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Even for those who believed that brutal treatment could produce results, the official said, “seeing these depths of human misery and degradation has a traumatic effect.”

A footnote to another of the memos described a rift between line officers questioning Abu Zubaydah at a secret C.I.A. prison in Thailand and their bosses at headquarters, and asserted that the brutal treatment may have been “unnecessary.”

In March 2002, when Abu Zubaydah was captured in Pakistan after a gunfight with Pakistani security officers backed by F.B.I. and C.I.A. officers, Bush administration officials portrayed him as a Qaeda leader. That judgment was reflected in the Aug. 1, 2002, legal opinion signed by Jay S. Bybee, then head of the Justice Department’s Office of Legal Counsel.The memo summarizes the C.I.A.’s judgment that Abu Zubaydah, then 31, had risen rapidly to “third or fourth man in Al Qaeda” and had served as “senior lieutenant” to Osama bin Laden. It said he had “managed a network of training camps” and had been “involved in every major terrorist operation carried out by Al Qaeda.”

The memo reported the C.I.A.’s portrayal of “a highly self-directed individual who prizes his independence,” a deceptive narcissist, healthy and tough, who agency officers believed was the most senior terrorist caught since the attacks of Sept. 11, 2001.

His interrogation, according to multiple accounts, began in Pakistan and continued at the secret C.I.A. site in Thailand, with a traditional, rapport-building approach led by two F.B.I. agents, who even helped care for him as his gunshot wounds healed.

A C.I.A. interrogation team that arrived a week or two later, which included former military psychologists, did not change the approach to questioning, but began to keep him awake night and day with blasting rock music, have his clothes removed and keep his cell cold.

The legal basis for this treatment is uncertain, but lawyers at C.I.A. headquarters were in constant touch with interrogators, as well as with Mr. Bybee’s subordinate in the Office of Legal Counsel, John C. Yoo, who was drafting memos on the legal limits of interrogation.

Through the summer of 2002, Abu Zubaydah continued to provide valuable information. Interrogators began to surmise that he was not a leader, but rather a helpful training camp personnel clerk who would arrange false documents and travel for jihadists, including Qaeda members.

He knew enough to give interrogators “a road map of Al Qaeda operatives,” an agency officer said. He also repeated talk he had heard about possible plots or targets in the United States, though when F.B.I. agents followed up, most of it turned out to be idle discussion or preliminary brainstorming.At the time, former C.I.A. officials say, his tips were extremely useful, helping to track several other important terrorists, including Mr. Mohammed.

But senior agency officials, still persuaded, as they had told President George W. Bush and his staff, that he was an important Qaeda leader, insisted that he must know more.“You get a ton of information, but headquarters says, ‘There must be more,’ ” recalled one intelligence officer who was involved in the case. As described in the footnote to the memo, the use of repeated waterboarding against Abu Zubaydah was ordered “at the direction of C.I.A. headquarters,” and officials were dispatched from headquarters “to watch the last waterboard session.”

The memo, written in 2005 and signed by Steven G. Bradbury, who worked in the Office of Legal Counsel, concluded that the waterboarding was justified even if the prisoner turned out not to know as much as officials had thought.

And he did not, according to the former intelligence officer involved in the Abu Zubaydah case. “He pleaded for his life,” the official said. “But he gave up no new information. He had no more information to give.”

Since 2002, the C.I.A. has downgraded its assessment of Abu Zubaydah’s significance, while continuing to call his revelations important. In an interview, an intelligence officer said that the current view was that Abu Zubaydah was “an important terrorist facilitator” who disclosed “essential raw material for successful counterterrorist action.”

Amid the high alert following the Sept. 11 terrorist attacks, a small CIA unit examined the potential for targeted assassinations of al Qaeda operatives, according to the three former officials. The Ford administration had banned assassinations in the response to investigations into intelligence abuses in the 1970s. Some officials who advocated the approach were seeking to build teams of CIA and military Special Forces commandos to emulate what the Israelis did after the Munich Olympics terrorist attacks, said another former intelligence official.

"It was straight out of the movies," one of the former intelligence officials said. "It was like: Let's kill them all."

Also in September 2001, as CIA operatives were preparing for an offensive in Afghanistan, officials drafted cables that would have authorized assassinations of specified targets on the spot.

