The Plots and Designs of Al Qaeda’s Engineer

KARACHI, Pakistan â€”  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.

“The way he is managing their affairs, the way he is controlling things, he is not an ordinary man,� said one top Pakistani intelligence official. “He is very sharp and brave -- an unusual combination.�

Sometimes Mohammed’s escapes have been abetted by the caution of his pursuers. In one instance, in 1996, U.S. intelligence had determined that Mohammed was in Doha, Qatar. Some American officials wanted to organize what they call a “snatch and grab,� essentially a commando raid, to seize him.

“Good intel had placed him in Qatar. This was, ‘Oh my God! This bastard is in Doha -- let’s get him,� said one person involved in the investigation.

This plan was defeated when high-level managers complained during a White House meeting that it was too risky and might result in American deaths, according to two people involved in the decision. They said this failure to act decisively characterized the U.S. government’s lack of a serious approach to terrorism before the Sept. 11 attacks.

“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. We absolutely believe that,� said Neil Herman, a former top FBI counter-terrorism officer. “He is right there. He is a common denominator. If he had been caught in 1996, who knows what could have been prevented.�

Pakistani and American officials say catching Mohammed now could turn the tide in the war on terrorism. The senior Pakistani intelligence official said: “If you catch Khalid Shaikh at this point, you will break the backbone of the entire network.�

Almost every Al Qaeda suspect whom the Pakistanis have arrested since last year has had some connection to Mohammed, authorities say. Many of those arrested have no links to one another, but they all know Mohammed.

Even those investigators who have been most involved in the hunt for Mohammed say they know very little about him. In the small, closed world of international counter-terrorism, he has become a mythic figure -- a ghost in the machine -- whose vague presence lurks behind innumerable plots but never comes completely into view.

Kuwait: Oil Town

Khalid Shaikh Mohammed was born in 1965, according to records, and reared in Fahaheel, a busy oil settlement south of Kuwait City, on the road to Saudi Arabia. The town was historically part of a sleepy agricultural zone on the edge of an oasis, a traditional site of palm and vegetable cultivation. Older Kuwaitis recall driving the route from Kuwait City through miles of desert, with the occasional vehicle, camel and Bedouin tent as the only landmarks.

That changed with the explosive growth of the petroleum business. By the late 1950s, Fahaheel boomed with a jaunty, cosmopolitan rhythm all its own. Palestinians, Lebanese, Syrians, Egyptians, Jordanians -- even the British and Americans -- were drawn here by the oil. Almost none of them were able to become Kuwaiti citizens, no matter how long they stayed, creating an enduring anxiety among many of the overseas workers. Even now, a majority of Kuwait’s 2 million people are noncitizens.

Mohammed attended high school at a three-story, 1960s-style brick all-boys school that housed as many as 1,200 students. Fahaheel teachers and alumni said they recall him as a studious youth who concentrated on science. School was, and is, a serious thing in Kuwait: Schoolboys wear white shirts and gray slacks and the headmaster walks around with a bamboo cane, to be used on obstreperous students.

Mohammed’s oldest brother, Zahed Shaikh, attended Kuwait University in the 1980s 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 Assn. of Palestinian Students was also formed on campus then; one of its leaders went on to become head of the political bureau of the militant Islamic group Hamas. This was the initial politicization of Mohammed, the friend said.

Much of the Middle East, following the devastating Arab loss to Israel in the 1967 war and the death of Egyptian President Gamal Abdel Nasser -- failed champion of the drive for a secular and united Arab world -- embarked on a gradual but inexorable turn toward religion, leading up to the Islamic Revolution in Iran. Analysts say it seemed that the secular path had been exposed as lacking, and religion was an alternative source of identity and regional esteem.

“It was like a huge vacuum, and nobody was able to fill this vacuum better than the rising Islamists,� said Shafeeq Ghabra, a political scientist in Kuwait.

The Kuwaiti government acknowledges that Mohammed was born in Kuwait, but that is about as far as the authorities will go in admitting any relationship with him.

“Just because he lived in Kuwait, or may have been born here, doesn’t mean that this man is a Kuwaiti,� Foreign Ministry Undersecretary Khalid al Jarallah said recently. “He is definitely not a Kuwaiti.�

The Pakistani government also seeks to disown Mohammed, even though his first known passport was issued by Pakistan.

“Why do the Kuwaitis want to shift the blame to us?� said Muhammad Khalid, head of chancery at the Pakistani Embassy in Kuwait City.

Although much remains murky about Mohammed’s background, it seems clear that his parents came from Baluchistan, which encompasses great swaths of southwestern Pakistan, southern Iran and Afghanistan. As avid coastal traders, the Baluchis have an extended history throughout the Gulf. Generations ago, area sheiks brought in fearsome Baluchi tribesmen to serve as palace guards.

Mohammed’s parents had religious callings, according to local press reports. His father, Shaikh Mohammed Ali Doustin Baluchi, who died decades ago, according to Mohammed’s acquaintances, has been described as a former imam, or preacher, at a mosque in the sprawling Ahmadi municipality. Mohammed’s mother, Halema, was said to have worked cleaning women’s bodies for burial. This is considered a prestigious job in Islam, however ill-paid.

