On October 12, 2000, in the deep-water port of Aden, Yemen, the U.S.S. Cole, a guided-missile destroyer weighing eighty-three hundred tons, was docked at a fuelling buoy. The Cole, which cost a billion dollars to build, was one of the most “survivable” ships in the U.S. Navy, with seventy tons of armor, a hull that could withstand an explosion of fifty-one thousand pounds per square inch, and stealth technology designed to make the ship less visible to radar. As the Cole filled its tank, a fibreglass fishing boat containing plastic explosives approached. Two men brought the skiff to a halt amidships, smiled and waved, then stood at attention. The symbolism of this moment was exactly what Osama bin Laden, the leader of Al Qaeda, had hoped for when he approved a plan to attack an American naval vessel. “The destroyer represented the West,” bin Laden said later. “The small boat represented Muhammad.”

The shock wave from the blast shattered windows onshore. Two miles away, people thought there had been an earthquake. The fireball that rose from the waterline swallowed a sailor who had leaned over the rail to see what the men in the skiff were up to. The blast opened a hole, forty feet by forty feet, in the port side of the ship, tearing apart sailors belowdecks who were waiting for lunch. Seventeen of them perished, and thirty-nine were wounded. Several sailors swam through the blast hole to escape the flames. The great man-of-war looked like a gutted animal.

It was Al Qaeda’s second successful strike against American targets. In August, 1998, operatives had bombed the United States Embassies in Kenya and Tanzania simultaneously, killing two hundred and twenty-four people. Yet an important part of the Cole plot had failed: Fahd al-Quso, a member of Al Qaeda’s support team in Aden, was supposed to videotape the blast for propaganda purposes, but he slept through a morning alarm and did not set up his camera in time. Quso was in a taxi at the moment of the explosion, and he immediately went into hiding.

Shortly after the attack, Ali Soufan, a twenty-nine-year-old Lebanese-American, was driving across the Brooklyn Bridge when he received a page from the New York office of the F.B.I., where he was employed as a special agent. He was told to report to work at once. At the time, Soufan was the only F.B.I. agent in the city who spoke Arabic, and one of only eight in the country. He had joined the New York office in the fall of 1997, and his talents were quickly spotted by John O’Neill, the head of the F.B.I.’s National Security Division, which is devoted to combatting terrorism. The following February, when bin Laden issued a fatwa declaring war on America, Soufan wrote a trenchant report on Islamic fundamentalism that O’Neill distributed to his supervisors. After the 1998 embassy bombings, Soufan helped assemble the initial evidence linking them to bin Laden. Soufan’s language skills, his relentlessness, and his roots in the Middle East made him invaluable in helping the F.B.I. understand Al Qaeda, an organization that few Americans were even aware of before the embassy bombings. O’Neill, who had joined the F.B.I. twenty-five years earlier, referred to the young agent as a “national treasure.” Despite Soufan’s youth and his relatively short tenure, O’Neill placed him in charge of the Cole investigation. As it turned out, Soufan became America’s best chance to stop the attacks of September 11th.

Soufan speaks rapidly, and there is still a hint of Lebanon in his voice. He has an open face and an engaging smile, although there are circles under his eyes from too many long nights. Soufan is a Muslim, but he doesn’t follow any particular school of Islam; instead, he is drawn to mystical thought, especially that of Kahlil Gibran, the Lebanese-American poet. He told me that he has an interest in the Kabbalah, because “it appeared at a time when the political environment for the Jews was so harsh that they used this philosophy to escape their anguish.” When he wants to relax, he watches reruns of “Seinfeld”—he’s seen every episode three or four times—or Bugs Bunny cartoons. One of his favorite writers is Karen Armstrong, whose biographies of Muhammad and the Buddha knit together history and religion in a way that makes sense to him.

Soufan grew up in Lebanon during the calamitous civil war, when cities were destroyed and terrorists were empowered by lawlessness and chaos. His father was a journalist in Beirut, and as a child Soufan helped out at the business magazine his father produced, often carrying galleys to the printshop. In 1987, when Soufan was sixteen, the family moved to the United States. Soufan’s most vivid initial impression of his adopted country was that it was safe. “Also, it allowed me to dream,” he said.

Soufan lived in Pennsylvania, and he never suffered from prejudice because he was a Muslim Arab. In high school, he won many academic awards. He attended Mansfield University, in central Pennsylvania, where he was elected president of the student government. In 1997, he received a master’s degree in international relations from Villanova University, outside Philadelphia. He initially planned to continue his studies in a Ph.D. program. But he had developed a fascination with the U.S. Constitution—in particular, with its guarantees of freedom of speech, religion, and assembly, and the right to a speedy trial. “People who are born into this system may take it for granted,” he said. “You don’t know how important these rights are if you haven’t lived in a country where you can be arrested or killed and not even know why.” Like many naturalized citizens, Soufan felt indebted for the new life he had been given. Although he was poised for an academic career, he decided—“almost as a joke,” he says—to send his résumé to the F.B.I. He thought it was nearly inconceivable that the bureau would hire someone with his background. Yet in July, 1997, a letter arrived instructing him to report to the F.B.I. Academy, in Quantico, Virginia, in two weeks.

Upon graduation, Soufan went to the New York bureau. He was soon assigned to the I-40 squad, which concentrated mainly on the Islamist paramilitary group Hamas, but, in 1998, on the day after the East African embassy bombings, O’Neill drafted him into I-49, which had become the lead unit in the F.B.I.’s investigation of Al Qaeda.

O’Neill was one of a few top managers in the F.B.I. who recognized early the danger that Al Qaeda posed to America. His intensity was unyielding, and his manner was often abrasive; he could be brutal not only to those under him but to superiors who he felt were not fully committed to an investigation. Soufan proved to be a tireless ally, willing to work nights and holidays. “O’Neill adored him, and Ali felt the same way,” Carlos Fernandez, an agent who knew both men well, observed. “They were equals, in many ways. If you say something to Ali, he’ll remember it, word for word, ten years from now. John was also great at remembering names and connecting the dots. They could go on for hours, putting things together.” The fact that a novice like Soufan had direct access to O’Neill aroused some resentment among the other agents, but the bureau had nobody else with his skills and dedication. “John and I often talked about the need to clone Ali,” Kenneth Maxwell, an F.B.I. official who was then Soufan’s superior, told me.