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Senior Pakistani and American intelligence officials say the operational commander of Al Qaeda, the man who planned the Sept. 11 attacks on the United States, narrowly avoided capture in a raid that took his two sons into custody here.

It was one of at least half a dozen missed opportunities over eight years to seize Khalid Sheik 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 young sons in custody since September. One senior U.S. investigator said authorities came “within moments” of capturing Mohammed in the same raid.

Pakistani intelligence officials said that in recent months they have seen evidence that Mohammed, even as he has been on the run, has been aggressively directing terrorist cells.

“Despite being so much in danger, he has not gone into hibernation or [made efforts] to hide,” 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 U.S. as far back as 1993, but his importance in the overall Al Qaeda structure became clear only after Sept. 11, U.S. officials say. Now, some officials say, stopping Mohammed is at least as important as capturing Osama bin Laden, perhaps more.

Mohammed, believed to be 37, has traveled the world as one of the chief designers of Al Qaeda, using Egyptian, Qatari, Saudi, British and Kuwaiti identities. He has used more than three dozen aliases. 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 a mechanical engineering degree at a college in North Carolina.

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 was forced to retreat to rural hide-outs he sent messages by donkey.

Even at the height of the U.S. bombing campaign against Al Qaeda in Afghanistan, Mohammed planned, staffed and directed new terrorist attacks, according to intelligence documents. Mohammed planned a bombing campaign in Southeast Asia that was scheduled to occur late in 2001, according to the documents.

Mohammed the Pakistani, as the Asian bombers knew him, housed a young Canadian recruit named Jabarah for weeks in his Karachi apartment, instructing him on communication protocols–e-mail passwords, telephone codes. He then sent him to coordinate and finance the bomb squads. With just a few days’ notice, Mohammed delivered $50,000 to the recruit to pay for bombmaking 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 the terrorist networks of that region, including the cell responsible for the recent attack in Bali, Indonesia, in which nearly 200 people died.

It is the same role U.S. investigators believe he has played around the world. If bin Laden has been the architect of Al Qaeda, they say, Mohammed has been its engineer.

Al Qaeda members in custody have told interrogators that Mohammed had operational cells in place in the U.S. 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 FBI 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.”

Although born in Kuwait, Mohammed is a Pakistani national whose family is from Baluchistan, an area that straddles Pakistan’s borders with Iran and Afghanistan. Mohammed was born in 1965, according to records, and raised in Fahaheel, south of Kuwait City. His oldest brother, Zahed, attended Kuwait University and was a leader of the Muslim Brotherhood, a militant pan-Arab organization that functioned as an underground opposition throughout the region.

A man who knew the family said a group called the Islamic Association of Palestinian Students also was formed on campus then; one of its leaders went on to become head of the political bureau of the militant Islamic group Hamas. That was the initial politicization of Mohammed, the friend said.

Mohammed attended high school in Kuwait then left for college in the United States. He enrolled first at Chowan College, a tiny Baptist school in eastern North Carolina.

Chowan did not require the English proficiency exam then widely mandated for international students. Foreign enrollees often spent a semester or two at Chowan, improved their English and then transferred to four-year universities. By 1984, Chowan had a sizable contingent of Middle Easterners.

Mohammed spent just a semester at Chowan, then transferred to North Carolina A&T, a historically black college in Greensboro. He was a part of a group of Arab students there that other Middle Easterners called the “mullahs” because of their religious zeal.

`In the mosque all the time’

Students who recall Mohammed describe him as studious and private, a devotee of the library and Allah, but friendly enough in a casual way and capable of a laugh.

“All anyone knows about him is that he was in the mosque all the time,” said Faisal Al-Munifi, who studied mechanical engineering at the same time as Mohammed.

He didn’t spout anti-Western or anti-American rhetoric. “Something must have happened later that caused that feeling,” said Badawi Hindieh, who knew Mohammed at Chowan and Greensboro. “I never remember him saying anything like that.”

Mohammed earned a degree in mechanical engineering at the end of 1986 and is believed to have left the United States for Pakistan, where he joined two older brothers active in the Afghan resistance in Peshawar. A man who knew the three brothers said Mohammed emulated Abed, who was more militant than Zahed, who ran a Kuwaiti charity organization.

