The roots of the Abu Ghraib prison scandal lie not in the criminal inclinations of a few Army reservists but in a decision, approved last year by Secretary of Defense Donald Rumsfeld, to expand a highly secret operation, which had been focussed on the hunt for Al Qaeda, to the interrogation of prisoners in Iraq. Rumsfeld’s decision embittered the American intelligence community, damaged the effectiveness of élite combat units, and hurt America’s prospects in the war on terror.

According to interviews with several past and present American intelligence officials, the Pentagon’s operation, known inside the intelligence community by several code words, including Copper Green, encouraged physical coercion and sexual humiliation of Iraqi prisoners in an effort to generate more intelligence about the growing insurgency in Iraq. A senior C.I.A. official, in confirming the details of this account last week, said that the operation stemmed from Rumsfeld’s long-standing desire to wrest control of America’s clandestine and paramilitary operations from the C.I.A.

Rumsfeld, during appearances last week before Congress to testify about Abu Ghraib, was precluded by law from explicitly mentioning highly secret matters in an unclassified session. But he conveyed the message that he was telling the public all that he knew about the story. He said, “Any suggestion that there is not a full, deep awareness of what has happened, and the damage it has done, I think, would be a misunderstanding.” The senior C.I.A. official, asked about Rumsfeld’s testimony and that of Stephen Cambone, his Under-Secretary for Intelligence, said, “Some people think you can bullshit anyone.”

The Abu Ghraib story began, in a sense, just weeks after the September 11, 2001, attacks, with the American bombing of Afghanistan. Almost from the start, the Administration’s search for Al Qaeda members in the war zone, and its worldwide search for terrorists, came up against major command-and-control problems. For example, combat forces that had Al Qaeda targets in sight had to obtain legal clearance before firing on them. On October 7th, the night the bombing began, an unmanned Predator aircraft tracked an automobile convoy that, American intelligence believed, contained Mullah Muhammad Omar, the Taliban leader. A lawyer on duty at the United States Central Command headquarters, in Tampa, Florida, refused to authorize a strike. By the time an attack was approved, the target was out of reach. Rumsfeld was apoplectic over what he saw as a self-defeating hesitation to attack that was due to political correctness. One officer described him to me that fall as “kicking a lot of glass and breaking doors.” In November, the Washington Post reported that, as many as ten times since early October, Air Force pilots believed they’d had senior Al Qaeda and Taliban members in their sights but had been unable to act in time because of legalistic hurdles. There were similar problems throughout the world, as American Special Forces units seeking to move quickly against suspected terrorist cells were compelled to get prior approval from local American ambassadors and brief their superiors in the chain of command.

Rumsfeld reacted in his usual direct fashion: he authorized the establishment of a highly secret program that was given blanket advance approval to kill or capture and, if possible, interrogate “high value” targets in the Bush Administration’s war on terror. A special-access program, or sap—subject to the Defense Department’s most stringent level of security—was set up, with an office in a secure area of the Pentagon. The program would recruit operatives and acquire the necessary equipment, including aircraft, and would keep its activities under wraps. America’s most successful intelligence operations during the Cold War had been saps, including the Navy’s submarine penetration of underwater cables used by the Soviet high command and construction of the Air Force’s stealth bomber. All the so-called “black” programs had one element in common: the Secretary of Defense, or his deputy, had to conclude that the normal military classification restraints did not provide enough security.

“Rumsfeld’s goal was to get a capability in place to take on a high-value target—a standup group to hit quickly,” a former high-level intelligence official told me. “He got all the agencies together—the C.I.A. and the N.S.A.—to get pre-approval in place. Just say the code word and go.” The operation had across-the-board approval from Rumsfeld and from Condoleezza Rice, the national-security adviser. President Bush was informed of the existence of the program, the former intelligence official said.

The people assigned to the program worked by the book, the former intelligence official told me. They created code words, and recruited, after careful screening, highly trained commandos and operatives from America’s élite forces—Navy seals, the Army’s Delta Force, and the C.I.A.’s paramilitary experts. They also asked some basic questions: “Do the people working the problem have to use aliases? Yes. Do we need dead drops for the mail? Yes. No traceability and no budget. And some special-access programs are never fully briefed to Congress.”

In theory, the operation enabled the Bush Administration to respond immediately to time-sensitive intelligence: commandos crossed borders without visas and could interrogate terrorism suspects deemed too important for transfer to the military’s facilities at Guantánamo, Cuba. They carried out instant interrogations—using force if necessary—at secret C.I.A. detention centers scattered around the world. The intelligence would be relayed to the sap command center in the Pentagon in real time, and sifted for those pieces of information critical to the “white,” or overt, world.