Mohammed is one of at least five siblings -- four boys and a girl. The brothers’ names -- Khalid (meaning man of eternal life); Zahed (pious); Abed (worshiper) and Aref (knowledgeable) -- reflect the family’s religious orientation.

What little is known about the sister includes one compelling piece of information: She is thought to be the mother of Abdul Karim Basit, better known as Ramzi Ahmed Yousef, the man convicted of masterminding the 1993 bombing of the World Trade Center in New York.

Chowan College: Abbie Dahbies

Mohammed’s first extended encounter with the West occurred at Chowan College, a tiny Baptist school nestled among the cotton farms, tobacco patches and thick forests of eastern North Carolina, just south of the Virginia line.

The school was founded in 1848 as a refuge of learning for proper Southern women. Later, it became a two-year junior college, a place where young adults could gain an academic foothold. Its entry standards were liberal, but its values were bedrock and its leafy setting in isolated Murfreesboro, with no bars and a single pizza shop, pretty much ensured that everyone remained on the straight and narrow. Generations of small-town ministers, teachers and other community mainstays passed through Chowan’s colonnaded facade.

After World War II, the school’s missionary alumni began referring students from overseas. Dominating the international contingent by the 1980s were Middle Eastern men.

Chowan did not require the standardized English proficiency exam then widely mandated for international students, a fact that spread through the global academic network. Foreign enrollees often spent a semester or two at Chowan, improved their English and then transferred to four-year universities.

Mohammed applied to Chowan as a Pakistani citizen shortly after graduating from Fahaheel Secondary in 1983, according to college records. He told school administrators that he had heard of the college from a friend in Kuwait. His bill -- $2,245 for the spring semester -- was paid in full the day of matriculation, Jan. 10, 1984. He told fellow students that his father was dead and that his brothers picked up the tab.

“He took his studies seriously and was a very good Muslim,� said Badawi Hindieh, a Palestinian from Fahaheel who attended Chowan at the same time.

Acquaintances knew him as Khalid Shaikh, a name that stuck in people’s minds. Mohammed, acquaintances said, was culturally integrated into Arab and Kuwaiti society and could have passed as a Kuwaiti Arab.

“Khalid Shaikh spoke very good Arabic, like a Kuwaiti, but introduced himself as a Pakistani,� Hindieh said. “We knew he was Baluchi.�

Later in life, as Mohammed used multiple identities and moved from the Gulf to Afghanistan, the West and beyond, this ability to immerse in varying cultures would serve him well.

By 1984, about 50 of the 650 or so male students at Chowan were Middle Easterners, including a sizable contingent from Fahaheel and elsewhere in Kuwait. The local boys had a name for them: “Abbie Dahbies.�

The Arab students were frequent recipients of anti-Iranian epithets in the years after the 1979 takeover of the U.S. Embassy in Tehran. The foreigners were sometimes viewed as cliquish.

“They seemed to be praying all the time,� recalled John Franklin Timberlake, a 1984 Chowan graduate, now a police officer in Murfreesboro. “Just chanting, like. We never understood a word of it. Sometimes we’d come home late on a weekend night, maybe after we’d had a few beers, and they’d still be praying.�

At Chowan, Mohammed embarked on a pre-engineering curriculum -- popular among the foreigners.

“He was a good student -- a bit better than a B-type student,� Garth D. Faile, chairman of the science department, said in an interview this fall.

Mohammed, like every student, was required to attend a once-a-week chapel service based on Christian doctrine.

One large bloc of Middle Easterners lived in Parker Hall, a brick tower overlooking the campus’ Lake Vann, a restful crescent of water frequented by migrating birds and couples holding hands.

Groups of Arab students would gather in a fifth-floor dorm room and follow a kind of ritual: boil a chicken, share it with rice among all present, pray and commence intense discussions, before praying anew.

In the Middle Eastern tradition, they would leave their shoes in the corridor. Some U.S. students could not resist the temptation: The footwear sometimes ended up in the lake. Another prank involved filling 55-gallon garbage containers with water and propping the vessels against the doors of the “Abbie Dahbies,� knocking and running away. When the door opened, water flooded the room.

The hijinks did not appear to discourage the visitors, many of whom remained in the States and completed their degrees. Years later, one alumnus interviewed at his office in Kuwait City recalled his time at Chowan with great affection, remembering in particular the becalmed lake -- an extravagance for Arabs reared in parched latitudes.

“In a place like Chowan, some students became more insular -- speaking only to Arab students, while others tried to mix with the Americans,� he recalled. “I tried to mix, but others did it differently.�

Mohammed completed his semester at Chowan and moved on.

Greensboro: The Mullahs

In summer 1984, Mohammed enrolled as an engineering major at North Carolina Agricultural & Technical State University in Greensboro, a historically black college on the Piedmont plain in the central part of the state.

On Feb. 1, 1960, students at A&T -- whose most famous graduate is Jesse Jackson -- staged the first lunch-counter sit-in at a downtown Greensboro Woolworth’s, a galvanizing action that spread throughout the South.

College abroad was a rite of passage for legions of Middle Eastern students -- overwhelmingly men. Typically, this was their initial long-term exposure to Western life. Some left appalled at what they witnessed. Others ate it up.

