On Sept. 11, 2001, the core of al-Qaeda was concentrated in a single city: Karachi, Pakistan.

At a hospital, the accused mastermind of the bombing of the USS Cole was recovering from a tonsillectomy. Nearby, the alleged organizer of the 2002 bombing in Bali, Indonesia, was buying lab equipment for a biological weapons program. And in a safe house, the man who would later describe himself as the intellectual author of the Sept. 11 attacks was with other key al-Qaeda members watching the scenes from New York and Washington unfold on television.

Within a day, much of the al-Qaeda leadership was on the way back to Afghanistan, planning for a long war.

A cache of classified military documents obtained by the anti-secrecy organization WikiLeaks presents new details of their whereabouts on Sept. 11, 2001, and their movements afterward. The documents also offer some tantalizing glimpses into the whereabouts and operations of Osama bin Laden and his Egyptian deputy, Ayman al-Zawahiri.

The documents, provided to European and U.S. news outlets, including The Washington Post, are intelligence assessments of nearly every one of the 779 individuals who have been held at Guantanamo Bay, Cuba, since 2002. In them, analysts have created detailed portraits of detainees based on raw intelligence, including material gleaned from interrogations.

Detainees are assessed “high,” “medium” or “low” in terms of their intelligence value, the threat they pose while in detention and the continued threat they might pose to the United States if released.

The documents tend to take a bleak view of the detainees, even those who have been ordered released by the federal courts because of a lack of evidence to justify their continued detention. And the assessments are often based, in part, on reporting by informants at the military detention center, sources that some judges have found wanting.

In a statement, the Pentagon, which described the decision to publish some of the material as “unfortunate,” stressed the incomplete and snapshot nature of the assessments, known as Detainee Assessment Briefs, or DABs.

“The Guantanamo Review Task Force, established in January 2009, considered the DABs during its review of detainee information,” said Pentagon press secretary Geoff Morrell and Ambassador Daniel Fried, the Obama administration’s special envoy on detainee issues. “In some cases, the Task Force came to the same conclusions as the DABs. In other instances the Review Task Force came to different conclusions, based on updated or other available information. Any given DAB illegally obtained and released by Wikileaks may or may not represent the current view of a given detainee.”

Regardless of how detainees are currently assessed, many of the documents shed light on their histories, particularly those of the 14 high-value detainees whose assessments were made available. When pieced together, they capture some of the drama of al-Qaeda’s scattering in the wake of the Sept. 11 attacks. They also point to tensions between certain members of the terrorist group.

Among other previously unknown meetings, the documents describe a major gathering of some of al-Qaeda’s most senior operatives in early December 2001 in Zormat, a mountainous region of Afghanistan between Kabul and Khost. There, the operatives began to plan new attacks, a process that would consume them, according to the assessments, until they were finally captured.

A hectic three months

According to the documents, four days after the Sept. 11 attacks, bin Laden visited a guesthouse in Afghanistan’s Kandahar province. He told the Arab fighters gathered there “to defend Afghanistan against the infidel invaders” and to “fight in the name of Allah.”

It was beginning of a peripatetic three months for bin Laden and Zawahiri. Traveling by car among several locations in Afghanistan, bin Laden handed out assignments to his followers, met with some of the Taliban leadership and delegated control of al-Qaeda to the group’s Shura Council, presumably because he feared being captured or killed as U.S. forces closed in.

At some point, bin Laden and Zawahiri used a secret guesthouse in or relatively near Kabul. The al-Qaeda leader welcomed a stream of visitors and issued a series of orders, including instructions to continue operations against Western targets. He dispersed his fighters from training camps and instructed women and children, including some of his wives, to flee to Pakistan.

In October, bin Laden met in Kabul with two Malaysians, Yazid Zubair and Bashir Lap — both of whom are now at Guantanamo Bay — and lectured them on history and religion. On the day that the U.S.-led coalition began bombing Afghanistan, bin Laden met in Kandahar with Taliban official Mullah Mansour. Bin Laden and Zawahiri also met that month with Taliban leader Jalaluddin Haqqani, who continues to lead a deadly insurgency against the United States and its allies in Afghanistan.