Mohammed taught at a university established by an Afghan warlord and at an adjacent refugee camp, according to a friend. His brother Abed was killed in an explosion either in battle or in a jihad training camp in 1989, friends said.

Mohammed’s first known involvement in terrorism occurred in 1992, when he sent money to his nephew, Ramzi Yousef, as Yousef was in New Jersey preparing to bomb the World Trade Center.

He and Yousef later teamed up on plots in the Philippines to assassinate the pope and President Bill Clinton and to place bombs aboard a dozen U.S. airliners. Those plots were foiled by authorities in 1995. Mohammed escaped and moved to the Persian Gulf, according to American investigators.

Investigators say Mohammed spent the next year building and maintaining a fundraising network in the gulf.

“Throughout the region, there was this classic sort of money collector–the guy who was hanging out at the mosque, checking out the scene, basically casing the mark, who would invariably be some old guy with lots of money. A religious guy, probably. The collector would come up alongside him, make his pitch very persistently and the mark would write him a check,” said one American official who worked in the gulf region throughout the 1990s.

“Khalid Sheik Mohammed was a collector, a guy who would collect the money from the street collectors. . . . A guy in the Philippines would call a guy in Dubai who would call Khalid Sheik Mohammed. It would be a chain of telephone calls and Khalid would send the money.”

Misdirected attention

U.S. understanding of Islamic terrorism then was inchoate. Al Qaeda was barely on the screen. Potential state-sponsored terrorism was deemed more dangerous, so more attention was given to Iran, which had become the chief international proponent of Islamist goals.

Mohammed lived openly in the Persian Gulf region. “He wasn’t even using an alias,” one official said. U.S. agents tracked him through Italy, Egypt, Singapore, Jordan, Thailand, the Philippines and Qatar. In Qatar, American officials say, he stayed as the guest of a member of the country’s ruling family, Abdullah bin Khallad al-Thani, who was then the country’s minister of religious affairs.

“Abdullah bin Khallad had a farm outside of [Doha]. A lot of these guys had what were basically gentlemen’s truck farms. It was a hobby. Grow cabbages, raise ducks,” said one U.S. official. “So he has this farm and he always had a lot of people around, the house was always overstaffed, a lot of unemployed Afghan Arabs. . . . There were always these guys hanging around and maybe a couple of Kalashnikovs in the corner.”

U.S. intelligence figured out that one of the guys on the farm was Mohammed. A grand jury in New York had indicted Mohammed for the Manila airliner plot, and a debate occurred on what exactly to do about it.

FBI Director Louis Freeh met with Qatar officials seeking permission to arrest him. One FBI official said months passed without approval, even though Qatar acknowledged that Mohammed was there. At one point, according to documents, Qatar told the U.S. they feared Mohammed was constructing an explosive device. They also said he then possessed more than 20 passports; still, they delayed granting U.S. permission to seize him.

Some officials felt strongly that the U.S. should act as quickly and with as much force as necessary to capture him. Others were more wary. A meeting was called in Washington in early 1996. Caution prevailed.

“That D.C. meeting . . . struck me as one of the great lessons in politics,” said a person who attended the meeting. “Here was this opportunity to get this bad guy, and we didn’t do it. The Qatar government had no interest in screwing up its fragile relationship with us. If we had gone in and nabbed this guy, or just cut his head off, the Qatari government would not have complained a bit.

“Everyone around the table for their own reasons refused to go after someone who fundamentally threatened American interests. . . . The FBI can’t go anywhere overseas without the CIA providing the intel, the DOD providing the logistics and military muscle in the event we have to shoot our way in. And none of that happened.”

Another participant said the real obstacle was the Pentagon, which feared another “Black Hawk Down” debacle and insisted the “snatch and grab” job would require hundreds if not thousands of troops.

In the end, rather than sending a kidnap squad, Freeh sent a letter to the Qatari government. By the time permission was granted, Mohammed was gone.

He is thought to have fled to Afghanistan, where he joined Al Qaeda and eventually rose to its highest ranks.

“Look at what has happened in the last six years–you would have to assume that he played a role in everything from that point on,” said Neil Herman, a former top FBI counterterrorism officer. “He is right there. He is a common denominator. If he had been caught in 1996, who knows what could have been prevented?”