A Rare Look Inside The C.I.A.’s Secret Interrogation Program.

by Jane Mayer

In March, Mariane Pearl, the widow of the murdered Wall Street Journal reporter Daniel Pearl, received a phone call from Alberto Gonzales, the Attorney General. At the time, Gonzales's role in the controversial dismissal of eight United States Attorneys had just been exposed, and the story was becoming a scandal in Washington. Gonzales informed Pearl that the Justice Department was about to announce some good news: a terrorist in U.S. custody-Khalid Sheikh Mohammed, the Al Qaeda leader who was the primary architect of the September 11th attacks-had confessed to killing her husband. (Pearl was abducted and beheaded five and a half years ago in Pakistan, by unidentified Islamic militants.) The Administration planned to release a transcript in which Mohammed boasted, "I decapitated with my blessed right hand the head of the American Jew Daniel Pearl in the city of Karachi, Pakistan. For those who would like to confirm, there are pictures of me on the Internet holding his head."

Pearl was taken aback. In 2003, she had received a call from Condoleezza Rice, who was then President Bush's national-security adviser, informing her of the same news. But Rice's revelation had been secret. Gonzales's announcement seemed like a publicity stunt. Pearl asked him if he had proof that Mohammed's confession was truthful; Gonzales claimed to have corroborating evidence but wouldn't share it. "It's not enough for officials to call me and say they believe it," Pearl said. "You need evidence." (Gonzales did not respond to requests for comment.)

The circumstances surrounding the confession of Mohammed, whom law-enforcement officials refer to as K.S.M., were perplexing. He had no lawyer. After his capture in Pakistan, in March of 2003, the Central Intelligence Agency had detained him in undisclosed locations for more than two years; last fall, he was transferred to military custody in Guantánamo Bay, Cuba. There were no named witnesses to his initial confession, and no solid information about what form of interrogation might have prodded him to talk, although reports had been published, in the Times and elsewhere, suggesting that C.I.A. officers had tortured him. At a hearing held at Guantánamo, Mohammed said that his testimony was freely given, but he also indicated that he had been abused by the C.I.A. (The Pentagon had classified as "top secret" a statement he had written detailing the alleged mistreatment.) And although Mohammed said that there were photographs confirming his guilt, U.S. authorities had found none. Instead, they had a copy of the video that had been released on the Internet, which showed the killer's arms but offered no other clues to his identity.

Further confusing matters, a Pakistani named Ahmed Omar Saeed Sheikh had already been convicted of the abduction and murder, in 2002. A British-educated terrorist who had a history of staging kidnappings, he had been sentenced to death in Pakistan for the crime. But the Pakistani government, not known for its leniency, had stayed his execution. Indeed, hearings on the matter had been delayed a remarkable number of times-at least thirty-possibly because of his reported ties to the Pakistani intelligence service, which may have helped free him after he was imprisoned for terrorist activities in India. Mohammed's confession would delay the execution further, since, under Pakistani law, any new evidence is grounds for appeal.

A surprising number of people close to the case are dubious of Mohammed's confession. A longtime friend of Pearl's, the former Journal reporter Asra Nomani, said, "The release of the confession came right in the midst of the U.S. Attorney scandal. There was a drumbeat for Gonzales's resignation. It seemed like a calculated strategy to change the subject. Why now? They'd had the confession for years." Mariane and Daniel Pearl were staying in Nomani's Karachi house at the time of his murder, and Nomani has followed the case meticulously; this fall, she plans to teach a course on the topic at Georgetown University. She said, "I don't think this confession resolves the case. You can't have justice from one person's confession, especially under such unusual circumstances. To me, it's not convincing." She added, "I called all the investigators. They weren't just skeptical-they didn't believe it."

Special Agent Randall Bennett, the head of security for the U.S. consulate in Karachi when Pearl was killed-and whose lead role investigating the murder was featured in the recent film "A Mighty Heart"-said that he has interviewed all the convicted accomplices who are now in custody in Pakistan, and that none of them named Mohammed as playing a role. "K.S.M.'s name never came up," he said. Robert Baer, a former C.I.A. officer, said, "My old colleagues say with one-hundred-per-cent certainty that it was not K.S.M. who killed Pearl." A government official involved in the case said, "The fear is that K.S.M. is covering up for others, and that these people will be released." And Judea Pearl, Daniel's father, said, "Something is fishy. There are a lot of unanswered questions. K.S.M. can say he killed Jesus-he has nothing to lose."

Mariane Pearl, who is relying on the Bush Administration to bring justice in her husband's case, spoke carefully about the investigation. "You need a procedure that will get the truth," she said. "An intelligence agency is not supposed to be above the law."

Mohammed's interrogation was part of a secret C.I.A. program, initiated after September 11th, in which terrorist suspects such as Mohammed were detained in "black sites"-secret prisons outside the United States-and subjected to unusually harsh treatment. The program was effectively suspended last fall, when President Bush announced that he was emptying the C.I.A.'s prisons and transferring the detainees to military custody in Guantánamo. This move followed a Supreme Court ruling, Hamdan v. Rumsfeld, which found that all detainees-including those held by the C.I.A.-had to be treated in a manner consistent with the Geneva Conventions. These treaties, adopted in 1949, bar cruel treatment, degradation, and torture. In late July, the White House issued an executive order promising that the C.I.A. would adjust its methods in order to meet the Geneva standards. At the same time, Bush's order pointedly did not disavow the use of "enhanced interrogation techniques" that would likely be found illegal if used by officials inside the United States. The executive order means that the agency can once again hold foreign terror suspects indefinitely, and without charges, in black sites, without notifying their families or local authorities, or offering access to legal counsel.