“We were all excited about going to the States,� said Khalil A. Abdullah, a 1987 A&T graduate. “In high school we had seen all the movies, heard the music. We wondered so much about it.�

In Greensboro, Mohammed was part of the large Middle Eastern bloc in the university’s expansive engineering department -- a natural major for Kuwaitis and others from oil-producing nations. By all accounts, there were three distinct student groups at the school: African Americans (by far the largest group), white Americans and Middle Easterners.

“It wasn’t like there was tension or anything, but that’s just the way it was,� said Winfred S. Kenner, who studied mechanical engineering at the sprawling, tree-lined campus east of downtown.

The Middle Easterners tended to live off campus in anonymous complexes like the Yorktown and the Colonial, seldom ate in the cafeteria and skipped organized events. While “Aggies� trundled off in merry droves to Saturday football games, the foreign students arranged soccer matches in the park. They socialized mainly with one another.

“It was the college life: We used to get together three, four times a week, watch the games, chat, drink, you know,� said Sami Zitawi, a Kuwaiti native who recalled large get-togethers of Arabs on Friday, the Muslim holy day. “We used to go to the farmers, buy a lamb or a goat. Butcher it with a knife.... Every Friday night someone would have a big dinner: 15, 20, 25 students.�

Political discussions inevitably occurred. The year before Mohammed’s arrival, students in Greensboro marched in protest of the 1982 massacres of Palestinians at refugee camps in Lebanon -- though the Arab visitors learned to mute their criticisms.

The Middle Eastern students were far from a monolith. Differences in politics, culture and, especially, in the practice of Islam tore at regional solidarity.

“Basically, what you saw was a micro-society of our home,� explained Mahmood Zubaid, a Kuwaiti architectural engineer. “Everybody fit in where they felt most comfortable.�

A social barrier separated the elite scholarship boys like Zubaid and students like Mohammed, the Baluchi, and the Palestinians, reliant on their families or smaller grants for tuition and living expenses. But religion was the real dividing line.

Wherever large concentrations of Middle Eastern students gathered on Western campuses, graduates say, groups of religious conservatives sprung up. These self-appointed moral overseers endeavored to ensure adherence to Koranic values and avoidance of wine, women, drugs and other vices. They grew beards as religious statements and prayed five times a day, typically in makeshift mosques in apartments or university-provided centers. And they actively recruited fellow students.

“We called them the mullahs,� recalled Waleed M. Qimlass, a 1980s A&T graduate who now directs environmental affairs for Kuwait City. “Basically, the students at Greensboro were divided into the mullahs and the non-mullahs.�

At A&T, several Arab graduates say, Mohammed was among the mullahs. Even back at Chowan, one student recalled, Mohammed had reproached him for eating pork.

There was plenty at A&T for Mohammed and other true believers to be distressed about. Some Arab students drank, flirted and frequented clubs -- indulging in hedonistic pursuits absent back home. A few motored about the expansive campus in Porsches and Mercedeses.

The party crowd attempted to keep their indiscretions private, fearing that word might get back to their families. But the mullahs took notice and exercised pressure both intense and subtle.

Islamists at Greensboro and other U.S. universities made a point of seeking out newly arrived Arab students at airports. Qimlass recalled how three “guys with beards� intercepted him and a friend as the two Kuwaitis waited for their luggage at the airport in Tulsa, Okla., where Qimlass studied before transferring to A&T. The trio immediately ushered the two arriving Kuwaiti students to a kind of rooming house that doubled as a mosque, reproaching a fatigued Qimlass when he lighted up a cigarette.

If they missed new arrivals at the airport, the bearded ones would seek them out on campus. Their advances were sometimes rejected but often welcomed among vulnerable newcomers who were homesick and out of place.

“Your first day in Greensboro, you didn’t know anybody, maybe your English is not so good, and they met you at the airport and helped you get started,� Zubaid said.

One former Kuwaiti student wasn’t so thrilled: He would place a bottle of Johnnie Walker on his table whenever the mullahs came by, like a cross proffered to Dracula.

The disproportionate influence of religious students overseas has long troubled Arab capitals. The region’s mostly autocratic rulers aren’t keen to subsidize the training of would-be ayatollahs who would return and espouse revolt. Nor did the prospect of religious indoctrination abroad thrill secular parents seeking to broaden their children’s horizons.

“Pre-Sept. 11, I knew many mothers here who worried about their children going to America and coming back very radical in their thinking as Islamists,� said Ghabra, the political scientist at Kuwait University.

The Kuwaiti government would disperse U.S.-based scholarship students if fears emerged that any kind of religious-political cabal was gaining traction, according to several former students. The precise reason remains unexplained but, in the late 1980s, the steady stream of Kuwaitis attending North Carolina Agricultural & Technical State University dwindled. Few Arab students attend the school today.

In the aftermath of Sept. 11, the religious recruitment inevitably takes on a sinister slant. Yet former A&T students stress that the Muslim evangelizing there was largely spiritual and cultural, common enough throughout the Islamic world, where communal prayer is encouraged.

Students who recall Mohammed invariably describe a studious and private 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 Munifi, who studied mechanical engineering at the same time.

