NARRATOR: To protect the hundreds of investigators on the ground, O’Neill and American military commanders wanted to show the Yemenis a forceful presence — guns ready, perimeters established. But much to O’Neill’s surprise, that approach quickly angered the American ambassador, Barbara Bodine, who felt his actions were harming U.S.-Yemeni government relations. RICHARD CLARKE, NSC Chief of Counterterrorism ’92-’01: You had an ambassador who wanted to be fully in control of everything that every American official did in the country and resented the fact that suddenly there were hundreds of FBI personnel in the country and only a handful of State Department personnel. She wanted good relations with Yemen as the number-one priority. John O’Neill wanted to stop terrorism as the number-one priority. And the two conflicted. FRAN TOWNSEND, Deputy U.S. Attorney general ’95-’01: This results in meetings between the attorney general and State, FBI, C.I.A. and Justice. But Ambassador Pickering is at it, the undersecretary, and the attorney general. Things are getting raised to that kind of a level, this has become such a bone of contention between them. RICHARD CLARKE: Almost all of us who were following the details in Washington, whether we were in the Justice Department, the FBI, the White House, the State Department, the Defense Department — almost all of us thought that John O’Neill was doing the right thing. NARRATOR: But not the higher-ups at the FBI. BARRY MAWN, Director FBI NYC ’00-’02: There may have been people at FBI headquarters that were going, “See? I told you so.” You know, “John does upset people and get them upset. And maybe he wasn’t the right guy.” But that’s — I mean, that’s all childish gossip and rumoring, as far as I’m concerned. NARRATOR: But on the ground in Yemen, the law enforcement agents saw a very different John O’Neill. MICHAEL DORSEY: I think he developed a real sense of closeness with the senior Yemeni officials. They referred to him in Arabic as “Alach [sp?],” which is “the brother,” and oftentimes referred to him as “the commander” or “your commander.” They had a real sense of appreciation for his seniority in the U.S. government and for what he represented. And I knew that they came to trust John. NARRATOR: For six years at the center of the FBI’s counterterrorism effort, O’Neill and his team had built the evidence on the mounting bin Laden threat: failed plots to kill hundreds of Americans in Jordan, Ressam’s explosives headed to LAX, an aborted Al Qaeda plot to blow up another American warship, the USS The Sullivans, and now the Cole. The Yemenis finally agreed to let the FBI join in the interrogation of one of their most prominent suspects, Fahad al Quso. O’Neill and his agents believed al Quso knew about bin Laden’s desire to videotape the destruction of the Cole, and possibly a whole lot more. O’Neill worked his newly developed Yemeni police officials and old allies in the CIA. NARRATOR: He had come to believe that some Yemeni officials were not being forthcoming about information from al Quso and other suspects. It was the Khobar Towers investigation all over again. (emphasis mine) But the weeks were taking their toll. O’Neill needed a break. He’d get back to al Quso after he returned from New York at the first of the year. VALERIE JAMES (O’Neill’s wife) : I have to tell you, when John came home — he got home, I think it was two days before Thanksgiving because he kept telling me he was going to try to be home for Thanksgiving. He — John had dropped 20, 25 pounds. NARRATOR: In New York, he plotted his return to Yemen. He had taken a Yemeni police delegation on a tour of Elaine’s and other hotspots. He was working them, trying to get unfettered access to al Quso and what he knew. But then he was told he wouldn’t be allowed to return to Yemen. Ambassador Bodine denied his visa. CHRIS ISHAM, ABC News: I mean, John was not rational on the topic of Ambassador Barbara Bodine. He was — I mean, “livid” would be putting it mildly. I mean, one can’t forget that John was — he very American, but he was also very Irish. INTERVIEWER: And that means? CHRIS ISHAM: That means when he got hot, he got hot. And he was hot. There’s no question about it. I think he felt that she was on the wrong side. NARRATOR: Ambassador Bodine would not grant FRONTLINE’s request for an interview. She was quoted in The New Yorker magazine. “The idea that John or his people or the FBI 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 10 months.” For weeks, the ambassador had been making the case against O’Neill, even lobbying Louis Freeh. Finally, her accusations had their intended effect. Headquarters supported her decision not to let O’Neill back into Yemen. BARRY MAWN: John was upset. She was bad-mouthing him. She had caused a stir at headquarters. I actually think John was more disappointed that our headquarters didn’t back us, as far as sending him back and taking a stronger stand with the State Department. Eventually, our headquarters said, “Well, let’s try and work around not having John go back.” And so that’s what I had to do. NARRATOR: So O’Neill would not be in Yemen. The investigation slowed to a crawl. MICHAEL SHEEHAN, Chief Counterterrorism, State Dept. ’98-’01: I watched with dismay as the issue of the USS Cole completely disappeared from the U.S. scene, completely — again, in a new administration. It was just not on their agenda. Clearly, it was not on the agenda of the Congress, the media or anyone else. Again, it went into oblivion. NARRATOR: By spring, intelligence about Al Qaeda forces in Yemen convinced O’Neill they were about to target his agents. O’Neill pleaded with Barry Mawn to pull them out, and Mawn agreed. O’Neill’s investigation in Yemen was effectively over. CHRIS ISHAM: We don’t know what would have happened if John could have done his job in Yemen and had really had the full back-up to go and to really push in Yemen and what kind of networks he could have exposed. But you know, we do know there were Yemenis involved in the attacks of September 11th. So is it possible that if he had been able to really open up that network and really expose that network, that he could have in some way deterred the tragedy of September 11th? I don’t think we know, but it’s sad because we won’t know the answer to that. But I think there is a fighting — he would have had had a fighting chance if he’d been able to do his job.