Agents Saw Mohammed’s Stamp Behind Many Plots

When, after Sept. 11, evidence and interrogations made apparent to American investigators that Khalid Shaikh Mohammed was a key planner of the attacks, they began reexamining past terrorist plots. The more they looked, the more they saw Mohammed.

They eventually concluded, to their dismay, that he had been involved in every significant Al Qaeda operation they were aware of, including a 1995 plot to blow up U.S. airliners over the Pacific, the 1998 bombings of two U.S. embassies in Africa and the 2000 attack on an American warship in Yemen.

“He was under everybody’s radar. We don’t know how he did it. We wish we knew,” a senior FBI official said recently. “He’s the guy nobody ever heard of.”

Investigators believe that the idea to use airliners as bombs was Mohammed’s; they believe he recruited and supervised the hijack teams that carried out the Sept. 11 attacks.

Mohammed’s capture Saturday closes one of the longest and most frustrating episodes in the history of counter-terrorism. Investigators tracked him over a decade through five continents and a dozen plots and in the end still didn’t know much more about him than a collection of three dozen aliases.

In the small, closed world of international counter-terrorism, Mohammed became a mythic figure -- a ghost in the machine. He traveled the world as one of the chief designers of Al Qaeda. If Osama bin Laden was the network’s visionary architect, Mohammed was its engineer, the builder of its plots.

Mohammed communicated with Al Qaeda cells around the world by courier, e-mail, coded telephone conversations and short-wave radio. German intelligence agents have said that when he was forced to retreat to rural hide-outs along the Afghan-Pakistani border, he sent messages out by donkey.

Even at the height of the U.S. bombing campaign in Afghanistan in late 2001, Mohammed allegedly planned, staffed and directed more attacks. He is believed to have planned a post-Sept. 11 bombing of a synagogue in Tunisia. Several captured Al Qaeda operatives mentioned his interests in chemical and radioactive “dirty bombs.”

He used Egyptian, Qatari, Saudi, British and Kuwaiti identities, investigators say. He posed as a rich Persian Gulf oil sheik, an electronics import-export man and a religious advisor. He speaks Arabic with a Kuwaiti accent and is fluent in Urdu, a principal language of Pakistan, and English, acquired in part as he studied for a mechanical engineering degree at a college in North Carolina.

Over the years, investigators came close to capturing Mohammed at least half a dozen times, missing him sometimes by weeks, other times by what they guessed was mere minutes. Last fall, Pakistani authorities captured one of his principal aides and his two young sons, but Mohammed got away.

Mohammed’s persistence earned the grudging admiration of some investigators, who marveled at his ability to stay one step ahead.

In Pakistan, attempts to capture him involved a small army of agents from the military, police and multiple countries and intelligence agencies.

“The way he is managing their [Al Qaeda] affairs, the way he is controlling things, he is not an ordinary man,” said one top Pakistani intelligence official.

Almost every Al Qaeda suspect the Pakistanis have arrested over the last year had some connection to Mohammed, authorities say. Many had no relationship to one another, but they all knew Mohammed.

Mohammed was born in 1965, according to records, and was reared in Kuwait. His parents were Pakistanis from Baluchistan, an area that straddles Pakistan’s borders with Iran and Afghanistan. They were among the thousands of foreigners who were lured to the Persian Gulf by the oil boom but who were usually regarded as outsiders no matter how long they stayed.

Mohammed was the youngest of five children. His oldest brother, Zahed Shaikh, attended Kuwait University and was a leader of the Muslim Brotherhood, a pan-Arab organization that functioned as an underground opposition throughout the region. A man who knew the family in Kuwait said Mohammed’s initial politicization occurred through Zahed.

Mohammed attended high school in Kuwait, then left for tiny Chowan College, a Baptist school nestled among the cotton farms, tobacco patches and thick forests of eastern North Carolina.

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

The Arab students were frequently the targets of anti-Iranian epithets in the years after the 1979 takeover of the U.S. Embassy in Tehran. Locals called them “Abbie Dahbies.” American students played pranks on them, stealing the shoes the Arabs routinely left in the hallway outside their doors. Another prank involved filling 55-gallon garbage containers with water and propping them against the doors, knocking and running away. When the door opened, water flooded the room.

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

Students who recall Mohammed describe him as studious and private, a devotee of the library and of Allah.

“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 as Mohammed.

Mohammed 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 at Greensboro. “I never remember him saying anything like that.”

Mohammed earned a degree in mechanical engineering in late 1986 and is believed to have left the United States for Pakistan, where he joined his brother Zahed, who by then was running a Kuwaiti charity that aided Afghan refugees in Peshawar. Another brother fought and died in the Afghan resistance against Soviet occupation.

Mohammed taught at a university established by an Afghan warlord and at an adjacent refugee camp, according to a friend. His first known involvement in terrorism occurred in 1992, when he sent money to his nephew Ramzi Yousef as Yousef was in New Jersey planning the first bombing of the World Trade Center, in 1993.

Mohammed and Yousef later teamed up in a series of plots in the Philippines that included plans to assassinate Pope John Paul II and President Clinton and to bomb a dozen U.S. airliners, investigators say. Various people in Manila later described Mohammed as a fun-loving high-roller who entertained at plush hotels and took scuba-diving lessons.

Authorities foiled the Manila plots in 1995. Mohammed escaped and moved to the Persian Gulf, according to American investigators.

He spent the next year building and maintaining a terrorist fund-raising network in the gulf, investigators say.

He lived openly in the region.

“He wasn’t even using an alias,” said one official.

American agents tracked him through Italy, Egypt, Singapore, Jordan, Thailand, the Philippines and Qatar. In Qatar, U.S. officials say, he was a guest of Abdullah ibn Khalid al Thani, a member of the ruling family, who was then the country’s minister of religious affairs.

Then-FBI Director Louis J. Freeh met with Qatari officials seeking permission to arrest Mohammed. Some officials felt strongly that the U.S. should act as quickly and with as much force as necessary to capture him. Others were wary. A meeting was called in Washington in early 1996. Caution prevailed.

In the end, rather than sending a squad to capture Mohammed, Freeh sent a letter to the Qatari government. By the time permission was granted, Mohammed was gone. He is believed to have fled to Afghanistan and then to have joined Al Qaeda and risen 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 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?”

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Times staff writers Patrick J. McDonnell and Josh Meyer contributed to this report.