The C.I.A.'s director, General Michael Hayden, has said that the program, which is designed to extract intelligence from suspects quickly, is an "irreplaceable" tool for combatting terrorism. And President Bush has said that "this program has given us information that has saved innocent lives, by helping us stop new attacks." He claims that it has contributed to the disruption of at least ten serious Al Qaeda plots since September 11th, three of them inside the United States.

According to the Bush Administration, Mohammed divulged information of tremendous value during his detention. He is said to have helped point the way to the capture of Hambali, the Indonesian terrorist responsible for the 2002 bombings of night clubs in Bali. He also provided information on an Al Qaeda leader in England. Michael Sheehan, a former counterterrorism official at the State Department, said, "K.S.M. is the poster boy for using tough but legal tactics. He's the reason these techniques exist. You can save lives with the kind of information he could give up." Yet Mohammed's confessions may also have muddled some key investigations. Perhaps under duress, he claimed involvement in thirty-one criminal plots-an improbable number, even for a high-level terrorist. Critics say that Mohammed's case illustrates the cost of the C.I.A.'s desire for swift intelligence. Colonel Dwight Sullivan, the top defense lawyer at the Pentagon's Office of Military Commissions, which is expected eventually to try Mohammed for war crimes, called his serial confessions "a textbook example of why we shouldn't allow coercive methods."

The Bush Administration has gone to great lengths to keep secret the treatment of the hundred or so "high-value detainees" whom the C.I.A. has confined, at one point or another, since September 11th. The program has been extraordinarily "compartmentalized," in the nomenclature of the intelligence world. By design, there has been virtually no access for outsiders to the C.I.A.'s prisoners. The utter isolation of these detainees has been described as essential to America's national security. The Justice Department argued this point explicitly last November, in the case of a Baltimore-area resident named Majid Khan, who was held for more than three years by the C.I.A. Khan, the government said, had to be prohibited from access to a lawyer specifically because he might describe the "alternative interrogation methods" that the agency had used when questioning him. These methods amounted to a state secret, the government argued, and disclosure of them could "reasonably be expected to cause extremely grave damage." (The case has not yet been decided.)

Given this level of secrecy, the public and all but a few members of Congress who have been sworn to silence have had to take on faith President Bush's assurances that the C.I.A.'s internment program has been humane and legal, and has yielded crucial intelligence. Representative Alcee Hastings, a Democratic member of the House Select Committee on Intelligence, said, "We talk to the authorities about these detainees, but, of course, they're not going to come out and tell us that they beat the living daylights out of someone." He recalled learning in 2003 that Mohammed had been captured. "It was good news," he said. "So I tried to find out: Where is this guy? And how is he being treated?" For more than three years, Hastings said, "I could never pinpoint anything." Finally, he received some classified briefings on the Mohammed interrogation. Hastings said that he "can't go into details" about what he found out, but, speaking of Mohammed's treatment, he said that even if it wasn't torture, as the Administration claims, "it ain't right, either. Something went wrong."

Since the drafting of the Geneva Conventions, the International Committee of the Red Cross has played a special role in safeguarding the rights of prisoners of war. For decades, governments have allowed officials from the organization to report on the treatment of detainees, to insure that standards set by international treaties are being maintained. The Red Cross, however, was unable to get access to the C.I.A.'s prisoners for five years. Finally, last year, Red Cross officials were allowed to interview fifteen detainees, after they had been transferred to Guantánamo. One of the prisoners was Khalid Sheikh Mohammed. What the Red Cross learned has been kept from the public. The committee believes that its continued access to prisoners worldwide is contingent upon confidentiality, and therefore it addresses violations privately with the authorities directly responsible for prisoner treatment and detention. For this reason, Simon Schorno, a Red Cross spokesman in Washington, said, "The I.C.R.C. does not comment on its findings publicly. Its work is confidential."

The public-affairs office at the C.I.A. and officials at the congressional intelligence-oversight committees would not even acknowledge the existence of the report. Among the few people who are believed to have seen it are Condoleezza Rice, now the Secretary of State; Stephen Hadley, the national-security adviser; John Bellinger III, the Secretary of State's legal adviser; Hayden; and John Rizzo, the agency's acting general counsel. Some members of the Senate and House intelligence-oversight committees are also believed to have had limited access to the report.

Confidentiality may be particularly stringent in this case. Congressional and other Washington sources familiar with the report said that it harshly criticized the C.I.A.'s practices. One of the sources said that the Red Cross described the agency's detention and interrogation methods as tantamount to torture, and declared that American officials responsible for the abusive treatment could have committed serious crimes. The source said the report warned that these officials may have committed "grave breaches" of the Geneva Conventions, and may have violated the U.S. Torture Act, which Congress passed in 1994. The conclusions of the Red Cross, which is known for its credibility and caution, could have potentially devastating legal ramifications.

Concern about the legality of the C.I.A.'s program reached a previously unreported breaking point last week when Senator Ron Wyden, a Democrat on the intelligence committee, quietly put a "hold" on the confirmation of John Rizzo, who as acting general counsel was deeply involved in establishing the agency's interrogation and detention policies. Wyden's maneuver essentially stops the nomination from going forward. "I question if there's been adequate legal oversight," Wyden told me. He said that after studying a classified addendum to President Bush's new executive order, which specifies permissible treatment of detainees, "I am not convinced that all of these techniques are either effective or legal. I don't want to see well-intentioned C.I.A. officers breaking the law because of shaky legal guidance."

