Since that time, CIA case officers and FBI agents, working in coordination with Pakistan and other countries, have captured Atef's replacement, Khalid Sheik Mohammed, who U.S. officials charge was an organizer of the World Trade Center and Pentagon attacks, as well as three of Mohammed's lieutenants, Abu Zubaida, Ramzi Binalshibh and, last week, Tawfiq bin Attash, who was picked up in Pakistan along with a nephew of Muhammad's who had taken up some of Muhammad's operational duties.
All are cooperating to some degree with their CIA interrogators, according to intelligence sources.
"The nucleus [of al Qaeda leaders] was relatively small, and Atef and Muhammad were significant losses," one senior intelligence analyst said. "There are not many with senior operational capabilities left." In addition, bin Laden and Zawahiri and the remaining leadership have to operate differently with the loss of their haven in Afghanistan. "They must move around and keep their heads down, mainly concentrating during their waking hours every day on just surviving," the analyst said.
Those al Qaeda leaders still at large are believed to be hiding along the border between Afghanistan and Pakistan, and in Iran, according to intelligence officials. The senior intelligence analyst said it remains unclear to what extent those who have taken refuge in Iran are being protected by the Iranian government. Bin Laden and Zawahiri are suspected to be hiding separately along the Afghan-Pakistani border with a number of remaining operational chiefs, the analyst said. Those in Iran are largely ideological adherents to al Qaeda not directly involved with mounting terrorist attacks.
The denial of Afghanistan as a secure base of operations and training for al Qaeda severely affected the organization's global reach, officials said, though they point out that members of al Qaeda and their supporters in the ousted Taliban government are reappearing in the country.
"We always thought if we could cut the head off the rest would shrivel up but not vanish," one senior official said. That has largely happened, said intelligence officials and others. Terrorists still operate in South Asia, the Philippines, Indonesia, the Middle East and Chechnya, but, as one official put it, "they have lost some guidance on the international scale."
Rep. Porter J. Goss (R-Fla.), a former CIA case officer and chairman of the House Permanent Select Committee on Intelligence, said the progress in dismantling al Qaeda has been significant. "I think the intelligence community really has driven a lot of the terrorists back into their holes and broken down the command and control," he said. "I wouldn't deny that the success of the community has probably been underreported -- and for good reason."
Some key bin Laden associates, leaders with their own organizations that were inspired or supported by al Qaeda, are still at large and may be operating.
In Afghanistan, Mohammed Omar, leader of the Taliban, has not been found. The U.S. military is still carrying out missions against pockets of his supporters. "Afghanistan is no longer a den of terrorists, and we have 6,000 U.S. troops there to keep overt terrorist camps from ever operating there again," a senior intelligence analyst said.
Abu Musab Zarqawi, a Jordanian whose organization maintained connections with al Qaeda and was said by U.S. officials to be a link between bin Laden and former Iraqi president Saddam Hussein, "is still at large and still a threat," a senior administration official said. The official said U.S. military units in Baghdad last week picked up one Zarqawi aide, Abu Muaz, who was part of the cell that Secretary of State Colin L. Powell told the United Nations in February was operating in Iraq with Hussein's permission.
The training camp in the Kurdish area of northern Iraq that Zarqawi was said to have run was hit by U.S. bombs and cruise missiles and later overrun by U.S. Special Forces and Kurdish militia. The attacks scattered the occupants, with some fleeing to Afghanistan and others to Turkey or Iran, intelligence officials said.
Initial reports said U.S. searchers found traces of cyanide and ricin along with laptop computers at the training camp. Subsequent reports, however, said only traces of cyanide were found and that the laptops were either destroyed or rendered useless in the airstrikes.