One draft cable, later scrapped, authorized officers on the ground to "kill on sight" certain al Qaeda targets, according to one person who saw it. The context of the memo suggested it was designed for the most senior leaders in al Qaeda, this person said. Eventually Mr. Bush issued the finding that authorized the capturing of several top al Qaeda leaders, and allowed officers to kill the targets if capturing proved too dangerous or risky.

Lawmakers first learned specifics of the CIA initiative the day after Mr. Panetta did, when he briefed them on it for 45 minutes

On Sunday, lawmakers criticized the Bush administration's decision not to tell Congress. Senate Intelligence Committee Chairman Dianne Feinstein, a Democrat from California, hinted that the Bush administration may have broken the law by not telling Congress.

Ms. Feinstein said Mr. Panetta told the lawmakers that Mr. Cheney had ordered that the information be withheld from Congress. Mr. Cheney on Sunday couldn't be reached for comment through former White House aides.

Iran rejected the report, saying the US was guilty of double standards. Foreign Minister Manouchehr Mottaki said the US had no right to accuse others in light of its actions at Abu Ghraib and Guantanamo Bay.

The report charges that Iran's involvement in countries like Lebanon, Iraq, Afghanistan and in the Palestinian territories threatens efforts to promote peace, economic stability in the Gulf and democracy.

The report singles out the Quds force, an elite branch of Iran's Revolutionary Guard as the channel through which Iran supports terrorist activities and groups abroad. The report also takes to task Syria, an Iranian ally in the region.

Of equal concern, our correspondent notes, is the advance of al-Qaeda in Pakistan and Afghanistan where terrorist attacks are sharply on the rise while the rest of the world, including Iraq, has seen terrorist attacks decrease. The acting coordinator for counter-terrorism for the state department, Ronald Schlicher, told journalists that al-Qaeda was using border areas of Pakistan to regroup. "Al-Qaeda and al-Qaeda associated networks remain the greatest terrorist threat to the US and its partners," he said.

Mr Schlicher said they were using the Afghan-Pakistan border area "as a safe haven where they can hide, where they can train, where they can communicate with their followers, where they can plot attacks and where they can make plans to send fighters to support the insurgency in Afghanistan".

Washington is worried that the government in Islamabad might collapse, and last week US Secretary of State Hillary Clinton said the Taleban fighters posed an existential threat to Pakistan, which is a nuclear power, our correspondent adds.

The memo said the CIA waterboarded Mohammed only after it became apparent that standard interrogation techniques were not working, a judgment that appears to have been reached rapidly. Mohammed, according to the memo, resisted giving any answers to questions about future attacks, saying, "Soon you will know."

A 2005 memo by the Justice Department's Office of Legal Counsel said that Mohammed and Abu Zubaida, the nom de guerre of Zayn al-Abidin Muhammed Hussein, an al-Qaeda associate who was also subjected to coercive interrogation, have been "pivotal sources because of their ability and willingness to provide their analysis and speculation about the capabilities, methodologies and mindsets of terrorists."

One of the Justice Department memos said waterboarding "may be used on a High Value Detainee only if the CIA has 'credible intelligence that a terrorist attack is imminent.' " It also stated that waterboarding can be employed only if "other interrogation methods have failed to elicit the information [or] CIA has clear indications that other methods are unlikely to elicit this information within the perceived time limit for preventing the attack."

The memo, while saying it discussed only a fraction of the important intelligence gleaned from Abu Zubaida and Mohammed, cited three specific successes: the identification of alleged "dirty bomber" Jose Padilla; the discovery of a "Second Wave" attack targeting Los Angeles; and the break-up of the Indonesian Jemaah Islamiya cell, an al-Qaeda ally led by Riduan Isamuddin, better known as Hambali. The last example was an undoubted success that led to the capture of several suspects, but the other two are much less clear-cut.

The Office of Legal Counsel memo said Abu Zubaida provided significant information on two operatives, including Jose Padilla, who "planned to build and detonate a dirty bomb in the Washington D.C area."

now he has started a review of policy toward Afghanistan and Pakistan intended to find a new strategy, and he signaled that reconciliation could emerge as an important initiative, mirroring the strategy used by Gen. David H. Petraeus in Iraq.