A former C.I.A. officer, who supports the agency's detention and interrogation policies, said he worried that, if the full story of the C.I.A. program ever surfaced, agency personnel could face criminal prosecution. Within the agency, he said, there is a "high level of anxiety about political retribution" for the interrogation program. If congressional hearings begin, he said, "several guys expect to be thrown under the bus." He noted that a number of C.I.A. officers have taken out professional liability insurance, to help with potential legal fees.

Paul Gimigliano, a spokesman for the C.I.A., denied any legal impropriety, stressing that "the agency's terrorist-detention program has been implemented lawfully. And torture is illegal under U.S. law. The people who have been part of this important effort are well-trained, seasoned professionals." This spring, the Associated Press published an article quoting the chairman of the House intelligence committee, Silvestre Reyes, who said that Hayden, the C.I.A. director, "vehemently denied" the Red Cross's conclusions. A U.S. official dismissed the Red Cross report as a mere compilation of allegations made by terrorists. And Robert Grenier, a former head of the C.I.A.'s Counterterrorism Center, said that "the C.I.A.'s interrogations were nothing like Abu Ghraib or Guantánamo. They were very, very regimented. Very meticulous." He said, "The program is very careful. It's completely legal."

Accurately or not, Bush Administration officials have described the prisoner abuses at Abu Ghraib and Guantánamo as the unauthorized actions of ill-trained personnel, eleven of whom have been convicted of crimes. By contrast, the treatment of high-value detainees has been directly, and repeatedly, approved by President Bush. The program is monitored closely by C.I.A. lawyers, and supervised by the agency's director and his subordinates at the Counterterrorism Center. While Mohammed was being held by the agency, detailed dossiers on the treatment of detainees were regularly available to the former C.I.A. director George Tenet, according to informed sources inside and outside the agency. Through a spokesperson, Tenet denied making day-to-day decisions about the treatment of individual detainees. But, according to a former agency official, "Every single plan is drawn up by interrogators, and then submitted for approval to the highest possible level-meaning the director of the C.I.A. Any change in the plan-even if an extra day of a certain treatment was added-was signed off by the C.I.A. director."

On September 17, 2001, President Bush signed a secret Presidential finding authorizing the C.I.A. to create paramilitary teams to hunt, capture, detain, or kill designated terrorists almost anywhere in the world. Yet the C.I.A. had virtually no trained interrogators. A former C.I.A. officer involved in fighting terrorism said that, at first, the agency was crippled by its lack of expertise. "It began right away, in Afghanistan, on the fly," he recalled. "They invented the program of interrogation with people who had no understanding of Al Qaeda or the Arab world." The former officer said that the pressure from the White House, in particular from Vice-President Dick Cheney, was intense: "They were pushing us: 'Get information! Do not let us get hit again!' " In the scramble, he said, he searched the C.I.A.'s archives, to see what interrogation techniques had worked in the past. He was particularly impressed with the Phoenix Program, from the Vietnam War. Critics, including military historians, have described it as a program of state-sanctioned torture and murder. A Pentagon-contract study found that, between 1970 and 1971, ninety-seven per cent of the Vietcong targeted by the Phoenix Program were of negligible importance. But, after September 11th, some C.I.A. officials viewed the program as a useful model. A. B. Krongard, who was the executive director of the C.I.A. from 2001 to 2004, said that the agency turned to "everyone we could, including our friends in Arab cultures," for interrogation advice, among them those in Egypt, Jordan, and Saudi Arabia, all of which the State Department regularly criticizes for human-rights abuses.

The C.I.A. knew even less about running prisons than it did about hostile interrogations. Tyler Drumheller, a former chief of European operations at the C.I.A., and the author of a recent book, "On the Brink: How the White House Compromised U.S. Intelligence," said, "The agency had no experience in detention. Never. But they insisted on arresting and detaining people in this program. It was a mistake, in my opinion. You can't mix intelligence and police work. But the White House was really pushing. They wanted someone to do it. So the C.I.A. said, 'We'll try.' George Tenet came out of politics, not intelligence. His whole modus operandi was to please the principal. We got stuck with all sorts of things. This is really the legacy of a director who never said no to anybody."

Many officials inside the C.I.A. had misgivings. "A lot of us knew this would be a can of worms," the former officer said. "We warned them, It's going to become an atrocious mess." The problem from the start, he said, was that no one had thought through what he called "the disposal plan." He continued, "What are you going to do with these people? The utility of someone like K.S.M. is, at most, six months to a year. You exhaust them. Then what? It would have been better if we had executed them."

The C.I.A. program's first important detainee was Abu Zubaydah, a top Al Qaeda operative, who was captured by Pakistani forces in March of 2002. Lacking in-house specialists on interrogation, the agency hired a group of outside contractors, who implemented a regime of techniques that one well-informed former adviser to the American intelligence community described as "a 'Clockwork Orange' kind of approach." The experts were retired military psychologists, and their backgrounds were in training Special Forces soldiers how to survive torture, should they ever be captured by enemy states. The program, known as SERE-an acronym for Survival, Evasion, Resistance, and Escape-was created at the end of the Korean War. It subjected trainees to simulated torture, including waterboarding (simulated drowning), sleep deprivation, isolation, exposure to temperature extremes, enclosure in tiny spaces, bombardment with agonizing sounds, and religious and sexual humiliation. The SERE program was designed strictly for defense against torture regimes, but the C.I.A.'s new team used its expertise to help interrogators inflict abuse. "They were very arrogant, and pro-torture," a European official knowledgeable about the program said. "They sought to render the detainees vulnerable-to break down all of their senses. It takes a psychologist trained in this to understand these rupturing experiences."