Fewer than two hundred operatives and officials, including Rumsfeld and General Richard Myers, chairman of the Joint Chiefs of Staff, were “completely read into the program,” the former intelligence official said. The goal was to keep the operation protected. “We’re not going to read more people than necessary into our heart of darkness,” he said. “The rules are ‘Grab whom you must. Do what you want.’ ”

One Pentagon official who was deeply involved in the program was Stephen Cambone, who was named Under-Secretary of Defense for Intelligence in March, 2003. The office was new; it was created as part of Rumsfeld’s reorganization of the Pentagon. Cambone was unpopular among military and civilian intelligence bureaucrats in the Pentagon, essentially because he had little experience in running intelligence programs, though in 1998 he had served as staff director for a committee, headed by Rumsfeld, that warned of an emerging ballistic-missile threat to the United States. He was known instead for his closeness to Rumsfeld. “Remember Henry II—‘Who will rid me of this meddlesome priest?’ ” the senior C.I.A. official said to me, with a laugh, last week. “Whatever Rumsfeld whimsically says, Cambone will do ten times that much.”

Cambone was a strong advocate for war against Iraq. He shared Rumsfeld’s disdain for the analysis and assessments proffered by the C.I.A., viewing them as too cautious, and chafed, as did Rumsfeld, at the C.I.A.’s inability, before the Iraq war, to state conclusively that Saddam Hussein harbored weapons of mass destruction. Cambone’s military assistant, Army Lieutenant General William G. (Jerry) Boykin, was also controversial. Last fall, he generated unwanted headlines after it was reported that, in a speech at an Oregon church, he equated the Muslim world with Satan.

Early in his tenure, Cambone provoked a bureaucratic battle within the Pentagon by insisting that he be given control of all special-access programs that were relevant to the war on terror. Those programs, which had been viewed by many in the Pentagon as sacrosanct, were monitored by Kenneth deGraffenreid, who had experience in counter-intelligence programs. Cambone got control, and deGraffenreid subsequently left the Pentagon. Asked for comment on this story, a Pentagon spokesman said, “I will not discuss any covert programs; however, Dr. Cambone did not assume his position as the Under-Secretary of Defense for Intelligence until March 7, 2003, and had no involvement in the decision-making process regarding interrogation procedures in Iraq or anywhere else.”

In mid-2003, the special-access program was regarded in the Pentagon as one of the success stories of the war on terror. “It was an active program,” the former intelligence official told me. “It’s been the most important capability we have for dealing with an imminent threat. If we discover where Osama bin Laden is, we can get him. And we can remove an existing threat with a real capability to hit the United States—and do so without visibility.” Some of its methods were troubling and could not bear close scrutiny, however.

By then, the war in Iraq had begun. The sap was involved in some assignments in Iraq, the former official said. C.I.A. and other American Special Forces operatives secretly teamed up to hunt for Saddam Hussein and—without success—for Iraqi weapons of mass destruction. But they weren’t able to stop the evolving insurgency.

In the first months after the fall of Baghdad, Rumsfeld and his aides still had a limited view of the insurgency, seeing it as little more than the work of Baathist “dead-enders,” criminal gangs, and foreign terrorists who were Al Qaeda followers. The Administration measured its success in the war by how many of those on its list of the fifty-five most wanted members of the old regime—reproduced on playing cards—had been captured. Then, in August, 2003, terror bombings in Baghdad hit the Jordanian Embassy, killing nineteen people, and the United Nations headquarters, killing twenty-three people, including Sergio Vieira de Mello, the head of the U.N. mission. On August 25th, less than a week after the U.N. bombing, Rumsfeld acknowledged, in a talk before the Veterans of Foreign Wars, that “the dead-enders are still with us.” He went on, “There are some today who are surprised that there are still pockets of resistance in Iraq, and they suggest that this represents some sort of failure on the part of the Coalition. But this is not the case.” Rumsfeld compared the insurgents with those true believers who “fought on during and after the defeat of the Nazi regime in Germany.” A few weeks later—and five months after the fall of Baghdad—the Defense Secretary declared,“It is, in my view, better to be dealing with terrorists in Iraq than in the United States.”

Inside the Pentagon, there was a growing realization that the war was going badly. The increasingly beleaguered and baffled Army leadership was telling reporters that the insurgents consisted of five thousand Baathists loyal to Saddam Hussein. “When you understand that they’re organized in a cellular structure,” General John Abizaid, the head of the Central Command, declared, “that . . . they have access to a lot of money and a lot of ammunition, you’ll understand how dangerous they are.”

