KARACHI, Pakistan — Senior Pakistani and American intelligence officials say the operational commander of Al Qaeda, the man believed to have planned the Sept. 11 attacks on the United States, narrowly avoided capture during a raid in which authorities took his two young sons into custody.
It was one of at least half a dozen missed opportunities over eight years to seize Khalid Shaikh Mohammed, who is described by intelligence analysts on three continents as the man most responsible for Al Qaeda's continuing terrorist attacks.
Pakistan's Inter-Services Intelligence agency has had Mohammed's two sons, ages 7 and 9, in custody since September. One senior American investigator said authorities believe that they might have come "within moments" of capturing Mohammed in the raid at a Karachi apartment.
In family photos seized at the apartment, Mohammed is pictured playing with the boys.
Pakistani intelligence officials said that in recent months they have seen persistent evidence that Mohammed -- even on the run -- has been aggressively directing Al Qaeda terrorist cells.
"Despite being so much in danger, he has not gone into hibernation," one senior Pakistani official said. "He is trying to protect what they have. He would like to consolidate first and then rebuild on the same edifice. And he is doing that. He remains active."
Mohammed has been linked to attacks against the United States as far back as 1993, but his importance in the Al Qaeda structure became clear only after Sept. 11 last year, U.S. officials say. Now, some officials say, stopping Mohammed is as important as capturing Osama bin Laden is, perhaps even more so.
Mohammed, believed to be 37, has traveled the world as one of the chief managers of the Al Qaeda network, using Egyptian, Qatari, Saudi, British and Kuwaiti identities. He is said to speak Arabic with a Kuwaiti accent and to be fluent in Urdu, the principal language of Pakistan, and English, acquired in part as he studied for his mechanical engineering degree at a university in North Carolina.
Although born in Kuwait, he is a Pakistani national whose family is from Baluchistan, an area that straddles Pakistan's borders with Iran and Afghanistan. He has used more than three dozen aliases, including one -- Mukhtar al Baluchi -- that honors this tribal heritage.
Mohammed has been operating out of Karachi on and off for a decade. He communicates with Al Qaeda cells around the world by courier, e-mail, coded telephone conversations and shortwave radio; German intelligence agents say that when he has been forced to retreat to rural hide-outs he sends his messages by donkey.
Even during the U.S. bombing campaign against Al Qaeda in Afghanistan late last year, Mohammed continued to plan, staff and direct new terrorist attacks, according to intelligence documents made available to The Times. The documents detail Mohammed's orchestration of a bombing campaign in Southeast Asia.
Mohammed the Pakistani, as the Asian bombers knew him, housed a young Canadian recruit for weeks in his Karachi apartment, personally instructing him on communication protocols -- e-mail passwords, telephone codes. He then sent him off to coordinate and finance the bomb squads. With just a few days' notice, Mohammed was able to deliver $50,000 to the recruit to pay for bomb-making materials. The money was delivered in packs of $100 bills at a shopping mall in Kuala Lumpur, Malaysia, according to the intelligence documents.
That plot was foiled, but Mohammed's intimate involvement in it underscores his leadership in building regional terrorist networks. One network linked to Al Qaeda is allegedly behind the October bombing in Bali, Indonesia, in which nearly 200 people died.
It is the same role that American investigators believe he played not just in Asia but also around the world: If Bin Laden has been the architect of Al Qaeda, Mohammed has been its engineer. Al Qaeda members in custody have told their interrogators that Mohammed had operational cells in place in the United States after the Sept. 11 attacks and that he was the principal proponent within Al Qaeda of developing radioactive "dirty bombs," according to European intelligence officers.
The FBI acknowledges that it underestimated Mohammed's significance for years, a senior agency official said. "He was under everybody's radar. We don't know how he did it. We wish we knew.... He's the guy nobody ever heard of. The others had egos. He didn't."
Mohammed's persistence has earned the grudging admiration of some investigators, who marvel at his uncanny ability to stay one step ahead of unprecedented dragnets. In Pakistan, where the FBI believes Mohammed is still hiding, those attempts have involved a small army of agents from the military, police and multiple countries and intelligence agencies.