The use of psychologists was also considered a way for C.I.A. officials to skirt measures such as the Convention Against Torture. The former adviser to the intelligence community said, "Clearly, some senior people felt they needed a theory to justify what they were doing. You can't just say, 'We want to do what Egypt's doing.' When the lawyers asked what their basis was, they could say, 'We have Ph.D.s who have these theories.' " He said that, inside the C.I.A., where a number of scientists work, there was strong internal opposition to the new techniques. "Behavioral scientists said, 'Don't even think about this!' They thought officers could be prosecuted."

Nevertheless, the SERE experts' theories were apparently put into practice with Zubaydah's interrogation. Zubaydah told the Red Cross that he was not only waterboarded, as has been previously reported; he was also kept for a prolonged period in a cage, known as a "dog box," which was so small that he could not stand. According to an eyewitness, one psychologist advising on the treatment of Zubaydah, James Mitchell, argued that he needed to be reduced to a state of "learned helplessness." (Mitchell disputes this characterization.)

Steve Kleinman, a reserve Air Force colonel and an experienced interrogator who has known Mitchell professionally for years, said that "learned helplessness was his whole paradigm." Mitchell, he said, "draws a diagram showing what he says is the whole cycle. It starts with isolation. Then they eliminate the prisoners' ability to forecast the future-when their next meal is, when they can go to the bathroom. It creates dread and dependency. It was the K.G.B. model. But the K.G.B. used it to get people who had turned against the state to confess falsely. The K.G.B. wasn't after intelligence."

As the C.I.A. captured and interrogated other Al Qaeda figures, it established a protocol of psychological coercion. The program tied together many strands of the agency's secret history of Cold War-era experiments in behavioral science. (In June, the C.I.A. declassified long-held secret documents known as the Family Jewels, which shed light on C.I.A. drug experiments on rats and monkeys, and on the infamous case of Frank R. Olson, an agency employee who leaped to his death from a hotel window in 1953, nine days after he was unwittingly drugged with LSD.) The C.I.A.'s most useful research focussed on the surprisingly powerful effects of psychological manipulations, such as extreme sensory deprivation. According to Alfred McCoy, a history professor at the University of Wisconsin, in Madison, who has written a history of the C.I.A.'s experiments in coercing subjects, the agency learned that "if subjects are confined without light, odors, sound, or any fixed references of time and place, very deep breakdowns can be provoked."

Agency scientists found that in just a few hours some subjects suspended in water tanks-or confined in isolated rooms wearing blacked-out goggles and earmuffs-regressed to semi-psychotic states. Moreover, McCoy said, detainees become so desperate for human interaction that "they bond with the interrogator like a father, or like a drowning man having a lifesaver thrown at him. If you deprive people of all their senses, they'll turn to you like their daddy." McCoy added that "after the Cold War we put away those tools. There was bipartisan reform. We backed away from those dark days. Then, under the pressure of the war on terror, they didn't just bring back the old psychological techniques-they perfected them."

The C.I.A.'s interrogation program is remarkable for its mechanistic aura. "It's one of the most sophisticated, refined programs of torture ever," an outside expert familiar with the protocol said. "At every stage, there was a rigid attention to detail. Procedure was adhered to almost to the letter. There was top-down quality control, and such a set routine that you get to the point where you know what each detainee is going to say, because you've heard it before. It was almost automated. People were utterly dehumanized. People fell apart. It was the intentional and systematic infliction of great suffering masquerading as a legal process. It is just chilling."

The U.S. government first began tracking Khalid Sheikh Mohammed in 1993, shortly after his nephew Ramzi Yousef blew a gaping hole in the World Trade Center. Mohammed, officials learned, had transferred money to Yousef. Mohammed, born in either 1964 or 1965, was raised in a religious Sunni Muslim family in Kuwait, where his family had migrated from the Baluchistan region of Pakistan. In the mid-eighties, he was trained as a mechanical engineer in the U.S., attending two colleges in North Carolina.

As a teen-ager, Mohammed had been drawn to militant, and increasingly violent, Muslim causes. He joined the Muslim Brotherhood at the age of sixteen, and, after his graduation from North Carolina Agricultural and Technical State University, in Greensboro-where he was remembered as a class clown, but religious enough to forgo meat when eating at Burger King-he signed on with the anti-Soviet jihad in Afghanistan, receiving military training and establishing ties with Islamist terrorists. By all accounts, his animus toward the U.S. was rooted in a hatred of Israel.

In 1994, Mohammed, who was impressed by Yousef's notoriety after the first World Trade Center bombing, joined him in scheming to blow up twelve U.S. jumbo jets over two days. The so-called Bojinka plot was disrupted in 1995, when Philippine police broke into an apartment that Yousef and other terrorists were sharing in Manila, which was filled with bomb-making materials. At the time of the raid, Mohammed was working in Doha, Qatar, at a government job. The following year, he narrowly escaped capture by F.B.I. officers and slipped into the global jihadist network, where he eventually joined forces with Osama bin Laden, in Afghanistan. Along the way, he married and had children.