“He very much kept to himself,� said Zitawi, now a gas station owner in the Greensboro area. “We’d see each other at the Burger King for coffee or lunch. That was our hangout.... He was always polite. He wasn’t a funny guy, but when he’s talking to you, you feel like he’s smiling. He wasn’t rude or anything.�

Nor did Mohammed spout anti-Western or anti-American rhetoric. “Something must have happened later that caused that feeling,� said Hindieh, who knew Mohammed at both Chowan and Greensboro. “I never remember him saying anything like that.�

There is an unmistakable similarity between descriptions of Mohammed and the later accounts of the men, like Mohamed Atta, he sent to attack the United States: all Western-educated scions of middle-class Arab families; dedicated young men from discerning backgrounds who came to embrace a volatile creed of religion, politics and resentment.

By the end of 1986, after just 2 1/2 years, Mohammed had completed his work. He graduated Dec. 18, one of 28 mechanical engineering graduates, almost a third of them Middle Easterners. As at Chowan, there is no photo of him in the yearbook.

None of almost a dozen faculty members in the department from that era recalled Mohammed. For most of his classmates and teachers, the future terrorist mastermind with a $25-million price on his head did not cast a long shadow, if any at all.

Peshawar: The Call

Jihad, Abdullah Azzam wrote, is the way of everlasting glory, and the only way to get there is behind the barrel of a gun. “Jihad and the rifle alone: no negotiations, no conferences and no dialogues,� he said.

Azzam, more than any man, created the modern notion of a Muslim’s duty to wage war against all comers in order to reestablish the reign of Islam on Earth. It is a duty, he said, that commands all Muslims to its banner.

Azzam was born in the West Bank in 1941, land later occupied by Israel. He answered his first call to battle with the Palestinian resistance there, which he criticized because it was, he said, mere politics insufficiently rooted in Islam.

He departed for Cairo and an academic career, then left that when the Soviet Union invaded Afghanistan in 1979. He was among the first of the Afghan Arabs to arrive in Peshawar, Pakistan, in an upland basin ringed by hills that rise into mountains north and west en route to the Khyber Pass and Afghanistan.

Peshawar, capital of Pakistan’s unruly Northwest Frontier Province, has for centuries been an international crossroads for traders, warriors and rough statesmen. In the 1980s, Azzam made it the capital of the Afghan resistance and the destination for tens of thousands of Muslims who joined the holy war.

Saudi Arabia’s national airline offered special jihad fares. Arab governments sent emissaries and opened offices for dozens of state-sponsored charities to assist the fighters.

For a decade, parts of Peshawar were transformed into a sort of Little Mecca.

“It was a bustling Arab town -- Arab restaurants, bazaars, bakeries. During the jihad there were Arab newspapers and magazines published here. There were men in kaffiyeh, women fully covered in black,� said Rahimullah Yusufzai, a Pakistani journalist who became a leading chronicler of the Afghan wars.

It was, said Gen. Hamid Gul, who formerly headed Pakistan’s Inter-Services Intelligence, “the first international brigade of the modern time.�

Among those who answered Azzam’s call was a former student, Osama bin Laden. Azzam’s intellectual fervor and Bin Laden’s bank book combined in an organization that eventually became Al Qaeda.

The Saudi government sent dozens of missionaries and millions of dollars. The United States funneled arms and more millions through Peshawar.

Gun violence had been a way of life and death in the region long before the Soviet war. As one Pushtun saying puts it: A man’s jewelry is his gun. But there had never been anything on this scale before.

Pakistani intelligence, the ISI, was installed as executor of American and Saudi interests. The service created a new logistics operation just to distribute the flood of armaments. Convoys of 10-ton trucks filled with rifles, machine guns, grenade launchers and antiaircraft missiles were sent out daily on the cross-country trip from the docks in Karachi to Peshawar and the Afghan interior beyond.

“The original jihadis started in old Peshawar with very little money, in the pre-Saudi, pre-CIA days,� Yusufzai said. “Later, they all rented places in University Town, the most expensive neighborhood in Peshawar.�

The Arab neighborhoods in University Town were, oddly, the most westernized in the city. Old Peshawar is a crooked tangle of alleys and bazaars rich with the smells, smoke and people of Central Asia. A thick haze of exhaust, dust and brick kiln smoke lies over it.

University Town is clean and rectangular, laid out on a grid filled with walled compounds of big three-story stucco houses that would be at home in Orange County. The new villas were filled by the Arabs and an even larger militia of camp followers. Armies used to be trailed by merchants of flesh and other entertainments; modern armies, even ragtag agglomerations like the moujahedeen, are as likely to be followed by a social worker as a streetwalker. The Afghan wars, because of the international nature of their combatants and finances, were the apotheosis of this.

The biggest industry in Peshawar in the ‘80s and ‘90s, after the arms trade, was good works. More than 150 charities, development and refugee care organizations opened offices.

There was plenty to do. Afghanistan at the time of the Russian invasion had a population of 15 million. Over a decade, that would shrink by almost half. Many fled through the mountain passes to Pakistan.

One of the largest aid agencies was a Kuwaiti charity called Lajnat al Dawa al Islamia, the Committee for Islamic Appeal. The charity at one point had more than 1,000 employees in Pakistan and was spending $4 million a year in the region. Its regional manager was Zahed Shaikh -- Khalid Shaikh Mohammed’s older brother.

As head of one of the largest charities in town, Zahed became a figure of importance. He knew local diplomats, the Afghan warlords; when Pakistani politicians came to town, he shared the dais with them.

