You can read part one of this article here.

A week after Robert Mueller took over as FBI director, the terrorist attacks of September 11, 2001, transformed his job. Gone were the days when the American people would be satisfied with after-the-fact prosecution. The emphasis now was on preventing the next attack.

Mueller, whose experiences as a Marine and a federal prosecutor shaped his leadership style, has overseen the deployment of FBI agents to the front lines of the war on terror around the world.

In December 2001, just after the US invasion of Afghanistan, the first FBI team of eight agents arrived in Kandahar—the first combat deployment of FBI agents since World War II.

Since then, more than 500 FBI personnel have been sent to Iraq and Afghanistan to investigate bombings and attacks and to collect biometric data on detainees and interrogate them. Another 500 have worked at the US base at Guantánamo Bay, Cuba. Agents have worked on cases in Iraq such as the Jordanian and Turkish embassy bombings and attacks on the headquarters of the Red Cross and United Nations.

The most controversial aspect of the FBI’s role in the war on terror has been its participation in “extreme interrogations” by the military and the CIA at sites such as Abu Ghraib prison in Iraq and Guantánamo Bay, known in military parlance as Gitmo.

The terrorism investigations posed three challenges to the FBI: First, in the war zones, the agents were dependent on military protection and so worked hard to maintain cordial relations; second, the FBI usually was not the lead investigative agency, so it didn’t have control over the treatment of detainees; and last, given the intelligence-gathering emphasis in the military zones, the typical evidentiary rules of US Article III courts didn’t necessarily apply.

According to documents and interviews, agents in Iraq, Afghanistan, and Gitmo all raised the issue of detainee treatment and the use of “extreme” or “enhanced” interrogations with their superiors, FBI headquarters staff, the military, and other agencies. One FBI commander at Gitmo told his agents that the FBI was “not in that business,” but as one former FBI section chief said, the military’s view was “You have your way, and we have our way.”

Agents raised concerns about the military’s use of such techniques as prolonged shackling of detainees in “stress positions.” One agent reported being especially disturbed after seeing the military duct-tape the head and face of a detainee to prevent him from chanting the Koran. Another reported a detainee’s being subjected to strobe lights and loud music for 16 hours.

According to the Justice Department’s inspector general, FBI agents at Gitmo went so far as to open a “war crimes” file to detail what they considered detainee abuse by the military and CIA but were told to abandon the project because it wasn’t the bureau’s role to investigate such allegations. That file has never surfaced.

Back in Washington, FBI counterterrorism chief Pasquale D’Amuro told Mueller that the FBI someday would be called to testify about the treatment of detainees and that he wanted the FBI to be able to say that it hadn’t taken part in the abuses. He told Mueller, “We don’t do that.” He felt that abusive interrogations helped al-Qaeda as a propaganda tool. D’Amuro—who now is with Giuliani Partners security consulting in New York—pointed to the fact that the East Africa bombing trials had been open, followed rules of evidence, and been hailed as a testament to the rule of law.

Another agent who raised abuse concerns with Army major general Geoffrey Miller, who ran the detainee interrogation program, said the general responded with words to the effect of “Thank you, gentlemen, but my boys know what they’re doing.”

FBI agents on the scene disagreed. The inspector general’s 2008 report paints a portrait of a detainee-interrogation program led by the CIA and the Department of Defense that was poorly planned and executed, with those involved making up the rules as they went along. The CIA’s and military’s “enhanced interrogations” were based mostly on a Survival, Evasion, Resistance, and Escape (SERE) training program—given to new CIA officers and military personnel including fighter pilots—that was designed to simulate the torture they might undergo if captured by an enemy. The program was approved at the highest levels of the US government with little discussion or debate. The ad hoc nature of the program was, FBI agents reported, “exacerbated by the fact that the DOD interrogators were often inexperienced and not particularly well trained about al-Qaeda.”

The FBI instructs its agents in interrogation techniques during their training at Quantico, and these skills are put to use regularly during the myriad criminal investigations they pursue over their careers. Bureau agents reported being appalled by the amateurism of military and CIA interrogators. The FBI agents found the DOD’s and CIA’s methods “clumsy” as well as “stupid, demeaning, and ineffective” and reported chastising DOD and military police officers for such unprofessional conduct as drawing smiley faces on the hoods of detainees.

The FBI believed it could get more useful information out of detainees by using its standard long-term-rapport-building techniques. The New York Times reported this summer that the CIA was most successful in interrogating 9/11 mastermind Khalid Shaikh Mohammed when it turned to rapport-building techniques rather than the “enhanced interrogations” that many human-rights groups say constitute torture.