“If you talk to General Petraeus, I think he would argue that part of the success in Iraq involved reaching out to people that we would consider to be Islamic fundamentalists, but who were willing to work with us because they had been completely alienated by the tactics of Al Qaeda in Iraq,” Mr. Obama said. At the same time, he acknowledged that outreach may not yield the same success. “The situation in Afghanistan is, if anything, more complex,” he said. “You have a less governed region, a history of fierce independence among tribes. Those tribes are multiple and sometimes operate at cross purposes, and so figuring all that out is going to be much more of a challenge.”

administration officials have criticized the Pakistani government for its own reconciliation deal with local Taliban leaders in the Swat Valley, where Islamic law has been imposed and radical figures hold sway. Pakistani officials have sought to reassure administration officials that their deal was not a surrender to the Taliban, but rather an attempt to drive a wedge between hard-core Taliban leaders and local Islamists.

During the interview, Mr. Obama also left open the option for American operatives to capture terrorism suspects abroad even without the cooperation of a country where they were found. “There could be situations — and I emphasize ‘could be’ because we haven’t made a determination yet — where, let’s say that we have a well-known Al Qaeda operative that doesn’t surface very often, appears in a third country with whom we don’t have an extradition relationship or would not be willing to prosecute, but we think is a very dangerous person,” he said.“I think we still have to think about how do we deal with that kind of scenario,”

The president went on to say that “we don’t torture” and that “we ultimately provide anybody that we’re detaining an opportunity through habeas corpus to answer to charges.”Aides later said Mr. Obama did not mean to suggest that everybody held by American forces would be granted habeas corpus or the right to challenge their detention. In a court filing last month, the Obama administration agreed with the Bush administration position that 600 prisoners in a cavernous prison on the American air base at Bagram in Afghanistan have no right to seek their release in court.

Cheney restated his claim that "there was a relationship between al Qaeda and Iraq that stretched back 10 years. It's not something I made up. ... We know for a fact that Saddam Hussein was a sponsor -- a state sponsor -- of terror. It's not my judgment. That was the judgment of our [intelligence community] and State Department." Cheney identified former CIA Director George Tenet as the "prime source of information" on the relationship between Iraq and al Qaeda.

Tenet "testified, if you go back and check the record, in the fall of [2002] before the Senate Intelligence Committee -- in open session -- that there was a relationship," Cheney said.

He reiterated his call for President Obama to declassify documents detailing the results of "enhanced interrogations" of high-value detainees. Since Obama has already released memos detailing the interrogation methods, Cheney said, it is important to share the results of those interrogations with the public as well. "I would not ordinarily be leading the charge to declassify classified information, otherwise they wouldn't call me Darth Vader for nothing," Cheney said. But "once the [Obama] administration released the legal memos that gave the opinions that were used to guide the interrogation program, they'd given away the store. ... I [therefore] thought it was important to have the results that were gained from that interrogation program front and center as well."

On May 21, Cheney gave a full-throated defense of the Bush administration's enhanced interrogations of al Qaeda prisoners during an appearance at the conservative American Enterprise Institute. He has said that the interrogations saved the lives of "thousands, perhaps hundreds of thousands." He called the techniques the Bush administration approved "legal, essential, justified, successful and the right thing to do."

The 2005 memo also says that the C.I.A. used waterboarding 183 times in March 2003 against Khalid Shaikh Mohammed, the self-described planner of the Sept. 11, 2001, terrorist attacks.

Mr. Obama said C.I.A. officers who had used waterboarding and other harsh interrogation methods with the approval of the Justice Department would not be prosecuted. He has repeatedly suggested that he opposes Congressional proposals for a “truth commission” to examine Bush administration counterterrorism programs, including interrogation and warrantless eavesdropping.

The Senate Intelligence Committee has begun a yearlong, closed-door investigation of the C.I.A. interrogation program, in part to assess claims of Bush administration officials that brutal treatment, including slamming prisoners into walls, shackling them in standing positions for days and confining them in small boxes, was necessary to get information.

The fact that waterboarding was repeated so many times may raise questions about its effectiveness, as well as about assertions by Bush administration officials that their methods were used under strict guidelines.