After college in North Carolina, Khalid, according to Kuwaiti authorities, never returned home. Instead, he joined his big brother in Peshawar. Another brother, Abed, a schoolteacher, left his job in the Gulf emirate of Qatar and came east too. A man who knew all three said Zahed, the eldest, was the coolest head of the trio; Abed was more militant and Khalid tended to follow him.

At the center of the Afghan resistance movement in Peshawar was Pushtun warlord Abdul Rasul Sayyaf, who had been a junior lecturer at Kabul University and was known as the Professor. He had been schooled in Cairo and spoke fluent Arabic. He became the favored recipient of money from the Saudi and American governments.

The money funded his army, a political party, a newspaper, a huge refugee camp and a college called the University of Dawa al Jihad, which means Convert and Struggle.

The university became known as a place you could learn darker trades than mathematics -- bomb-making, for example. A student once described it to U.S. journalist Mary Anne Weaver as an Islamic Sandhurst, likening it to the famous British military academy. For a time, the college also had as many as 1,000 students studying engineering, medical technology and literature.

The abandoned school sits behind high mud walls amid the sprawling Jalozai refugee camp, which today has more than 200,000 residents and is less an encampment than a city. Pakistanis marvel at the ingenuity of the Afghans, who have built a thriving local economy that includes the manufacture of pottery, textile and latticed wooden roofs that are exported back to Afghanistan where timber to make such things is scarce. There’s even a carwash.

By 1989, Mohammed had gone to work at Sayyaf’s university, a friend said. He taught there and worked weekends at the refugee camp. The three Baluchi brothers became part of the small, semi-permanent Arab community that included Azzam, Islamic Jihad founder Ayman Zawahiri and Bin Laden, who came and went with his wives and children in his own airplane. Most of the Arabs in town worshiped at a small mosque on a dead-end alley called Arbat Road, across the street from Zahed’s office.

It was a different world then, said one man who was part of the scene. Everyone had the same goal: to oust the Soviets. Everyone knew one another, prayed and socialized together, and even went to the jihad training camps together.

Victory over the Soviets, who withdrew in 1989, should have been the crowning achievement of the jihad. But the various Afghan factions, deprived of a common enemy, began fighting one another. American support disappeared with the end of the Soviet campaign. Many felt that the U.S. actively opposed the establishment of an Islamic government in Kabul after the Soviet withdrawal. This was, to some, the cruelest cut of all.

Azzam, the heart of the Arab jihadi resistance, and two young sons were murdered by a bomb on the street outside the mosque in 1989. That same spring, Khalid’s brother, Abed, also was killed by a bomb.

The political and religious climate changed in Peshawar, and resentment of the American abandonment festered. Bin Laden replaced Azzam as head of the Arab moujahedeen and began preaching hatred against the U.S.

Then came the 1990 Iraqi invasion of Kuwait and the American-led counterattack, which deepened divisions in the Arab world. Bin Laden, for one, was furious that the Saudi royal family allowed the U.S. to base its soldiers in the kingdom, violating what he felt was a Koranic dictate to keep infidels out of the holy land.

Most of the moujahedeen who had gathered in Pakistan went home, warriors without a war. Those who stayed changed perceptibly. Khalid Shaikh Mohammed and his circle changed with the times, one friend said.

“In 1991-92, their whereabouts, their meetings, their thoughts, it became more secret,� he said. “The hatred for Americans -- it was among every Arab who came to Afghanistan.�

Karachi: The Next War

Peshawar in the jihad years was said to have more spies, secret agents and freelance schemers per capita than any city in the world. Conversations dripped intrigue and purpose. Among the plotters was Khalid Shaikh Mohammed’s nephew, Ramzi Yousef.

Like Khalid, Yousef had left Fahaheel and Kuwait for college -- in his case, to study electrical engineering in Wales. He first visited Peshawar on a summer break in 1988 and then returned in 1991. He would become the first of the next-generation jihadis to carry the fight beyond Afghanistan.

It has never been clear who, if anyone, recruited Yousef, but at some point over the next year he began to make plans to attack. He asked a boyhood friend who was studying at flight schools in the U.S. to suggest potential targets. The friend suggested the World Trade Center, and by the fall of 1992 Yousef was in New York, assembling a team to bomb the twin towers.

American investigators say that Mohammed in late 1992 wired several hundred dollars to Yousef, so he knew at least where Yousef was; investigators believe that he also knew what Yousef was doing.

Mohammed moved his base of operations to Karachi, the metropolis of Pakistan’s southern seaboard, with direct flights throughout the Gulf, to Europe, to Southeast Asia, to Africa and the Americas. It is Pakistan’s most cosmopolitan city, if also its most violent.

In 1995 alone, there were 1,742 slayings, most of them the result of sectarian political rivalries that made parts of the city the exclusive property of one political party or another. These districts are called “no-go areas�; even police have abandoned any pretext of controlling what goes on within them.

Mohammed lived off and on in Karachi, using the city as a base from which to travel the globe. He began using the first of dozens of aliases, often posing as a Gulf businessman. At various times he told people that he was a holy-water salesman, an electronics importer and a Saudi oil sheik.

When Yousef returned to Pakistan in 1993 after the first World Trade Center bombing, he and Mohammed began assembling a team to broaden the battleground. By 1994, both men were spending months at a time in the Philippines and Malaysia, meeting like-minded men.

