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.
Pakistani Interior Minister Faisal Saleh Hayat said that because of Pakistani efforts, the structure of al Qaeda "has certainly been weakened."
(Mian Khursheed -- Reuters)
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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."