Many journalistic accounts have presented Mohammed as a charismatic, swashbuckling figure: in the Philippines, he was said to have flown a helicopter close enough to a girlfriend's office window so that she could see him; in Pakistan, he supposedly posed as an anonymous bystander and gave interviews to news reporters about his nephew's arrest. Neither story is true. But Mohammed did seem to enjoy taunting authorities after the September 11th attacks, which, in his eventual confession, he claimed to have orchestrated "from A to Z." In April, 2002, Mohammed arranged to be interviewed on Al Jazeera by its London bureau chief, Yosri Fouda, and took personal credit for the atrocities. "I am the head of the Al Qaeda military committee," he said. "And yes, we did it." Fouda, who conducted the interview at an Al Qaeda safe house in Karachi, said that he was astounded not only by Mohammed's boasting but also by his seeming imperviousness to the danger of being caught. Mohammed permitted Al Jazeera to reveal that he was hiding out in the Karachi area. When Fouda left the apartment, Mohammed, apparently unarmed, walked him downstairs and out into the street.

In the early months of 2003, U.S. authorities reportedly paid a twenty-five-million-dollar reward for information that led to Mohammed's arrest. U.S. officials closed in on him, at 4 A.M. on March 1st, waking him up in a borrowed apartment in Rawalpindi, Pakistan. The officials hung back as Pakistani authorities handcuffed and hooded him, and took him to a safe house. Reportedly, for the first two days, Mohammed robotically recited Koranic verses and refused to divulge much more than his name. A videotape obtained by "60 Minutes" shows Mohammed at the end of this episode, complaining of a head cold; an American voice can be heard in the background. This was the last image of Mohammed to be seen by the public. By March 4th, he was in C.I.A. custody.

Captured along with Mohammed, according to some accounts, was a letter from bin Laden, which may have led officials to think that he knew where the Al Qaeda founder was hiding. If Mohammed did have this crucial information, it was time sensitive-bin Laden never stayed in one place for long-and officials needed to extract it quickly. At the time, many American intelligence officials still feared a "second wave" of Al Qaeda attacks, ratcheting the pressure further.

According to George Tenet's recent memoir, "At the Center of the Storm," Mohammed told his captors that he wouldn't talk until he was given a lawyer in New York, where he assumed he would be taken. (He had been indicted there in connection with the Bojinka plot.) Tenet writes, "Had that happened, I am confident that we would have obtained none of the information he had in his head about imminent threats against the American people." Opponents of the C.I.A.'s approach, however, note that Ramzi Yousef gave a voluminous confession after being read his Miranda rights. "These guys are egomaniacs," a former federal prosecutor said. "They love to talk!"

A complete picture of Mohammed's time in secret detention remains elusive. But a partial narrative has emerged through interviews with European and American sources in intelligence, government, and legal circles, as well as with former detainees who have been released from C.I.A. custody. People familiar with Mohammed's allegations about his interrogation, and interrogations of other high-value detainees, describe the accounts as remarkably consistent.

Soon after Mohammed's arrest, sources say, his American captors told him, "We're not going to kill you. But we're going to take you to the very brink of your death and back." He was first taken to a secret U.S.-run prison in Afghanistan. According to a Human Rights Watch report released two years ago, there was a C.I.A.-affiliated black site in Afghanistan by 2002: an underground prison near Kabul International Airport. Distinctive for its absolute lack of light, it was referred to by detainees as the Dark Prison. Another detention facility was reportedly a former brick factory, just north of Kabul, known as the Salt Pit. The latter became infamous for the 2002 death of a detainee, reportedly from hypothermia, after prison officials stripped him naked and chained him to the floor of his concrete cell, in freezing temperatures.

In all likelihood, Mohammed was transported from Pakistan to one of the Afghan sites by a team of black-masked commandos attached to the C.I.A.'s paramilitary Special Activities Division. According to a report adopted in June by the Parliamentary Assembly of the Council of Europe, titled "Secret Detentions and Illegal Transfers of Detainees," detainees were "taken to their cells by strong people who wore black outfits, masks that covered their whole faces, and dark visors over their eyes." (Some personnel reportedly wore black clothes made from specially woven synthetic fabric that couldn't be ripped or torn.) A former member of a C.I.A. transport team has described the "takeout" of prisoners as a carefully choreographed twenty-minute routine, during which a suspect was hog-tied, stripped naked, photographed, hooded, sedated with anal suppositories, placed in diapers, and transported by plane to a secret location.

A person involved in the Council of Europe inquiry, referring to cavity searches and the frequent use of suppositories during the takeout of detainees, likened the treatment to "sodomy." He said, "It was used to absolutely strip the detainee of any dignity. It breaks down someone's sense of impenetrability. The interrogation became a process not just of getting information but of utterly subordinating the detainee through humiliation." The former C.I.A. officer confirmed that the agency frequently photographed the prisoners naked, "because it's demoralizing." The person involved in the Council of Europe inquiry said that photos were also part of the C.I.A.'s quality-control process. They were passed back to case officers for review.

A secret government document, dated December 10, 2002, detailing "SERE Interrogation Standard Operating Procedure," outlines the advantages of stripping detainees. "In addition to degradation of the detainee, stripping can be used to demonstrate the omnipotence of the captor or to debilitate the detainee." The document advises interrogators to "tear clothing from detainees by firmly pulling downward against buttoned buttons and seams. Tearing motions shall be downward to prevent pulling the detainee off balance." The memo also advocates the "Shoulder Slap," "Stomach Slap," "Hooding," "Manhandling," "Walling," and a variety of "Stress Positions," including one called "Worship the Gods."

In the process of being transported, C.I.A. detainees such as Mohammed were screened by medical experts, who checked their vital signs, took blood samples, and marked a chart with a diagram of a human body, noting scars, wounds, and other imperfections. As the person involved in the Council of Europe inquiry put it, "It's like when you hire a motor vehicle, circling where the scratches are on the rearview mirror. Each detainee was continually assessed, physically and psychologically."