The American military and intelligence communities were having little success in penetrating the insurgency. One internal report prepared for the U.S. military, made available to me, concluded that the insurgents’ “strategic and operational intelligence has proven to be quite good.” According to the study:

**{: .break one} ** Their ability to attack convoys, other vulnerable targets and particular individuals has been the result of painstaking surveillance and reconnaissance. Inside information has been passed on to insurgent cells about convoy/troop movements and daily habits of Iraqis working with coalition from within the Iraqi security services, primarily the Iraqi Police force which is rife with sympathy for the insurgents, Iraqi ministries and from within pro-insurgent individuals working with the CPA’s so-called Green Zone. **

The study concluded, “Politically, the U.S. has failed to date. Insurgencies can be fixed or ameliorated by dealing with what caused them in the first place. The disaster that is the reconstruction of Iraq has been the key cause of the insurgency. There is no legitimate government, and it behooves the Coalition Provisional Authority to absorb the sad but unvarnished fact that most Iraqis do not see the Governing Council”—the Iraqi body appointed by the C.P.A.—“as the legitimate authority. Indeed, they know that the true power is the CPA.”

By the fall, a military analyst told me, the extent of the Pentagon’s political and military misjudgments was clear. Donald Rumsfeld’s “dead-enders” now included not only Baathists but many marginal figures as well—thugs and criminals who were among the tens of thousands of prisoners freed the previous fall by Saddam as part of a prewar general amnesty. Their desperation was not driving the insurgency; it simply made them easy recruits for those who were. The analyst said, “We’d killed and captured guys who had been given two or three hundred dollars to ‘pray and spray’ ”—that is, shoot randomly and hope for the best. “They weren’t really insurgents but down-and-outers who were paid by wealthy individuals sympathetic to the insurgency.” In many cases, the paymasters were Sunnis who had been members of the Baath Party. The analyst said that the insurgents “spent three or four months figuring out how we operated and developing their own countermeasures. If that meant putting up a hapless guy to go and attack a convoy and see how the American troops responded, they’d do it.” Then, the analyst said, “the clever ones began to get in on the action.”

By contrast, according to the military report, the American and Coalition forces knew little about the insurgency: “Human intelligence is poor or lacking . . . due to the dearth of competence and expertise. . . . The intelligence effort is not coördinated since either too many groups are involved in gathering intelligence or the final product does not get to the troops in the field in a timely manner.” The success of the war was at risk; something had to be done to change the dynamic.

The solution, endorsed by Rumsfeld and carried out by Stephen Cambone, was to get tough with those Iraqis in the Army prison system who were suspected of being insurgents. A key player was Major General Geoffrey Miller, the commander of the detention and interrogation center at Guantánamo, who had been summoned to Baghdad in late August to review prison interrogation procedures. The internal Army report on the abuse charges, written by Major General Antonio Taguba in February, revealed that Miller urged that the commanders in Baghdad change policy and place military intelligence in charge of the prison. The report quoted Miller as recommending that “detention operations must act as an enabler for interrogation.”

Miller’s concept, as it emerged in recent Senate hearings, was to “Gitmoize” the prison system in Iraq—to make it more focussed on interrogation. He also briefed military commanders in Iraq on the interrogation methods used in Cuba—methods that could, with special approval, include sleep deprivation, exposure to extremes of cold and heat, and placing prisoners in “stress positions” for agonizing lengths of time. (The Bush Administration had unilaterally declared Al Qaeda and other captured members of international terrorist networks to be illegal combatants, and not eligible for the protection of the Geneva Conventions.)

Rumsfeld and Cambone went a step further, however: they expanded the scope of the sap, bringing its unconventional methods to Abu Ghraib. The commandos were to operate in Iraq as they had in Afghanistan. The male prisoners could be treated roughly, and exposed to sexual humiliation.

“They weren’t getting anything substantive from the detainees in Iraq,” the former intelligence official told me. “No names. Nothing that they could hang their hat on. Cambone says, I’ve got to crack this thing and I’m tired of working through the normal chain of command. I’ve got this apparatus set up—the black special-access program—and I’m going in hot. So he pulls the switch, and the electricity begins flowing last summer. And it’s working. We’re getting a picture of the insurgency in Iraq and the intelligence is flowing into the white world. We’re getting good stuff. But we’ve got more targets”—prisoners in Iraqi jails—“than people who can handle them.”

Cambone then made another crucial decision, the former intelligence official told me: not only would he bring the sap’s rules into the prisons; he would bring some of the Army military-intelligence officers working inside the Iraqi prisons under the sap’s auspices. “So here are fundamentally good soldiers—military-intelligence guys—being told that no rules apply,” the former official, who has extensive knowledge of the special-access programs, added. “And, as far as they’re concerned, this is a covert operation, and it’s to be kept within Defense Department channels.”

The military-police prison guards, the former official said, included “recycled hillbillies from Cumberland, Maryland.” He was referring to members of the 372nd Military Police Company. Seven members of the company are now facing charges for their role in the abuse at Abu Ghraib. “How are these guys from Cumberland going to know anything? The Army Reserve doesn’t know what it’s doing.”