A footnote to another 2005 Justice Department memo released Thursday said waterboarding was used both more frequently and with a greater volume of water than the C.I.A. rules permitted.

Michael V. Hayden, director of the C.I.A. for the last two years of the Bush administration, would not comment when asked on the program “Fox News Sunday” if Mr. Mohammed had been waterboarded 183 times. He said he believed that that information was still classified.

Mr. Hayden said he had opposed the release of the memos, even though President Obama has said the techniques will never be used again, because they would tell Al Qaeda “the outer limits that any American would ever go in terms of interrogating an Al Qaeda terrorist.”

He also disputed an article in The New York Times on Saturday that said Abu Zubaydah had revealed nothing new after being waterboarded, saying that he believed that after unspecified “techniques” were used, Abu Zubaydah revealed information that led to the capture of another terrorist suspect, Ramzi Binalshibh.

Two suicide bombers struck within five minutes of each other on streets leading to the shrine of Imam Musa al-Kadhim and his grandson. One of the attacks, and perhaps both, were carried out by women, witnesses said.

Nearly half of those killed were Iranians making a pilgrimage to the shrine, a golden-domed landmark in the predominantly Shiite Kadhimiya neighborhood of Baghdad that is devoted to 2 of the 12 imams of Shiite Islam. At least 125 people were wounded, many of them also Iranians.

A loose coalition of Sunni militant forces, the Islamic State of Iraq, has claimed responsibility for carrying out many of the recent attacks.

The deadliest of the three bombings on Thursday struck a restaurant filled with Iranian travelers in Muqdadiya, a town in Diyala not far from the border. The toll in that attack rose to 56, with Iranians making up the majority of the dead. Over all, at least 89 people were killed in the bombings on Thursday, and more than 100 were wounded.

After the attacks on Friday, angry Iraqis who gathered amid the bloody debris blamed lax security and corruption of the police and government officials for what had happened. Some of their anger had a strongly sectarian cast.“They have been ruling us for 1,400 years,” said a Shiite army soldier who identified himself only as Abu Haidar, referring to the Sunni domination of Shiites in Iraq. “We took it over for four years, and they are slaughtering us.”

The Islamic State of Iraq, an umbrella insurgent group that includes Al Qaeda in Mesopotamia, says the recent attacks as part of a campaign called Harvest of the Good, which it announced in March.

In a statement distributed on extremist Web sites at the time, the group’s leader, Abu Omar al-Baghdadi, ridiculed President Obama as “Washington’s black man” and called his plan to withdraw American forces by 2011 an “implied avowal of defeat.”

On Thursday, Iraq’s military claimed to have arrested Mr. Baghdadi, but what was touted as a major success appeared to be in question. Extremist Web sites denied his arrest, according to the SITE Intelligence Group, which monitors claims and other statements by terrorist and extremist groups. The American military command also said in a statement that it could not confirm “the arrest or capture” of the leader, who the American military believes to be a fictitious Iraqi figurehead of a movement that includes many foreign fighters.

A senior national police official on Friday bluntly cited the limitations of Iraq’s security forces and their equipment for detecting explosives, typically hand-held wands used at checkpoints that the official described as fakes.

The new assessment is in keeping with the high number of videos from Afghanistan attacking German government policy. At the end of last week, a new propaganda film by the Islamic Jihad Union emerged and threatened attacks. In early 2009, Bonn-based Islamist Bekkay Harrach, who has gone underground in Afghanistan, threatened attacks on Germany. Harrach is believed to play an important role in al-Qaida.

Some Republicans in Congress have mounted stiff resistance to closing Guantánamo, and officials in some American communities, fearing that terrorism suspects could be tried or held in their courts or prisons, said they would fight any such plans. Also, while some European governments have promised to resettle detainees, specific agreements have been slow in coming.

The Yemenis not only are the biggest group of detainees, but also are widely seen as the most difficult to transfer out of Guantánamo. Other countries are wary of many of the Yemeni detainees because jihadist groups have long had deep roots in Yemen, one of the poorest countries in the Arab world and the homeland of Osama bin Laden’s father. If the Yemenis are not sent home, there may be few other options for many of the 97 men, detainees’ lawyers and human rights groups say.