According to sources, Mohammed said that, while in C.I.A. custody, he was placed in his own cell, where he remained naked for several days. He was questioned by an unusual number of female handlers, perhaps as an additional humiliation. He has alleged that he was attached to a dog leash, and yanked in such a way that he was propelled into the walls of his cell. Sources say that he also claimed to have been suspended from the ceiling by his arms, his toes barely touching the ground. The pressure on his wrists evidently became exceedingly painful.

Ramzi Kassem, who teaches at Yale Law School, said that a Yemeni client of his, Sanad al-Kazimi, who is now in Guantánamo, alleged that he had received similar treatment in the Dark Prison, the facility near Kabul. Kazimi claimed to have been suspended by his arms for long periods, causing his legs to swell painfully. "It's so traumatic, he can barely speak of it," Kassem said. "He breaks down in tears." Kazimi also claimed that, while hanging, he was beaten with electric cables.

According to sources familiar with interrogation techniques, the hanging position is designed, in part, to prevent detainees from being able to sleep. The former C.I.A. officer, who is knowledgeable about the interrogation program, explained that "sleep deprivation works. Your electrolyte balance changes. You lose all balance and ability to think rationally. Stuff comes out." Sleep deprivation has been recognized as an effective form of coercion since the Middle Ages, when it was called tormentum insomniae. It was also recognized for decades in the United States as an illegal form of torture. An American Bar Association report, published in 1930, which was cited in a later U.S. Supreme Court decision, said, "It has been known since 1500 at least that deprivation of sleep is the most effective torture and certain to produce any confession desired."

Under President Bush's new executive order, C.I.A. detainees must receive the "basic necessities of life, including adequate food and water, shelter from the elements, necessary clothing, protection from extremes of heat and cold, and essential medical care." Sleep, according to the order, is not among the basic necessities.

In addition to keeping a prisoner awake, the simple act of remaining upright can over time cause significant pain. McCoy, the historian, noted that "longtime standing" was a common K.G.B. interrogation technique. In his 2006 book, "A Question of Torture," he writes that the Soviets found that making a victim stand for eighteen to twenty-four hours can produce "excruciating pain, as ankles double in size, skin becomes tense and intensely painful, blisters erupt oozing watery serum, heart rates soar, kidneys shut down, and delusions deepen."

Mohammed is said to have described being chained naked to a metal ring in his cell wall for prolonged periods in a painful crouch. (Several other detainees who say that they were confined in the Dark Prison have described identical treatment.) He also claimed that he was kept alternately in suffocating heat and in a painfully cold room, where he was doused with ice water. The practice, which can cause hypothermia, violates the Geneva Conventions, and President Bush's new executive order arguably bans it.

Some detainees held by the C.I.A. claimed that their cells were bombarded with deafening sound twenty-fours hours a day for weeks, and even months. One detainee, Binyam Mohamed, who is now in Guantánamo, told his lawyer, Clive Stafford Smith, that speakers blared music into his cell while he was handcuffed. Detainees recalled the sound as ranging from ghoulish laughter, "like the soundtrack from a horror film," to ear-splitting rap anthems. Stafford Smith said that his client found the psychological torture more intolerable than the physical abuse that he said he had been previously subjected to in Morocco, where, he said, local intelligence agents had sliced him with a razor blade. "The C.I.A. worked people day and night for months," Stafford Smith quoted Binyam Mohamed as saying. "Plenty lost their minds. I could hear people knocking their heads against the walls and doors, screaming their heads off."

Professor Kassem said his Yemeni client, Kazimi, had told him that, during his incarceration in the Dark Prison, he attempted suicide three times, by ramming his head into the walls. "He did it until he lost consciousness," Kassem said. "Then they stitched him back up. So he did it again. The next time, he woke up, he was chained, and they'd given him tranquillizers. He asked to go to the bathroom, and then he did it again." This last time, Kazimi was given more tranquillizers, and chained in a more confining manner.

The case of Khaled el-Masri, another detainee, has received wide attention. He is the German car salesman whom the C.I.A. captured in 2003 and dispatched to Afghanistan, based on erroneous intelligence; he was released in 2004, and Condoleezza Rice reportedly conceded the mistake to the German chancellor. Masri is considered one of the more credible sources on the black-site program, because Germany has confirmed that he has no connections to terrorism. He has also described inmates bashing their heads against the walls. Much of his account appeared on the front page of the Times. But, during a visit to America last fall, he became tearful as he recalled the plight of a Tanzanian in a neighboring cell. The man seemed "psychologically at the end," he said. "I could hear him ramming his head against the wall in despair. I tried to calm him down. I asked the doctor, 'Will you take care of this human being?' " But the doctor, whom Masri described as American, refused to help. Masri also said that he was told that guards had "locked the Tanzanian in a suitcase for long periods of time-a foul-smelling suitcase that made him vomit." (Masri did not witness such abuse.)

Masri described his prison in Afghanistan as a filthy hole, with walls scribbled on in Pashtun and Arabic. He was given no bed, only a coarse blanket on the floor. At night, it was too cold to sleep. He said, "The water was putrid. If you took a sip, you could taste it for hours. You could smell a foul smell from it three metres away." The Salt Pit, he said, "was managed and run by the Americans. It was not a secret. They introduced themselves as Americans." He added, "When anything came up, they said they couldn't make a decision. They said, 'We will have to pass it on to Washington.' " The interrogation room at the Salt Pit, he said, was overseen by a half-dozen English-speaking masked men, who shoved him and shouted at him, saying, "You're in a country where there's no rule of law. You might be buried here."

