The C.I.A. may also have been protecting an overseas operation and was afraid that the F.B.I. would expose it. Moreover, Mihdhar and Hazmi could have seemed like attractive recruitment possibilities—the C.I.A. was desperate for a source inside Al Qaeda, having failed to penetrate the inner circle or even to place someone in the training camps, even though they were largely open to anyone who showed up. However, once Mihdhar and Hazmi entered the United States they were the province of the F.B.I. The C.I.A. has no legal authority to operate inside the country.

In the end, the C.I.A.’s failure to inform the F.B.I. may be best explained by the fact that the agency was drowning in a flood of threats and warnings, and simply did not see the pivotal importance of this intelligence. Whatever the reason for the C.I.A.’s lapse, many F.B.I. investigators remain furious that they were not informed of the presence of Al Qaeda operatives inside America. Mihdhar and Hazmi arrived twenty months before September 11th. Kenneth Maxwell, Soufan’s former supervisor, told me, “Two Al Qaeda guys living in California—are you kidding me? We would have been on them like white on snow: physical surveillance, electronic surveillance, a special unit devoted entirely to them.” Of course, the F.B.I. had other opportunities to prevent September 11th. In July, 2001, an F.B.I. agent in Phoenix suggested interviewing Arabs enrolled in American flight schools; a month later, the bureau’s Minnesota office requested permission to aggressively investigate Zacarias Moussaoui, who later confessed to being an Al Qaeda associate. Both proposals were rejected by F.B.I. supervisors. But Mihdhar and Hazmi were directly involved in the September 11th conspiracy. Because of their connection to bin Laden, who had a federal indictment against him, the F.B.I. had all the authority it needed to use every investigative technique to penetrate and disrupt the Al Qaeda cell. Instead, the hijackers were free to develop their plot until it was too late to stop them.

In Yemen, the security situation deteriorated rapidly. Soufan and the other F.B.I. agents were quartered at the Aden Hotel, crammed in with other U.S. military and government employees, including Marine guards, and billeted three and four to a room; several dozen slept on bedrolls in the hotel ballroom. Gunfire erupted outside the hotel so frequently that the agents slept in their clothes, with their weapons at their sides. Agents learned from a mechanic in Aden that, after the bombing, some men brought to his shop a truck similar to the one used by the bombers; the men wanted to have metal plates installed in such a way that they could direct the force of an explosion. Certainly, the most tempting target for such a bomb would be the Aden Hotel. It wasn’t clear that the Yemeni government troops who were guarding the hotel with machine-gun nests would truly protect the Americans. “We were prisoners,” an agent recalled.

One night, shots were fired on the street while O’Neill was running a meeting inside the hotel. The marines and the hostage-rescue team adopted defensive positions. Soufan ventured out, unarmed, to talk to the Yemeni troops.

“Hey, Ali!” O’Neill called out. “Be careful!” He raced down the steps of the hotel to make sure Soufan was wearing his flak jacket. Frustration, stress, and danger, along with the enforced intimacy of their situation, had brought the two men even closer. O’Neill had begun to describe Soufan as his “secret weapon.” Speaking to the Yemenis, he called him simply “my son.”

Snipers covered Soufan as he approached a Yemeni officer, who assured him that everything was O.K.

“If everything is O.K., why are there no cars on the street?” Soufan asked.

The officer said that there must be a wedding nearby. Soufan looked around and saw that the hotel was surrounded by a large number of men in traditional dress—some in Jeeps, all carrying guns. They were civilians, not soldiers. They could be intelligence officers, or a tribal group bent on revenge. In either case, they easily outnumbered the Americans. Soufan was reminded of the 1993 uprising in Somalia, which ended with eighteen American soldiers dead, and one of the bodies being dragged through the streets of Mogadishu. The hotel backed up to the harbor, and the Americans were essentially trapped.

After Soufan went inside and offered his assessment of the situation, O’Neill ordered the marines to deploy two armored vehicles to block the street in front of the hotel. The night passed without further incident, but the next day O’Neill moved the investigators to the U.S.S. Duluth, stationed ten miles away, in the Bay of Aden. That proved to be a dangerous mistake. The next morning, when O’Neill and Soufan were flying back to town, their helicopter suddenly lurched into violent evasive maneuvers. The pilot reported that an SA-7 missile had locked in on them. O’Neill decided to send most of the investigators home; those who remained returned to the deserted hotel.