Bin Laden, accompanied by Zawahiri and a handful of close associates in his security detail, escaped to his cave complex in Tora Bora in November. Around Nov. 25, he was seen giving a speech to the leaders and fighters at the complex.

He told them to “remain strong in their commitment to fight, to obey the leaders, to help the Taliban, and that it was a grave mistake and taboo to leave before the fight was completed.”

According to the documents, bin Laden and his deputy escaped from Tora Bora in mid-December 2001. At the time, the al-Qaeda leader was apparently so strapped for cash that he borrowed $7,000 from one of his protectors — a sum he paid back within a year.

Internal tensions

In December, al-Qaeda’s top lieutenants gathered in Zormat. They included Khalid Sheik Mohammed, the self-described mastermind of the Sept. 11 attacks; Abd al-Rahim al-Nashiri, the alleged planner of the USS Cole attack; and Abu Faraj al-Libbi, a key facilitator for bin Laden.

The place was teeming with fighters who were awaiting for al-Qaeda to return their passports so they could flee across the border to Pakistan.

Mohammed later stated that while he and the others were in Zormat, they received a message from bin Laden in which he delegated control of al-Qaeda to the Shura Council. And the senior operatives began to plan new attacks.

Nashiri reported that while at Zormat he was approached by two Saudi nationals who wanted to strike U.S. and Israeli targets in Morocco. Nashiri said he had been considering an operation in the Strait of Gibraltar and thought that the British military base there, which he had seen in a documentary, would be a good target.

Nashiri’s willingness to approve a plot on his own was later the source of some tension within the organization, particularly with Mohammed.

In May or June 2002, Mohammed learned of the disrupted plan to attack the military base in Gibraltar and was upset that he had not been informed of it.

Nashiri separately complained that he was being pushed by bin Laden to continue planning aggressive operations against U.S. interests in the Persian Gulf region without much regard for his security.

It was an unusual complaint for someone who was so committed to al-Qaeda. According to documents, to avoid the distraction of women, he “reportedly received injections to promote impotence and recommended the injections to others so more time could be spent on the jihad.”

Back in Pakistan

After the Zormat conclave, Mohammed and other senior al-Qaeda figures began to return to Karachi.

The documents state that Mohammed “put together a training program for assassinations and kidnappings as well as pistol and computer training.” It was not intended for specific operations but to occupy the bored fighters stuck in safe houses.

At the time, money was flowing into the country for Mohammed, according to the documents, allowing him to acquire safe houses and fund operations.

In November 2002, his nephew Baluchi took a delivery of nearly $70,000 from a courier. Mohammed, at one point, gave $500,000 to a Pakistani businessman, who is also being held at Guantanamo Bay, for safekeeping, much of it wrapped in cellophane and inside a shopping bag. Mohammed also gave Riduan Isamuddin, the Indonesian known by the nom de guerre Hambali, $100,000 to congratulate him for the Bali bombing.

Gradually, Mohammed and the other operatives were picked off by Pakistanis working with the CIA and the FBI. When Ramzi Binalshibh, a key liaison between the Sept. 11 hijackers and al-Qaeda, was arrested at a safe house in Karachi on the first anniversary of the Sept. 11 attacks, there was a four-hour standoff while the Yemeni and two others held knives to their own throats and threatened to kill themselves rather than be taken.

There are few geographic references in the documents for bin Laden after his flight into Pakistan.

He apparently sent out letters from his hiding place through a trusted courier, who then handed them to Libbi, who had provided the secret guesthouse in Kabul immediately after the Sept. 11 attacks.

After the capture of Mohammed in March 2003, Zawahiri fled from the house where he had been staying. The documents state that Zawahiri left on his own and sought out an Afghan, who delivered him to Libbi.

In May 2005, while waiting for bin Laden’s courier at a drop point, Libi was arrested by Pakistani special forces.

Zawahiri, in response, moved again. His residence, documents state, “was changed to a good place owned by a simple old man.”

He remains at large.

Staff researcher Julie Tate contributed to this report.