The developments are significant for the Obama administration because the 97 Yemeni detainees make up more than 40 percent of the remaining 241 prisoners at Guantánamo Bay. The question of what to do with them “is integral to the process of closing Guantánamo,” said Ken Gude, an associate director at the Center for American Progress who has written about closing the prison camp.

Perhaps a dozen or more Yemeni detainees could face prosecution in the United States, including Ramzi bin al-Shibh, who was charged in the Bush administration’s military commission system with being a coordinator of the Sept. 11, 2001, attacks.

David H. Remes, a lawyer for 16 Yemeni detainees, said it appeared that many of the men might remain in American custody. “Unless President Obama reconsiders his decision to close Guantánamo,” Mr. Remes said, “the Yemeni detainees would have to be brought to the U.S. and put in some sort of prison.”

The complexities of the issues surrounding the detainees are a reflection of Yemen’s tangled domestic and international problems. It is a state that often appears on the verge of chaos. A weak central government is fighting a persistent insurgency in the north, restive separatists in the south and a growing Qaeda presence.

Some Yemeni officials say President Saleh, a wily former army officer, has used the internal threats — and perhaps even nurtured them — to press the United States and Yemen’s neighbor Saudi Arabia for more aid.As a result, people who have discussed the detainee issues with Yemeni officials say the Obama administration’s frustration with the Yemeni government may be well founded.

One senior Yemeni official, she said, seemed to suggest that Yemen would require a huge payment from the American government to resettle the detainees. A proper rehabilitation program, the official claimed, could cost as much as $1 million for each detainee, totaling nearly $100 million.

Often using the detainee's own words, the report offers a harrowing view of conditions at the secret prisons, where prisoners were told they were being taken "to the verge of death and back," according to one excerpt. During interrogations, the captives were routinely beaten, doused with cold water and slammed head-first into walls. Between sessions, they were stripped of clothing, bombarded with loud music, exposed to cold temperatures, and deprived of sleep and solid food for days on end. Some detainees described being forced to stand for days, with their arms shackled above them, wearing only diapers. "On a daily basis . . . a collar was looped around my neck and then used to slam me against the walls of the interrogation room," the report quotes detainee Tawfiq bin Attash, also known as Walid Muhammad bin Attash, as saying. Later, he said, he was wrapped in a plastic sheet while cold water was "poured onto my body with buckets." He added: "I would be wrapped inside the sheet with cold water for several minutes. Then I would be taken for interrogation."

President George W. Bush acknowledged the use of coercive interrogation tactics on senior al-Qaeda captives detained by the CIA in the aftermath of the Sept. 11, 2001, terrorist attacks, but he insisted that the measures complied with U.S. and international law. Former CIA director Michael V. Hayden confirmed last year that the measures included the use of waterboarding on three captives before 2003. President Obama outlawed such practices within hours of his inauguration in January. But Obama has expressed reluctance to conduct a legal inquiry into the CIA's policies.

Abu Zubaida was severely wounded during a shootout in March 2002 at a safe house he ran in Faisalabad, Pakistan, and survived thanks to CIA-arranged medical care, including multiple surgeries. After he recovered, Abu Zubaida describes being shackled to a chair at the feet and hands for two to three weeks in a cold room with "loud, shouting type music" blaring constantly, according to the ICRC report. He said that he was questioned two to three hours a day and that water was sprayed in his face if he fell asleep. At some point -- the timing is unclear from the New York Review of Books report -- Abu Zubaida's treatment became harsher. In July 2002, administration lawyers approved more aggressive techniques. Abu Zubaida said interrogators wrapped a towel around his neck and slammed him into a plywood wall mounted in his cell. He was also repeatedly slapped in the face, he said. After the beatings, he was placed in coffinlike wooden boxes in which he was forced to crouch, with no light and a restricted air supply, he said. "The stress on my legs held in this position meant my wounds both in my leg and stomach became very painful," he told the ICRC. After he was removed from a small box, he said, he was strapped to what looked like a hospital bed and waterboarded. "A black cloth was then placed over my face and the interrogators used a mineral bottle to pour water on the cloth so that I could not breathe," Abu Zubaida said. After breaks to allow him to recover, the waterboarding continued.

