet sites were scrubbed of such material. Danger Room was able to acquire some of these documents before they were removed.

Other materials reinforced the message delivered on the FBI’s internal network. A 2006 FBI intelligence assessment judged that “conversion” to Islam or intensifying Islamic faith (.PDF) could be early-warning signs of terrorism — a judgment that would apply to millions of American citizens. That assessment is still in official use, according to the FBI, even though one of its public responses to our expose was a public assurance that “Strong religious beliefs should never be confused with violent extremism. Views that are contrary should not and will not be taught to FBI employees.”

Asked to reconcile that statement with the 2006 assessment, FBI spokesman Christopher Allen replied, “The assessment you cite includes a series of indicators of radicalization. These indicators do not conflict with our statement that strong religious beliefs should never be confused with violent extremism.”

The FBI is now in damage-control mode. On Thursday afternoon, the FBI held a conference call with Muslim civil rights groups to apologize for its offensive training materials and admit that they were more extensive than it previously acknowledged. The FBI did not make any commitments on which outside experts or organizations it would consult for an updated training curriculum. But according to one participant, the FBI representative on the call said that many people within the Bureau disapproved of the anti-Islamic rhetoric. The FBI’s Allen declined to comment.

“We are glad that this very serious issue has finally received the attention of FBI leadership,” says Farhana Khera, executive director of the San Francisco-based civil rights group Muslim Advocates, “but an internal review is insufficient at this stage. In the last year, the FBI has either defended its use of bigoted trainers or emphatically assured the public that the various trainings were one-time, isolated incidents. Each time those assurances were later revealed to be false.”

Muslim Advocates sent a letter to the Justice Department Inspector General last week seeking an investigation. It has yet to receive a reply. However, the chairs of the Senate’s homeland security and intelligence committees have separately told Danger Room they will subject the FBI’s counterterrorism training to scrutiny.

For months, in fact, the chairman of the Senate Homeland Security and Government Affairs Committee, Joe Lieberman (I-Conn.), has raised concerns that law enforcement at all levels lacks “meaningful standards” for counterterrorism training. In the course of his ongoing inquiry on the subject, Lieberman’s staff became aware of a particularly problematic individual: an FBI intelligence analyst named William Gawthrop.

In April, Gawthrop presented a three-day briefing at the FBI’s Quantico training facility to counterterrorism agents in which he equated “mainstream” Islam with terrorism. In earlier interviews, he mused about triggering a “deteriorating cascade effect” upon Islam, convincing Muslims to abandon their religion by attacking “soft spots” in the Islamic faith. And he has lectured widely about the “threat” of Islam, ostensibly as a private citizen.

Lieberman staffers were appalled by the “inappropriate materials being used by Mr. Gawthrop and notified the FBI in mid-July of their concerns,” says Leslie Phillips, Communications Director of the Homeland Security Committee.

The FBI wouldn’t directly comment on the committee’s warning, instead reiterating the Bureau’s new commitment to a wide-ranging review — one that will stretch from Quantico to the FBI’s many field offices to the J. Edgar Hoover Building, its Washington headquarters.

“The senator hopes the FBI will take appropriate action to prohibit these and any other inaccurate training materials from being used in the future,” Phillips adds.

In the meantime, Gawthrop is, as of this writing, still an FBI counterterrorism analyst. And the message he helped inculcate in the Bureau lingers.