The events they planned were, in what would become a Mohammed signature, perversely spectacular: They would assassinate the pope, perhaps the American president, and in a stunning finale would blow up a dozen American airliners over the Pacific.

The plans were thwarted when bomb-making chemicals were ignited in a Manila apartment, leading to the discovery of their plots and the eventual arrest of fellow plotters. Yousef fled, just as he had after the first World Trade Center bombing, back to Pakistan. Mohammed had been careful; none of the other plotters even knew his name. It would be months before authorities figured out who he was and many years and thousands of deaths before they realized his significance.

Qatar: Slipping Away

Yousef wasn’t so careful. Some of the other plotters had known him for years; one told police that Yousef was the same man who had planned the Trade Center bombing. A worldwide manhunt ensued and within months Yousef’s whereabouts were betrayed. American and Pakistani agents stormed a hotel room in Islamabad, the Pakistani capital, in February 1995 and hauled Yousef away, kicking and screaming. At least that’s what another guest told a reporter.

“It was like a hurricane, a big panic,� the guest said. “He was shouting: ‘Why are you taking me? I am innocent! Show me papers if you are going to arrest me! Who are you?’ No one listened to him. They took him without his shoes. His eyes were blindfolded, his head was covered, his arms and legs were tied.�

The man giving this account identified himself as a Karachi businessman. He was registered under the name Khalid Shaikh. It was, American authorities eventually came to believe, Mohammed, hiding in plain sight. Mohammed’s caution -- he used three aliases on the Manila plot alone -- had paid off. He was still an unknown. That was about to end.

Yousef never gave up any valuable information. But investigators had recovered his laptop computer in Manila and a treasure trove of leads. The computer files included a letter seeking money for the plots. It was addressed to a potential donor, one who the letter-writer apparently felt was shirking his duty.

“Fear Allah, Mr. Siddiqui, there is a day of judgment,� the letter said.

It was signed Khalid Shaikh.

“We knew there was another person involved ... but he was very mysterious and we didn’t know who he was,� said Herman, who led the FBI investigation of the Manila plot. “He basically eluded us.�

The evidence they did have led investigators back to Peshawar and the circle of friends and acquaintances there. Zahed Shaikh -- Mohammed’s brother -- was scrutinized, and although there was never a formal accusation lodged against him, he disappeared from Peshawar.

Investigators say Mohammed spent the next year building and maintaining a fund-raising network in the Persian 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 throughout the 1990s.

“Khalid Shaikh 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 Shaikh Mohammed. It would be a chain of telephone calls, and Khalid would send the money.�

American understanding of Islamic terrorism then was still inchoate. Even Bin Laden was seen as just another guy with bad ideas and a lot of money. 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 Gulf. “He wasn’t even using an alias,� said one official. American agents tracked him to 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 ibn Khalid al Thani, who was then the country’s minister of religious affairs.

“Abdullah ibn Khalid had a farm outside� Doha, said one American official. “A lot of these guys had what were basically gentlemen’s truck farms. It was a hobby. Grow cabbages, raise ducks. 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.�

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

FBI Director Louis J. Freeh met with Qatari officials seeking permission to arrest him. One FBI official said months passed without approval, even though Qatar acknowledged that Mohammed, whom agents had begun referring to as KSM, was there. At one point, according to documents obtained by The Times, Qatar told the U.S. that it feared Mohammed was constructing an explosive device. They also said he possessed more than 20 different passports; still, they delayed granting the U.S. permission to arrest him.

Some officials strongly felt that the U.S. should act as quickly and with as much force as necessary to capture Mohammed. 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 one 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 [Department of Defense] providing the logistics and military muscle in the event we have to shoot our way in. And none of that happened.�

Another person at the meeting said the real obstacle was the Pentagon, which feared another “Black Hawk Down� debacle similar to the one in Somalia in 1993 and insisted that a raid would require hundreds, if not thousands, of troops.

In the end, rather than sending a kidnapping squad, Freeh sent a letter to Qatar’s government. By the time permission was granted and American agents went to Doha, Mohammed was gone.

“We reached out to every one of our friends out there to try and get him,� recalls one senior Justice Department official. “But he just kind of slipped off the screen.�

Afghanistan: Regrouping

Being on the run did not mean that Mohammed was out of commission.

He left Qatar about the same time Bin Laden was making common cause with the newly emergent Taliban in Afghanistan, who in exchange for his assistance gave him a secure base from which to operate.

A pair of attacks in Saudi Arabia marked the beginning of a new jihad, Bin Laden told British journalist Robert Fisk in 1996. He began expanding the reach of Al Qaeda across the world. Investigators now suspect that Mohammed was the key man in that effort. While Bin Laden and the men previously identified as his main deputies -- Zawahiri, Mohammed Atef and Abu Zubeida -- spent the bulk of their time in Afghanistan and Pakistan consolidating and rebuilding their training camps, Mohammed traveled the globe, searching out allies and recruits, and assembling what now seems like an omnipresent worldwide network.

“He was building a terrorism business. He was one of the key lieutenants in the entire Al Qaeda structure,� said the FBI’s Herman.

Investigators suspect that Mohammed developed direct personal relationships with several of the men who became Al Qaeda’s top regional operatives.

