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After the millennium roundup, O'Neill suspected that Al Qaeda had sleeper cells buried in America. "He started pulling the strings in Jordan and in Canada, and in the end they all led back to the United States," Clarke said. "There was a general disbelief in the F.B.I. that Al Qaeda had much of a presence here. It just hadn't sunk through to the organization, beyond O'Neill and Dale Watson"—the assistant director of the counter-terrorism division. Clarke's discussions with O'Neill and Watson over the next few months led to a strategic plan called the Millennium After-Action Review, which specified a number of policy changes designed to root out Al Qaeda cells in the United States. They included increasing the number of Joint Terrorism Task Forces around the country; assigning more agents from the Internal Revenue Service and the Immigration and Naturalization Service to monitor the flow of money and personnel; and creating a streamlined process for analyzing information obtained from wiretaps.

Many in the F.B.I. point to the millennium investigation as one of the bureau's great recent successes. A year earlier, O'Neill had been passed over when the position of assistant director in charge of national security that supporting him was a full-time job," Mawn said.

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(My headline: Barbara Bodine, typical Clinton appointeee sides with Yemen against the interest of the US military.)

On October 12, 2000, a small boat filled with C4 explosives motored alongside a U.S. destroyer, the Cole, which was fuelling up off the coast of Yemen. Two men aboard the small craft waved at the larger vessel, then blew themselves to pieces. Seventeen American sailors died, and thirty-nine others were seriously wounded.

O'Neill knew that Yemen was going to be an extremely difficult place in which to conduct an investigation. In 1992, bin Laden's network had bombed a hotel in Aden, hoping to kill a number of American soldiers. The country was filled with spies and with jihadis and was reeling from a 1994 civil war. "Yemen is a country of eighteen million citizens and 50 million machine guns," O'Neill reported. On the day the investigators arrived in Yemen, O'Neill warned them, "This may be the most hostile environment the F.B.I. has ever operated in."

The American Ambassador to Yemen, Barbara Bodine, saw things differently. In her eyes, Yemen was the poor and guileless cousin of the swaggering petro-monarchies of the Persian Gulf. Unlike other countries in the region, it was a constitutional democracy—however fragile—in which women were allowed to vote. Bodine had had extensive experience in Arab countries. During the Iraqi invasion and occupation of Kuwait, she had been the deputy chief of mission in Kuwait City, and she had stayed through the hundred-and-thirty-seven-day siege of the American Embassy by Iraqi troops until all the Americans were evacuated.

Bodine, who is on assignment from the State Department as diplomat-in-residence at the University of California at Santa Barbara, contends that she and O'Neill had agreed that he would bring in a team of no more than fifty. She was furious when three hundred investigators, support staff, and marines arrived, many carrying automatic weapons. "Try to imagine if a military plane from another country landed in Des Moines, and three hundred heavily armed people took over," she told me recently. Bodine recalled that she pleaded with O'Neill to consider the delicate diplomatic environment he was entering. She quoted him as responding, "We don't care about the environment. We're just here to investigate a crime."

"There was the F.B.I. way, and that was it," she said to me. "O'Neill wasn't unique. He was simply extreme." According to Michael Sheehan, who was the State Department's coördinator for counter-terrorism at the time, such conflicts between ambassadors and the bureau are not unusual, given their differing perspectives; however, Bodine had been given clear instructions from the outset of the investigation. "I drafted a cable under [then Secretary of State] Madeleine Albright's signature saying that there were three guiding principles," Sheehan said. "The highest priorities were the immediate safety of American personnel and the investigation of the attack. No. 3 was maintaining a relationship with the government of Yemen— but only to support those objectives."

O'Neill's investigators were billeted three or four to a room in an Aden hotel. "Forty-five F.B.I. personnel slept on mats on the ballroom floor," he later reported. He set up a command post on the eighth floor, which was surrounded by sandbags and protected by a company of fifty marines.

O'Neill spent much of his time coaxing the Yemeni authorities to coöperate. To build a case that would hold up in American courts, he wanted his agents present during interrogations by local authorities, in part to insure that none of the suspects were tortured. He also wanted to gather eyewitness testimony from residents who had seen the explosion. Both the Yemeni authorities and Bodine resisted these requests. "You want a bunch of six-foot-two Irish-Americans to go door-to-door?" Bodine remembers saying to O'Neill. "And, excuse me, but how many of your guys speak Arabic?"