He is to be replaced by Lt. Gen. Stanley A. McChrystal, a former commander of the Joint Special Operations Command. He served in Afghanistan as chief of staff of military operations in 2001 and 2002 and recently ran all commando operations in Iraq.

Forces under General McChrystal’s command were credited with finding and capturing Saddam Hussein and with tracking and killing Abu Musab al-Zarqawi, the leader of Al Qaeda in Mesopotamia. His success in using intelligence and firepower to track and kill insurgents, and his training in unconventional warfare that emphasizes the need to protect the population, made him the best choice for the command in Afghanistan, Defense Department officials said.

At the same time, he will be confronted with deep tensions over the conduct of Special Operations forces in Afghanistan, whose aggressive tactics are seen by Afghan officials as responsible for many of the American mistakes that have resulted in the deaths of civilians.

Pentagon officials have begun to describe Afghanistan as the military’s top priority, even more important than the war in Iraq. President Obama announced a major overhaul of American strategy in Afghanistan in March. Planned troop levels are expected to reach more than 60,000 Americans.

Mr. Obama seemed to connect with his audience in his 55-minute speech from Cairo University as he quoted repeatedly from the Koran and occasionally sprinkled his remarks with Arabic, even beginning his address with the traditional Arabic greeting “salaam aleikum,” or “peace be upon you.”

while he spoke uncompromisingly of the American fight against Al Qaeda, Mr. Obama never mentioned the words “terrorism” or “terrorist.” That was a departure from the language used by the Bush administration, but one that some Middle East experts suggested reflected a belief by the new administration that overuse had made the words inflammatory.

Paul D. Wolfowitz, a former top Bush administration official who was an architect of the war in Iraq and is a strong supporter of Israel, offered general praise for Mr. Obama’s address. “I could have used less moral equivalence, but he had to get through to his audience, and it’s in America’s interest for him to get through,” Mr. Wolfowitz said.

Mr. Obama’s stark statement that “the United States does not accept the legitimacy of continued Israeli settlements” is also likely to be seen as a sharp challenge to Israeli assumptions that existing West Bank settlements will always be allowed to remain.

It was noteworthy that the only Palestinian political group that Mr. Obama specifically mentioned was Hamas, the militant Islamic organization that won Palestinian legislative elections in 2006. Hamas governs Gaza, but is loathed by Israel. Mr. Obama called on Hamas to forswear violence and recognize Israel’s right to exist, but Middle East experts said that his mention was an acknowledgment that Hamas might have become a more important actor than the Fatah Party, controlled by Mahmoud Abbas, the Palestinian president. Mr. Obama said, “Hamas does have support among some Palestinians, but they also have to recognize they have responsibilities.”

Sometime during those early weeks, Mohammed started talking, providing information that supporters of harsh interrogations would later cite in defending the practices. Former vice president Richard B. Cheney has justified such interrogations by saying that intelligence gained from Mohammed resulted in the takedown of al-Qaeda plots.

Two former high-ranking officials with access to secret information said the interrogations yielded details of al-Qaeda's operations that resulted in the identification of previously unknown suspects, preventing future attacks. "The detainee-supplied data permitted us to round them up as they were being trained, rather than just before they came ashore," said one former intelligence official who spoke on the condition of anonymity because the cases are classified. "Not headline stuff, but the bread and butter of successful counterterrorism. And something that few people understand."

Other officials, including former high-ranking members of the Bush administration, argue that judging the program by whether it yielded information misses the point. "The systematic, calculated infliction of this scale of prolonged torment is immoral, debasing the perpetrators and the captives," said Philip D. Zelikow, a political counselor to then-Secretary of State Condoleezza Rice who reviewed secret Bush administration reports about the program in 2005. "Second, forfeiting our high ground, the practices also alienate needed allies in the common fight, even allies within our own government. Third, the gains are dubious when the alternatives are searchingly compared. And then, after all, there is still the law."

The Obama administration's top intelligence officer, Dennis C. Blair, has said the information obtained through the interrogation program was of "high value." But he also concluded that those gains weren't worth the cost. "There is no way of knowing whether the same information could have been obtained through other means," Blair said in a statement. "The bottom line is these techniques have hurt our image around the world, the damage they have done to our interests far outweighed whatever benefit they gave us and they are not essential to our national security."