According to two former C.I.A. officers, an interrogator of Mohammed told them that the Pakistani was kept in a cell over which a sign was placed: "The Proud Murderer of 3,000 Americans." (Another source calls this apocryphal.) One of these former officers defends the C.I.A.'s program by noting that "there was absolutely nothing done to K.S.M. that wasn't done to the interrogators themselves"-a reference to SERE-like training. Yet the Red Cross report emphasizes that it was the simultaneous use of several techniques for extended periods that made the treatment "especially abusive." Senator Carl Levin, the chairman of the Senate Armed Services Committee, who has been a prominent critic of the Administration's embrace of harsh interrogation techniques, said that, particularly with sensory deprivation, "there's a point where it's torture. You can put someone in a refrigerator and it's torture. Everything is a matter of degree."

One day, Mohammed was apparently transferred to a specially designated prison for high-value detainees in Poland. Such transfers were so secretive, according to the report by the Council of Europe, that the C.I.A. filed dummy flight plans, indicating that the planes were heading elsewhere. Once Polish air space was entered, the Polish aviation authority would secretly shepherd the flight, leaving no public documentation. The Council of Europe report notes that the Polish authorities would file a one-way flight plan out of the country, creating a false paper trail. (The Polish government has strongly denied that any black sites were established in the country.)

No more than a dozen high-value detainees were held at the Polish black site, and none have been released from government custody; accordingly, no first-hand accounts of conditions there have emerged. But, according to well-informed sources, it was a far more high-tech facility than the prisons in Afghanistan. The cells had hydraulic doors and air-conditioning. Multiple cameras in each cell provided video surveillance of the detainees. In some ways, the circumstances were better: the detainees were given bottled water. Without confirming the existence of any black sites, Robert Grenier, the former C.I.A. counterterrorism chief, said, "The agency's techniques became less aggressive as they learned the art of interrogation," which, he added, "is an art."

Mohammed was kept in a prolonged state of sensory deprivation, during which every point of reference was erased. The Council on Europe's report describes a four-month isolation regime as typical. The prisoners had no exposure to natural light, making it impossible for them to tell if it was night or day. They interacted only with masked, silent guards. (A detainee held at what was most likely an Eastern European black site, Mohammed al-Asad, told me that white noise was piped in constantly, although during electrical outages he could hear people crying.) According to a source familiar with the Red Cross report, Khalid Sheikh Mohammed claimed that he was shackled and kept naked, except for a pair of goggles and earmuffs. (Some prisoners were kept naked for as long as forty days.) He had no idea where he was, although, at one point, he apparently glimpsed Polish writing on a water bottle.

In the C.I.A.'s program, meals were delivered sporadically, to insure that the prisoners remained temporally disoriented. The food was largely tasteless, and barely enough to live on. Mohammed, who upon his capture in Rawalpindi was photographed looking flabby and unkempt, was now described as being slim. Experts on the C.I.A. program say that the administering of food is part of its psychological arsenal. Sometimes portions were smaller than the day before, for no apparent reason. "It was all part of the conditioning," the person involved in the Council of Europe inquiry said. "It's all calibrated to develop dependency."

The inquiry source said that most of the Poland detainees were waterboarded, including Mohammed. According to the sources familiar with the Red Cross report, Mohammed claimed to have been waterboarded five times. Two former C.I.A. officers who are friends with one of Mohammed's interrogators called this bravado, insisting that he was waterboarded only once. According to one of the officers, Mohammed needed only to be shown the drowning equipment again before he "broke."

"Waterboarding works," the former officer said. "Drowning is a baseline fear. So is falling. People dream about it. It's human nature. Suffocation is a very scary thing. When you're waterboarded, you're inverted, so it exacerbates the fear. It's not painful, but it scares the shit out of you." (The former officer was waterboarded himself in a training course.) Mohammed, he claimed, "didn't resist. He sang right away. He cracked real quick." He said, "A lot of them want to talk. Their egos are unimaginable. K.S.M. was just a little doughboy. He couldn't stand toe to toe and fight it out."

The former officer said that the C.I.A. kept a doctor standing by during interrogations. He insisted that the method was safe and effective, but said that it could cause lasting psychic damage to the interrogators. During interrogations, the former agency official said, officers worked in teams, watching each other behind two-way mirrors. Even with this group support, the friend said, Mohammed's interrogator "has horrible nightmares." He went on, "When you cross over that line of darkness, it's hard to come back. You lose your soul. You can do your best to justify it, but it's well outside the norm. You can't go to that dark a place without it changing you." He said of his friend, "He's a good guy. It really haunts him. You are inflicting something really evil and horrible on somebody."

Among the few C.I.A. officials who knew the details of the detention and interrogation program, there was a tense debate about where to draw the line in terms of treatment. John Brennan, Tenet's former chief of staff, said, "It all comes down to individual moral barometers." Waterboarding, in particular, troubled many officials, from both a moral and a legal perspective. Until 2002, when Bush Administration lawyers asserted that waterboarding was a permissible interrogation technique for "enemy combatants," it was classified as a form of torture, and treated as a serious criminal offense. American soldiers were court-martialled for waterboarding captives as recently as the Vietnam War.

A C.I.A. source said that Mohammed was subjected to waterboarding only after interrogators determined that he was hiding information from them. But Mohammed has apparently said that, even after he started coöperating, he was waterboarded. Footnotes to the 9/11 Commission report indicate that by April 17, 2003-a month and a half after he was captured-Mohammed had already started providing substantial information on Al Qaeda. Nonetheless, according to the person involved in the Council of Europe inquiry, he was kept in isolation for years. During this time, Mohammed supplied intelligence on the history of the September 11th plot, and on the structure and operations of Al Qaeda. He also described plots still in a preliminary phase of development, such as a plan to bomb targets on America's West Coast.