Just before Thanksgiving, the F.B.I. pulled O’Neill out of Yemen, apparently as a concession to Ambassador Bodine, who felt that the F.B.I. presence was straining diplomatic relations between America and Yemen. Soufan stayed on, but the threats in Aden became so acute that he and the other agents moved to the American Embassy in Sanaa, Yemen’s capital. The investigation was losing its momentum.

In the spring of 2001, Tom Wilshire, a C.I.A. liaison at F.B.I. headquarters, in Washington, was studying the relationship between Khaled al-Mihdhar, the Saudi Al Qaeda operative, and Khallad, the one-legged jihadi. Because of the similarity of the names, the C.I.A. had thought that they might be the same person, but, thanks in part to Ali Soufan’s investigations in Yemen, the agency now knew that they were not, and that Khallad had orchestrated the Cole attack. “O.K. This is important,” Wilshire said of Khallad, in an e-mail to his supervisors at the C.I.A. Counterterrorist Center. “This is a major-league killer.” Wilshire already knew that Hazmi, the other Saudi operative, had arrived in the United States and that Mihdhar was possibly with him. “Something bad [is] definitely up,” Wilshire wrote to a colleague. He asked permission to disclose this vital information to the F.B.I. His superiors at the C.I.A. never responded to his request. (In an official statement, the C.I.A. questioned the accuracy of this article but did not address specific allegations. It said, “Based on rigorous internal and external reviews of its shortcomings and successes before and after 9/11, the C.I.A. has improved its processing and sharing of intelligence. C.I.A.’s focus is on learning and even closer coöperation with partners inside and outside government, not on public finger pointing, which does not serve the American people well.”)

That summer, Wilshire asked an F.B.I. analyst to review the material on the Malaysia meeting, but he did not reveal that some of the participants might be in the United States. More important, he conveyed none of the urgency reflected in his e-mail; he told the analyst that she should examine the material in her free time. She didn’t get around to it until the end of July.

Wilshire did want to know, however, what the F.B.I. knew. He asked Dina Corsi, another F.B.I. analyst, to show three surveillance photos from the Malaysia meeting to several I-49 agents. The pictures showed Mihdhar and Hazmi and a man who, the C.I.A. believed, resembled Quso, the Cole cameraman. Wilshire told Corsi that one of the men was named Khaled al-Mihdhar, but he did not explain why the pictures had been taken, and he did not mention that Mihdhar had a U.S. visa.

According to the 9/11 Commission Report, on June 11th a C.I.A. supervisor went with the F.B.I. analyst and Corsi to New York to meet with F.B.I. case agents on the Cole investigation; Soufan, who was still in Yemen, did not attend. The meeting started in mid-morning, with the New York agents briefing the C.I.A. supervisor, Clark Shannon, for three or four hours on the progress of their investigation. Corsi then showed the three Malaysia photographs to her F.B.I. colleagues. They were high-quality surveillance photos. One, shot from a low angle, showed Mihdhar and Hazmi standing beside a tree in Malaysia. Shannon wanted to know if the agents recognized anyone. The I-49 agents asked who was in the pictures, and when and where they had been taken. “Were there any other photographs of this meeting?” one of the F.B.I. agents demanded. Shannon refused to say. Corsi promised that “in the days and weeks to come” she would try to get permission to pass that information along. The meeting became heated. The F.B.I. agents sensed that these photographs pertained directly to crimes they were trying to solve, but they couldn’t elicit any further information from Shannon. Corsi finally dropped the name Khaled al-Mihdhar. Steve Bongardt, Soufan’s top assistant in the Cole investigation, asked Shannon to provide a date of birth or a passport number to go with Mihdhar’s name. A name by itself was not sufficient to prevent his entry into the United States. Bongardt had just returned from Pakistan with a list of thirty names of suspected Al Qaeda associates and their dates of birth, which he had given to the State Department. That was standard procedure—the first thing most investigators would do. But Shannon declined to provide the additional information. Top C.I.A. officials had not authorized him to disclose the vital details of Mihdhar’s U.S. visa, his association with Hazmi, and their affiliation with Khallad and Al Qaeda.

There was a fourth photograph of the Malaysia meeting that Shannon did not produce. That was a picture of Khallad, the one-legged operative. Thanks to Soufan’s interrogation of Quso, the Cole investigators had an active file on Khallad and were preparing to indict him. Knowledge of that fourth photo would likely have prompted O’Neill to demand that the C.I.A. turn over all information relating to Khallad and his associates. By withholding the picture of Khallad attending the meeting with the future hijackers, the C.I.A. may in effect have allowed the September 11th plot to proceed. That summer, Mihdhar returned to Yemen and then went to Saudi Arabia, where, presumably, he helped the remaining hijackers secure entry into the United States. Two days after the frustrating June 11th meeting, Mihdhar received another American visa from the consulate in Jeddah, Saudi Arabia. Since the C.I.A. had not given his name to the State Department to post on its watch list, Mihdhar arrived in New York on the Fourth of July.

