In the more than two years since U.S. forces destroyed al Qaeda's haven and much of its leadership in Afghanistan, many U.S. intelligence officials and terrorism experts had come to believe that other Islamist extremist groups now posed the gravest threat.
From Istanbul to Madrid, local jihadists mounted daring and deadly attacks with little apparent support from Osama bin Laden's crippled network. President Bush and other U.S. officials boasted that two-thirds of al Qaeda's senior leadership had been captured or killed and that those who remained, including bin Laden, were desperate and on the run.
But the wave of arrests and intelligence discoveries in Pakistan in recent weeks that led to a new terrorism alert in the United States caught many U.S. officials and outside experts by surprise. It revealed a network of operatives connected to past al Qaeda operations and aligned with Khalid Sheik Mohammed, the imprisoned mastermind of the Sept. 11, 2001, attacks.
The new evidence suggests that al Qaeda is battered but not beaten, and that a motley collection of old hands and recent recruits has formed a nucleus in Pakistan that is pushing forward with plans for attacks in the United States, according to U.S. and Pakistani officials.
The key questions, according to intelligence officials and experts from both nations, are whether the new guard is capable of coordinating significant terrorist attacks and whether any coherent leadership has emerged to take the place of Mohammed and other senior al Qaeda leaders now in U.S. custody.
U.S. and Pakistani officials said in interviews this week that they are unsure whether bin Laden is still taking an active role in directing plots, although some evidence suggests that he is.
"We've been able get some information and some clue, an overview of the present structure of al Qaeda, how it functions," Pakistan's interior minister, Faisal Saleh Hayat, said in an interview in Islamabad this week. "This structure is in a continuous tailspin ever since the arrest of KSM [Khalid Sheik Mohammed]. It has certainly been weakened."
One senior U.S. counterterrorism official, however, said al Qaeda's "resiliency and their ability to reconstitute is truly remarkable."
"Until you put your hands on bin Laden and [deputy Ayman] Zawahiri and the other cast of characters, they are not going to switch gears or change careers. This is what they do," the official said.
"The challenge is to try to define the current al Qaeda and come to some consensus that the al Qaeda that took the embassies in 1998 remains today," the U.S. official added, referring to the bombings of U.S. embassies in East Africa. "We just don't know."
The trail leading to the latest revelations about al Qaeda began in Karachi on June 12, with the arrest of Abu Musab Baluchi, a nephew of Mohammed's and a cousin of Ramzi Yousef, who was convicted for carrying out the 1993 bombing of the World Trade Center. The capture -- part of a crackdown after failed assassination attempts on Gen. Pervez Musharraf, the Pakistani president -- led a month later to the arrest of Muhammad Naeem Noor Khan, a Pakistani computer engineer who allegedly sent coded communications to al Qaeda operatives around the globe.
Perhaps the most important break from Khan's arrest was the discovery of a laptop and computer disks containing scouting reports and hundreds of photographs of financial institutions in the United States -- targets that officials said were exhaustively surveilled by al Qaeda in 2000 and 2001.
The discovery, along with evidence that the files had been accessed as recently as this year, led U.S. officials to raise the terrorism alert status on Aug. 1 for the first time in six months, this time focusing on financial sectors in New York, Washington and Newark. Investigators were aided further when they used Khan in a sting operation by sending coded e-mails to al Qaeda operatives in order to flush them out.
A White House official this week called Khan "a critical operational node in the al Qaeda chain." The official said Kahn "certainly had links with those who were responsible for doing the casings here in the United States."
The arrests continued. Ahmed Khalfan Ghailani, a fugitive wanted in connection with the embassy bombings, was captured in Gujrat, Pakistan. In London, authorities apprehended two suspects: Eisa Hindi, suspected by some officials of conducting surveillance of the U.S. targets, and Babar Ahmad, who is a cousin of Khan's and who is accused of raising money for terrorists.
Counterterrorism officials said Hindi is an alias for Issa al-Britani, who is a subject of the recently completed Sept. 11 commission report. Under interrogation, Mohammed described al-Britani as a trusted al Qaeda operative whom he sent to conduct surveillance of possible economic and Jewish targets in New York. Mohammed told interrogators that the casing mission was ordered by bin Laden.
The FBI has launched its own search for possible accomplices in the casing of the World Bank, the New York Stock Exchange and other financial buildings. The suspects include Adnan G. el Shukrijumah, a highly sought fugitive who lived in Florida before the Sept. 11 attacks and who officials have long feared is planning an attack. Travel records and other circumstantial evidence suggest that Shukrijumah may have helped in the surveillance of financial buildings in New York before he left the country, according to law enforcement officials.
FBI agents in recent days located one man whom they suspected of casing the World Bank and International Monetary Fund headquarters in Washington, but it was a case of mistaken identity, one official said.
Many U.S. officials and terrorism experts view with alarm the arrests in Pakistan and London, in part because of the ties between the suspects and al Qaeda's old guard. The group is closely linked by blood or friendship, and several, particularly Khan, appeared to have access to the past surveillance plans and current communications within al Qaeda.
Juliette Kayyem, head of the national security program at Harvard University's Kennedy School of Government, called the suspects "descendants of the old guard," saying: "There is still this network. It may not be as big or as powerful, but it's still around."
The computer files were heavily encrypted, indicating significant sophistication within the network, officials said. And the targets selected for surveillance suggest the influence of Mohammed who, according to the Sept. 11 commission, was preoccupied with attacking symbols of American capitalism such as the World Trade Center.
"What this is showing with al Qaeda is that they have a deeper bench than we imagined," said Bruce Hoffman, a terrorism expert who heads the Washington office of the Rand Corp. "Even when they're nailing their top operational people, there's still a centralized command structure functioning. We thought KSM was really a deathblow. It wasn't. They just caught their breath and started up again."
Hayat, however, argued that al Qaeda's top leadership has lost much of its operational control.
"That element of directness is certainly not there," he said, attributing the loss to the "arrests and also the actions . . . taken earlier" by Pakistani authorities, including a May military assault on al Qaeda training facilities in the tribal region of South Waziristan.
Hayat also suggested that some important al Qaeda planners are still at large and "sitting outside Pakistan," although "it may not be appropriate to disclose their locations."
Martha Crenshaw, a professor of government at Wesleyan University who has studied terrorism since the late 1960s, said it is difficult to determine what the recent arrests and discoveries in Pakistan say about al Qaeda's viability.
"We don't know if this is the last gasp of what's left being rounded up, or whether they are much more resilient than we thought," Crenshaw said. "What we're not seeing is a lot of evidence of new leadership."
Crenshaw also noted that Khan's involvement in the sting may indicate a breakdown in loyalty to the outlaw network.
The Bush administration generally views the recent arrests and intelligence discoveries not only as a window into al Qaeda's operations, but also as a serious blow to what remains of the network. In a background briefing Thursday in Washington, one senior administration official characterized the arrests as "a strategic success against al Qaeda, as opposed to the wrapping up tactically of a single cell."
Some Pakistani intelligence officials are more cautious. They say that such arrests may have a limited impact both on al Qaeda, which they view as already dispersed, and Islamist terrorists who are inspired by bin Laden but not beholden to him.
"Almost every important al Qaeda arrest in Pakistan reinforced our analysis that al Qaeda breakaway cells, each consisting of no more than two dozen people, have emerged as more lethal and committed stand-alone groups," one Pakistani intelligence official said.
Lancaster reported from Islamabad. Staff writer Mike Allen in Washington and correspondent Kamran Khan in Pakistan contributed to this report.