In the war on terror, one historian says, the C.I.A. “didn’t just bring back the old psychological techniques—they perfected them.” Illustration by Guy Billout

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.”