The June 11th meeting was the culmination of a strange trend in the U.S. government toward hiding information from the people who most needed it. In this regard, the F.B.I. was as guilty as the C.I.A. A federal law at the time prohibited the sharing of information arising from grand-jury testimony, but the F.B.I. took it as a nearly absolute bar to revealing any investigative evidence and, as a result, repeatedly turned down requests for information from other intelligence agencies. (The Joint Congressional Inquiry on 9/11 claimed that the law “came to be used simply as an excuse for not sharing information.”)

In 1995, the Justice Department established a policy, known as “the Wall,” which regulated the exchange of foreign intelligence information between agents and criminal investigators. Managers at F.B.I. headquarters misinterpreted the policy, turning it into a straitjacket for their own investigators. Intelligence agents were warned that sharing such information with criminal agents could mean the end of their careers. The Wall, the F.B.I. decided, separated even people who were on the same squad. The F.B.I. also began withholding intelligence from the White House. Every morning on the classified computers of the National Security Council, there were at least a hundred reports, from the C.I.A., the N.S.A., and other intelligence branches, but the F.B.I. never disseminated information.

The C.I.A. embraced the idea of the Wall with equal vigor. The agency frequently decided not to share intelligence with the F.B.I. on the ground that it would compromise “sensitive sources and methods.” For example, the C.I.A. collected other crucial information about Mihdhar that it did not provide to the F.B.I. Mihdhar, it turned out, was the son-in-law of Ahmed al-Hada, the Al Qaeda loyalist in Yemen whose phone number operated as the network’s switchboard. After arriving in New York on July 4th, Mihdhar flew to San Diego and rented an apartment. From there, he made eight calls to the Hada phone to talk to his wife, who was about to give birth. In the I-49 squad’s office, there was a link chart showing the connections between Hada’s phone and other phones around the world. Had a line been drawn from Hada’s Yemen home to Mihdhar’s San Diego apartment, Al Qaeda’s presence in America would have been glaringly obvious.

After September 11th, the C.I.A. claimed that it had divulged Mihdhar’s identity to the F.B.I. in a timely manner; indeed, both George Tenet, the agency’s director, and Cofer Black, the head of its counterterrorism division, testified to Congress that this was the case. Later, the 9/11 Commission concluded that the statements of both were false. The C.I.A. was unable to produce evidence proving that the information had been passed to the bureau.

The I-49 squad responded to the secrecy in aggressive and creative ways. When the C.I.A. refused to share intercepts of bin Laden’s satellite phone, the squad came up with a plan to build two antennae to capture the signal—one on Palau, in the Pacific, and another on Diego Garcia, in the Indian Ocean. The squad also constructed an ingenious satellite telephone booth in Kandahar, hoping to provide a convenient facility for jihadis wanting to call home. The agents could listen in on the calls, and they received videos of callers through a camera hidden in the booth. Millions of dollars and thousands of hours of labor were consumed in replicating information that other U.S. officials refused to share. According to Soufan, the I-49 agents were so used to being denied access to intelligence that they bought a CD containing the Pink Floyd song “Another Brick in the Wall.” He recalled, “Whenever we got the speech about ‘sensitive sources and methods,’ we’d just hold up the phone to the CD player and push Play.”

Just days before the June 11th meeting took place in the New York office, new threats in Yemen created a security crisis for the Americans. Yemeni authorities arrested eight men who, they said, were part of a plot to blow up the American Embassy, where Soufan and other investigators had taken refuge. Louis Freeh, the director of the F.B.I., acting on O’Neill’s recommendation, withdrew the team entirely.

By then, Soufan had a much clearer idea of the relationship between Khallad and the Cole conspirators. In July, 2001, he sent a third formal request to the C.I.A. asking for information about a possible Al Qaeda meeting in Malaysia, and about Khallad’s trip to Bangkok to meet with Quso and the Cole suicide bomber. Yet again, the agency did not respond.

On August 22nd, John O’Neill was packing boxes in his office. It was his last day at the F.B.I. He had decided to retire from the bureau after he learned of a damaging leak to the Times. The paper had reported that O’Neill’s briefcase, containing sensitive documents, was stolen while he was attending an F.B.I. conference in Florida. The briefcase was quickly recovered, and it was determined that none of the sensitive material had been touched, but it ruined his prospects at the bureau.