There were only half a dozen Arabic speakers in the F.B.I. contingent, and even O'Neill acknowledged that their competence was sometimes in question. On one occasion, he complained to a Yemeni intelligence officer, "Getting information out of you is like pulling teeth." When his comment was translated, the Yemeni's eyes widened. The translator had told him, "If you don't give me the information I want, I'm going to pull out your teeth."

When O'Neill expressed his frustration to Washington, President Clinton sent a note to President Ali Abdullah Saleh. It had little effect. According to agents on the scene, O'Neill's people were never given the authority they needed for a proper investigation. Much of their time was spent on board the Cole, interviewing sailors, or lounging around the sweltering hotel. Some of O'Neill's requests for evidence mystified the Yemenis. They couldn't understand, for instance, why he was demanding a hat worn by one of the conspirators, which O'Neill wanted to examine for DNA evidence. Even the harbor sludge, which contained residue from the bomb, was off limits until the bureau paid the Yemeni government a million dollars to dredge it.

There were so many perceived threats that the agents often slept in their clothes and with their guns at their sides. Bodine thought that much of this fear was overblown. "They were deeply suspicious of everyone, including the hotel staff," she told me. She assured O'Neill that gunfire outside the hotel was probably not directed at the investigators but was simply the noise of wedding celebrations. Still, she added that, for the investigators' own safety, she wanted to lower the bureau's profile by reducing the number of agents and stripping them of heavy weapons. Upon receiving a bomb threat, the investigators evacuated the hotel and moved to an American vessel, the U.S.S. Duluth. After that, they had to request permission just to come ashore.

Relations between Bodine and O'Neill deteriorated to the point that Barry Mawn flew to Yemen to assess the situation. "She represented that John was insulting, and not getting along well with the Yemenis," he recalled. Mawn talked to members of the F.B.I. team and American military officers, and he observed O'Neill's interactions with Yemeni authorities. He told O'Neill that he was doing "an outstanding job." On Mawn's return, he reported favorably on O'Neill to Freeh, adding that Bodine was his "only detractor."

An ambassador, however, has authority over which Americans are allowed to stay in a foreign country. A month after the investigation began, Assistant Director Dale Watson told the Washington Post, "Sustained cooperation" with the Yemenis "has enabled the F.B.I. to further reduce its in-country presence. . . . The F.B.I. will soon be able to bring home the F.B.I.'s senior on-scene commander, John O'Neill." It appeared to be a very public surrender. The same day, the Yemeni Prime Minister told the Post that no link had been discovered between the Cole bombers and Al Qaeda.

The statement was premature, to say the least. In fact, it is possible that some of the planning for the Cole bombing and the September 11th attacks took place simultaneously. It is now believed that at least two of the suspected conspirators in the Cole bombing had attended a meeting of alleged bin Laden associates in Malaysia, in January, 2000. Under C.I.A. pressure, Malaysian authorities had conducted a surveillance of the gathering, turning up a number of faces but, in the absence of wiretaps, nothing of what was said. "It didn't seem like much at the time," a Clinton Administration official told me. "None of the faces showed up in our own files." Early last year, the F.B.I. targeted the men who were present at the Malaysia meeting as potential terrorists. Two of them were subsequently identified as hijackers in the September 11th attacks.

After two months in Yemen, O'Neill came home feeling that he was fighting the counter-terrorism battle without support from his own government. He had made some progress in gaining access to evidence, but so far the investigation had been a failure. Concerned about continuing threats against the remaining F.B.I. investigators, he tried to return in January of 2001. Bodine denied his application to reënter the country. She refuses to discuss that decision. "Too much is being made of John O'Neill's being in Yemen or not," she told me. "John O'Neill did not discover Al Qaeda. He did not discover Osama bin Laden. So the idea that John or his people or the F.B.I. were somehow barred from doing their job is insulting to the U.S. government, which was working on Al Qaeda before John ever showed up. This is all my embassy did for ten months. The fact that not every single thing John O'Neill asked for was appropriate or possible does not mean that we did not support the investigation."

After O'Neill's departure, the remaining agents, feeling increasingly vulnerable, retreated to the American Embassy in Sanaa, the capital of Yemen. In June, the Yemeni authorities arrested eight men who they said were part of a plot to blow up the Embassy. New threats against the F.B.I. followed, and Freeh, acting upon O'Neill's recommendation, withdrew the team entirely. Its members were, he told me, "the highest target during this period." Bodine calls the pullout "unconscionable." In her opinion, there was never a specific, credible threat against the bureau. The American Embassy, Bodine points out, stayed open. But within days American military forces in the Middle East were put on top alert.