His trail wound through Europe, Africa, the Gulf, Southeast Asia and even South America, according to investigators in Malaysia where Mohammed, traveling under an Egyptian passport, obtained a Brazilian visa.

At times, said one senior U.S. counter-terrorism official, Mohammed would travel to other countries to personally establish terrorist cells and provide them with plans for attack, money, manpower and logistical support. Other times, he would operate at a higher level, overseeing senior Al Qaeda commanders who led the attacks.

The official said Mohammed is believed to have been actively involved in the bombing of two U.S. embassies in Africa that killed 224 people in 1998, the bombing of the Cole in the Yemeni port of Aden in 2000, which killed 17 sailors and nearly sank the $1-billion U.S. warship, and many other attacks.

“There is a clear operational link between him and the execution of most, if not all, of the Al Qaeda plots over the past five years,� the official said.

American investigators acknowledge that this evaluation of Mohammed as a central figure in Al Qaeda is largely retrospective. It wasn’t until after Sept. 11 that his larger role became apparent.

“He popped up post 9/11 and then, looking back, we saw that he was the Zelig of Al Qaeda, involved in a lot of other things,� one investigator said.

Sept. 11

One of the hallmarks of Al Qaeda is its breadth, the dispersion of its resources. So, for example, parts of the network could be preparing to attack American warships in Yemen, others to bomb civilian targets in Europe and Asia, even as the larger organization was already planning Sept. 11.

In an interview with Al Jazeera television, recorded in May this year, Mohammed described himself as the head of Al Qaeda’s military committee. He said that “about 2 1/2years prior to the holy raids on Washington and New York, the military committee held a meeting during which we decided to start planning for a martyrdom operation inside America.�

That would date the inception of the plot to early 1999. Later that same year, the men who would execute it were chosen, he said. German intelligence agencies believe that Mohammed first came into contact with these men when they visited Al Qaeda camps in Afghanistan.

Several of the men were students in Hamburg, Germany, part of a small group of devout Muslims who were growing increasingly restive over the plight of the Islamic world.

They were largely middle class, some well educated, not dispossessed in any apparent way. One was an urban planner and architect, one an aeronautical engineering student and one a prospective marine engineering student. Mohammed, a mechanical engineering graduate, chose other engineers for Al Qaeda’s riskiest undertaking. They were, like him, devout but at home in the West, adept at languages and technically inclined.

The rest of the hijacking crews were made up of two veteran Al Qaeda operatives, a replacement pilot and a group of young Gulf Arab volunteers, chosen from what Mohammed described as “a big excess of brothers who were filled with desire for martyrdom,� whose job was mainly to effect the physical takeover of the airliners.

As Sept. 11 approached, intelligence agents in the West were nearly beside themselves with anxiety. They knew something was going to happen, but they couldn’t figure out what. Mohammed was already moving on. He spent the weeks before Sept. 11 instructing a new Canadian recruit on communications protocols. He was sending the recruit to Southeast Asia to coordinate a bombing campaign in the Philippines and Singapore. The only acknowledgment that something big was afoot was his suggestion that the recruit should probably leave Pakistan before Sept. 11.

It is that sort of unrelenting focus that makes Mohammed such a feared figure among those who pursue him. He simply does not stop.

In the months after Sept. 11, investigators think that Mohammed was moving back and forth between Pakistan and Afghanistan. One Afghan general, Ziaudeen Deldar, said intelligence reports indicate that “Khalid the Baluchi� was among hundreds of Al Qaeda fighters who escaped on foot to Pakistan from a camp near Shahi Kot in southeastern Afghanistan last spring when American forces launched Operation Anaconda -- an attempt, they said, to finish off Al Qaeda.

Instead, the Americans faced considerably more resistance than anticipated and backed off. The grasp of the anaconda relaxed and the prey, including Mohammed, slipped away. Weeks later, Al Qaeda operatives blew up a truck outside a synagogue in Tunisia, killing 19 people. In the days leading up to the attack, investigators say, one of the bombers was in frequent telephone contact with a man in Karachi -- Mohammed.

Mohammed was accompanied at the Al Jazeera interview by Ramzi Binalshibh, another Hamburg man who had wanted to become one of the suicide pilots but who tried and failed four times to obtain a U.S. visa. Binalshibh instead became Mohammed’s field coordinator for the plot.

It’s noteworthy that in the interview, Mohammed let Binalshibh do most of the talking. Even in granting an interview, the purpose of which ostensibly was to reveal, he exposed almost nothing.

Karachi: Behind Walls

Karachi is a reasonably modern, at times almost ordinary, place. Kids on bikes pass by on their way to school. Boys and girls giggle in one another’s presence and listen to music that offends their parents’ ears. Young hipsters scout the latest boutiques and restaurants with cool, enigmatic one-word names. Okra is one of the latest.

The city is by many measures a mess. It hasn’t had a comprehensive development plan since the 1920s, the air is foul, but cars are smaller and traffic manageable. Important people ride Toyota Corollas to work, some with chauffeurs and bodyguards.

It has some of the vanity and swagger of cities accustomed to dominating their surroundings. It is in love with the myth of itself as a place of danger and deception.

So maybe it is not surprising how many people here can tell you where Khalid Shaikh Mohammed is, would be or has recently been. For a ghost, he has made many appearances. You can, in a couple of weeks, collect half a dozen addresses and a great many more stories.