Ultimately, however, Mohammed claimed responsibility for so many crimes that his testimony became to seem inherently dubious. In addition to confessing to the Pearl murder, he said that he had hatched plans to assassinate President Clinton, President Carter, and Pope John Paul II. Bruce Riedel, who was a C.I.A. analyst for twenty-nine years, and who now works at the Brookings Institution, said, "It's difficult to give credence to any particular area of this large a charge sheet that he confessed to, considering the situation he found himself in. K.S.M. has no prospect of ever seeing freedom again, so his only gratification in life is to portray himself as the James Bond of jihadism."

By 2004, there were growing calls within the C.I.A. to transfer to military custody the high-value detainees who had told interrogators what they knew, and to afford them some kind of due process. But Donald Rumsfeld, then the Defense Secretary, who had been heavily criticized for the abusive conditions at military prisons such as Abu Ghraib and Guantánamo, refused to take on the agency's detainees, a former top C.I.A. official said. "Rumsfeld's attitude was, You've got a real problem." Rumsfeld, the official said, "was the third most powerful person in the U.S. government, but he only looked out for the interests of his department-not the whole Administration." (A spokesperson for Rumsfeld said that he had no comment.)

C.I.A. officials were stymied until the Supreme Court's Hamdan ruling, which prompted the Administration to send what it said were its last high-value detainees to Cuba. Robert Grenier, like many people in the C.I.A., was relieved. "There has to be some sense of due process," he said. "We can't just make people disappear." Still, he added, "The most important source of intelligence we had after 9/11 came from the interrogations of high-value detainees." And he said that Mohammed was "the most valuable of the high-value detainees, because he had operational knowledge." He went on, "I can respect people who oppose aggressive interrogations, but they should admit that their principles may be putting American lives at risk."

Yet Philip Zelikow, the executive director of the 9/11 Commission and later the State Department's top counsellor, under Rice, is not convinced that eliciting information from detainees justifies "physical torment." After leaving the government last year, he gave a speech in Houston, in which he said, "The question would not be, Did you get information that proved useful? Instead it would be, Did you get information that could have been usefully gained only from these methods?" He concluded, "My own view is that the cool, carefully considered, methodical, prolonged, and repeated subjection of captives to physical torment, and the accompanying psychological terror, is immoral."

Without more transparency, the value of the C.I.A.'s interrogation and detention program is impossible to evaluate. Setting aside the moral, ethical, and legal issues, even supporters, such as John Brennan, acknowledge that much of the information that coercion produces is unreliable. As he put it, "All these methods produced useful information, but there was also a lot that was bogus." When pressed, one former top agency official estimated that "ninety per cent of the information was unreliable." Cables carrying Mohammed's interrogation transcripts back to Washington reportedly were prefaced with the warning that "the detainee has been known to withhold information or deliberately mislead." Mohammed, like virtually all the top Al Qaeda prisoners held by the C.I.A., has claimed that, while under coercion, he lied to please his captors.

In theory, a military commission could sort out which parts of Mohammed's confession are true and which are lies, and obtain a conviction. Colonel Morris D. Davis, the chief prosecutor at the Office of Military Commissions, said that he expects to bring charges against Mohammed "in a number of months." He added, "I'd be shocked if the defense didn't try to make K.S.M.'s treatment a problem for me, but I don't think it will be insurmountable."

Critics of the Administration fear that the unorthodox nature of the C.I.A.'s interrogation and detention program will make it impossible to prosecute the entire top echelon of Al Qaeda leaders in captivity. Already, according to the Wall Street Journal, credible allegations of torture have caused a Marine Corps prosecutor reluctantly to decline to bring charges against Mohamedou Ould Slahi, an alleged Al Qaeda leader held in Guantánamo. Bruce Riedel, the former C.I.A. analyst, asked, "What are you going to do with K.S.M. in the long run? It's a very good question. I don't think anyone has an answer. If you took him to any real American court, I think any judge would say there is no admissible evidence. It would be thrown out."

The problems with Mohammed's coerced confessions are especially glaring in the Daniel Pearl case. It may be that Mohammed killed Pearl, but contradictory evidence and opinion continue to surface. Yosri Fouda, the Al Jazeera reporter who interviewed Mohammed in Karachi, said that although Mohammed handed him a package of propaganda items, including an unedited video of the Pearl murder, he never identified himself as playing a role in the killing, which occurred in the same city just two months earlier. And a federal official involved in Mohammed's case said, "He has no history of killing with his own hands, although he's proved happy to commit mass murder from afar." Al Qaeda's leadership had increasingly focussed on symbolic political targets. "For him, it's not personal," the official said. "It's business."

Ordinarily, the U.S. legal system is known for resolving such mysteries with painstaking care. But the C.I.A.'s secret interrogation program, Senator Levin said, has undermined the public's trust in American justice, both here and abroad. "A guy as dangerous as K.S.M. is, and half the world wonders if they can believe him-is that what we want?" he asked. "Statements that can't be believed, because people think they rely on torture?"

Asra Nomani, the Pearls' friend, said of the Mohammed confession, "I'm not interested in unfair justice, even for bad people." She went on, "Danny was such a person of conscience. I don't think he would have wanted all of this dirty business. I don't think he would have wanted someone being tortured. He would have been repulsed. This is the kind of story that Danny would have investigated. He really believed in American principles."

Jane Mayer has been a staff writer for The New Yorker since 1995.
© 2007 The New Yorker