The legend of John P. O’Neill, who lost his life at the World Trade Center on September 11th, begins with a story by Richard A. Clarke, the national coördinator for counter-terrorism in the White House from the first Bush Administration until last year. On a Sunday morning in February, 1995, Clarke went to his office to review intelligence cables that had come in over the weekend. One of the cables reported that Ramzi Yousef, the suspected mastermind behind the first World Trade Center bombing, two years earlier, had been spotted in Pakistan. Clarke immediately called the F.B.I. A man whose voice was unfamiliar to him answered the phone. “O’Neill,” he growled.

“Who are you?” Clarke said.

“I’m John O’Neill,” the man replied. “Who the hell are you?”

O’Neill had just been appointed chief of the F.B.I.’s counter-terrorism section, in Washington. He was forty-two years old, and had been transferred from the bureau’s Chicago office. After driving all night, he had gone directly to headquarters that Sunday morning without dropping off his bags. When he heard Clarke’s report about Yousef, O’Neill entered the F.B.I.’s Strategic Information Operations Center (SIOC) and telephoned Thomas Pickard, the head of the bureau’s National Security Division in New York. Pickard then called Mary Jo White, the United States Attorney for the Southern District of New York, who had indicted Yousef in the bombing case.

One of O’Neill’s new responsibilities was to put together a team to bring the suspect home. It was composed of agents who were working on the case, a State Department representative, a medical doctor, a hostage-rescue team, and a fingerprint expert whose job was to make sure that the suspect was, in fact, Ramzi Yousef. Under ordinary circumstances, the host country would be asked to detain the suspect until extradition paperwork had been signed and the F.B.I. could place the man in custody. There was no time for that. Yousef was reportedly preparing to board a bus for Peshawar. Unless he was apprehended, he would soon cross the Khyber Pass into Afghanistan, where he would be out of reach. There was only one F.B.I. agent in Pakistan at the time, along with several agents from the Drug Enforcement Administration and the State Department’s diplomatic-security bureau. “Our Ambassador had to get in his car and go ripping across town to get the head of the local military intelligence,” Clarke recalled. “The chief gave him his own personal aides, and this ragtag bunch of American law-enforcement officials and a couple of Pakistani soldiers set off to catch Yousef before he got on the bus.” O’Neill, working around the clock for the next three days, coördinated the entire effort. At 10 A.M. Pakistan time, on Tuesday, February 7th, SIOC was informed that the World Trade Center bomber was in custody.

During the next six years, O’Neill became the bureau’s most committed tracker of Osama bin Laden and his Al Qaeda network of terrorists as they struck against American interests around the world. Brash, ambitious, often full of himself, O’Neill had a confrontational personality that brought him powerful enemies. Even so, he was too valuable to ignore. He was the point man in the investigation of the terrorist attacks in Saudi Arabia, East Africa, and Yemen. At a time when the Clinton Administration was struggling to decide how to respond to the terrorist threat, O’Neill, along with others in the F.B.I. and the C.I.A., realized that Al Qaeda was relentless and resourceful and that its ultimate target was America itself. In the last days of his life, after he had taken a new job as the chief of security for the World Trade Center, he was warning friends, “We’re due.”

“I am the F.B.I.,” John O’Neill liked to boast. He had wanted to work for the bureau since boyhood, when he watched Efrem Zimbalist, Jr., as the buttoned-down Inspector Lewis Erskine in the TV series “The F.B.I.” O’Neill was born in 1952 and brought up in Atlantic City, where his mother drove a cab for a small taxi business that she and his father owned. After graduating from Holy Spirit High School, he got a job as a fingerprint clerk with the F.B.I. During his first semester in college, he married his high-school sweetheart, Christine, and when he was twenty their son, John P. O’Neill, Jr., was born. O’Neill put himself through a master’s program in forensics at George Washington University by serving as a tour guide at the F.B.I. headquarters. In 1976, he became a full-time agent in the bureau’s office in Baltimore; ten years later, he returned to headquarters and served as an inspector. In 1991, he was named assistant special agent in charge in the Chicago office. In 1994, he received the additional assignment of supervising VAPCON, a national investigation into violence against abortion providers. The following year, he transferred to headquarters to become the counter-terrorism chief.

John Lipka, an agent who met O’Neill during the VAPCON probe, marvelled at his ability to move so easily from investigating organized crime and official corruption to the thornier field of counter-terrorism. “He was a very quick study,” Lipka told me. “I’d been working terrorism since ’86, but he’d walk out of the Hoover building, flag a cab, and I’d brief him on the way to the White House. Then he’d give a presentation, and I’d be shocked that he grasped everything I had been working on for weeks.”

O’Neill entered the bureau in the J. Edgar Hoover era, and throughout his career he had something of the old-time G-man about him. He talked tough, in a New Jersey accent that many loved to imitate. He was darkly handsome, with black eyes and slicked-back hair. In a culture that favors discreet anonymity, he cut a memorable figure. He favored fine cigars and Chivas Regal and water with a twist, and carried a nine-millimetre automatic strapped to his ankle. His manner was bluff and dominating, but he was always immaculately, even fussily, dressed. One of his colleagues in Washington took note of O’Neill’s “night-club wardrobe”—black double-breasted suits, semitransparent black socks, and ballet-slipper shoes. “He had very delicate feet and hands, and, with his polished fingernails, he made quite an impression.”

In Washington, O’Neill became part of a close-knit group of counter-terrorism experts which formed around Richard Clarke. In the web of federal agencies concerned with terrorism, Clarke was the spider. Everything that touched the web eventually came to his attention. The members of this inner circle, which was known as the Counter-terrorism Security Group (C.S.G.), were drawn mainly from the C.I.A., the National Security Council, and the upper tiers of the Defense Department, the Justice Department, and the State Department. They met every week in the White House Situation Room. “John could lead a discussion at that level,” R. P. Eddy, who was an N.S.C. director at the time, told me. “He was not just the guy you turned to for a situation report. He was the guy who would say the thing that everybody in the room wishes he had said.”

In July of 1996, when T.W.A. Flight 800 crashed off the coast of Long Island, there was widespread speculation in the C.S.G. that it had been shot down by a shoulder-fired missile from the shore. Dozens of witnesses reported having seen an ascending flare that culminated in an explosion. According to Clarke, O’Neill, working with the Defense Department, determined the height of the aircraft and its distance from shore at the time of the explosion, and demonstrated that it was out of the range of a Stinger missile. He proposed that the flare could have been caused by the ignition of leaking fuel from the aircraft, and he persuaded the C.I.A. to do a video simulation of this scenario, which proved to be strikingly similar to the witnesses’ accounts. It is now generally agreed that mechanical failure, not terrorism, caused the explosion of T.W.A. Flight 800.