The stories start in the Defense Housing Society, a large, newer group of neighborhoods between the old city center and the sea. It was at a Defense apartment building that a big shootout occurred in September. Defense -- it’s named for its developer, army officers -- contains many of the finer districts in the city. Benazir Bhutto, the former prime minister, lives in one of them, a leafy area of big homes and older-model Mercedeses.

The shootout was just beyond the better neighborhoods, in a commercial-industrial tract full of five- and six-story buildings, most with low-rent light industrial tenants: textile plants, zipper and button factories and small machine shops. The streets are paved, but the buildings are separated by bare dirt and are shuttered in the front with metal roll-up doors. The night before, when police arrived, the streets were empty and dark.

Nothing happened that night. The police or, rather, the authorities -- there were more intelligence agents and army special forces than there were cops -- waited. This is the sort of thing that spawns rumors. Why did they wait? The simplest explanation, the one authorities give, is of course not trusted, but it is the one that makes sense. They waited because they didn’t know what else to do. They didn’t know what or who to expect and waited to see.

People would like to believe the opposite: that authorities knew everything and waited because that would confuse things afterward; that they waited to give the people they had come to get time to escape; that they waited because this is Karachi and nobody knows why they waited.

This is what happens in a place where everything has been secret for so long. And it is one of the reasons Karachi is such a great place to hide: Who couldn’t hide in a place where everything is hidden?

Khalid Shaikh Mohammed first came here to live and do business a decade ago, assembling money and people for plots that would occur everywhere in the world but here. An early co-conspirator said he first met Mohammed in an Arab neighborhood full of money changers and bucket shops. A man who was captured in another plot had a phone number for Mohammed that was traced to the other end of town, a middle-class preserve of single-family homes of clean modern lines behind pale stucco walls.

The walls, actually, are the one thing many of the neighborhoods have in common. Karachi is a city of walls.

Another address is in the neighborhood where Ramzi Yousef’s in-laws lived, a cramped, dense place where the food stalls are full of root vegetables and the women wear the richly embroidered dresses favored by Baluchis. At least 10% of Karachi’s 12 million people are from Baluchistan, the next province to the northwest, and there is a constant traffic to and from the rural precincts, and from there to Iran and Afghanistan. It’s where Mohammed’s people came from.

A man claimed that he met Mohammed and his family across the marsh flats in the mud huts of another neighborhood this past spring. Mohammed was posing as a spiritual advisor, a holy man on the run from Arab agents who didn’t like his brand of Islam. The story seemed preposterous, but police acknowledge that they received a tip from another source and searched the same neighborhood extensively.

The part about there being a family turned out to have some basis. The police and the agents and the army all gathered for the big shootout in Defense because of the family. Earlier that day, acting on a tip, the police raided an apartment a couple of miles away. Pakistini authorities say they had information, based on utility records, that a senior Al Qaeda leader might be there. Instead, they found three children, two women and a man.

One of the women was a caretaker, and one child was hers. The other woman was a “foster mother� of sorts to the other two children, and the man her companion. The two boys, ages 7 and 9, were named Omar and Abdullah. Pakistani and American officials believe that their father is Khalid Shaikh Mohammed.

American authorities say the house contained photographs of Mohammed with the children; there was also evidence of another woman, thought to be Mohammed’s wife. It seemed a happy, playful group, a senior FBI investigator said. Some thought that they might have missed Mohammed by mere minutes, so when the people they captured told them about a group of Arabs living at another address in Defense, the authorities called up reserves and hurried across town.

“Our officers moved immediately,� said a senior Pakistani official. “No, we didn’t know that he was there. But from the interviews and surveillance we knew there was something big going on. The number of people there, the weapons, the intelligence we gathered. “

After morning prayers, they found the caretaker, who told them that the entire top floor was filled with Arabs. They’d been there for two months, he said, and overpaid on the rent. The authorities went in, and all hell broke loose. They were fired on immediately, the Pakistani official said. “Then it was a free-for-all. We fired at the windowpanes, put in tear gas and stormed them.�

Hundreds of rounds and two dead men later, the authorities secured the building. They searched room by room and in a storage space under a stairwell found the would-be Sept. 11 pilot Ramzi Binalshibh.

Afterward, and still, Karachi was thick with rumor. Mohammed was dead, was captured, was there and got away, was there and was allowed to get away.

The police are about the only ones who claim not to know how near they were to catching him that morning. They think that they were close, but they don’t really know. They are, as they’ve been for a decade, still looking and they’re not quite sure who it is they’re trying to find.

They’re hesitant to talk about it much, but intelligence officers acknowledge that they have interrogated Khalid Shaikh Mohammed’s two young sons. Not surprisingly, the boys haven’t had much to say. Not even his children know much about the man who engineered Sept. 11.

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(BEGIN TEXT OF INFBOX)

Portrait in Terror

Names: Khalid Shaikh Mohammed and three dozen aliases

Age: 37

Background: Born and raised in Kuwait

College: Graduate of North Carolina Agricultural & Technical State University

Reward: $25 million offered for his capture as head of Al Qaeda military committee

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Times staff writer Sebastian Rotella in Spain, special correspondent Dirk Laabs in Germany and researcher Robert Patrick in Washington contributed to this report.