John O'Neill (1952-2001) became the chief of the Federal Bureau of Investigation (FBI) counterterrorism unit in 1995. Retiring from the Bureau in August 2001, he became chief of security for the World Trade Center, and died in the 9-11 Attack in New York. He was among the first in the United States intelligence community to recognize the threat of al-Qaeda, and pursued them intensely. By June 2001, however, he had reached a career dead end, and journalistic speculation that he warned of the 9-11 Attack does not reflect reality. While there were elements of information that might have been connected as a specific warning, he no longer had access to them when the final attack preparation was in progress.
He worked closely with Richard Clarke at the National Security Council, and also exchanged deputies with the Central Intelligence Agency. His relationship with Michael Scheuer at the CIA, however, was hostile.
O'Neill was a larger-than-life personality, challenging the law enforcement culture of the FBI and pushing toward an aggressive style of counterterrorism, and both giving and expecting personal loyalty.
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."
He would push the rules of the strict FBI. Even when his retirement was scheduled, he was investigated for misplacing a briefcase of classified documents, which he was authorized to have but was to safeguard. 
An apprenticeship for foreign terror?
O'Neill, in August 1994, was asked by Robert Bryant, assistant director of the FBI national security division, asked O'Neill if he would take on a special project, "fraught with a lot of internal, external, and political minefields." The project was violence against abortion providers, and was his first experience with religious fanaticism. One of his lovers, Valerie James, the daughter of a fundamentalist minister, said "At first he knew nothing about that, but he read everything there was about fundamentalism. He used to say, 'Fundamentalist anything, in the extreme, is wrong and dangerous." He told another agent, "As a Catholic boy from Atlantic City, I never knew what a third-trimester abortion was." 
In 1995, Richard Clarke discovered Ramzi Yousef, a suspect in the 1993 World Trade Center bombing, had been located in Pakistan, and called the FBI operations center, reaching O'Neill, who literally had just arrived chief of the F.B.I.'s counter-terrorism section, his suitcases not yet unpacked. O'Neill put together the team that apprehended Yousef and brought him back; while an Assistant U.S. Attorney and the Pakistani government were aware of the mission, it easily could be considered an extraordinary rendition; there was no formal international extradition hearing in Pakistan. 
As with the abortion clinic investigation, he immersed himself in study. "John made himself the terrorism expert, and then he started educating [FBI Director] Louis Freeh and his other bosses," according to a fellow agent. He differed with the prevailing view of much of the government, that Youssef's approach was not a grand but isolated crime, but the start of a pattern. The policy had been to investigate attacks, use diplomacy, and extradite them. Exploring broader conspiracies was not yet an idea, although this had failed in the investigation of the shooting of Meir Kahane, to which Youssef and colleagues were eventually linked. 
Another incident, not in the U.S., supported his view: the Aum Shinrikyo chemical weapons attack in the Tokyo subway on 3 March 1995. This made him more suspicious of a March 8 report on a relatively little-known individual named Osama bin Laden, who the Saudis wanted the government of Sudan, his sanctuary, to expel. O'Neill was the first to mention bin Laden to Bryant on March 8, then started discussing him with Clarke, saying that it was inconceivable to him that bin Laden's network did not reach into the United States. The FBI was not yet the lead agency in counterterrorism investigation — there was no central point — but the 1995 Oklahoma City bombing generated a Presidential directive assigning the subject to the FBI. 
1996 Khobar Towers bombing
He assembled the law enforcement investigation team for the 1996 Khobar Towers bombing, and later joined them in Saudi Arabia with FBI Director Louis Freeh. O'Neill became convinced the Saudis were obstructing the investigation, and, at first, Freh, who though there was progress, refused to speak to him. Eventually, however, O'Neill went back, but were "more close-mouthed than any police organization he had ever worked with."
USS Cole bombing
O'Neill was the field investigator for the 2000 bombing of the U.S. [destroyer]], USS Cole (DDG-67), in Yemen. It is generally agreed he had a personality conflict with the U.S. Ambassador to Yemen, Barbara Bodine.  Immediately after the news, O'Neill went to Barry Mawn, director of the New York FBI Office, and said "'It's Al Qaeda,' and I totally agreed with him. And he said, 'You got to get to the director, and we got to get this so the New York office responds initially.'" Headquarters debated if his potentially abrasive personality outweighed his investigative skill, but Freeh eventually decided to send him.
ABC News ran a miniseries on it in 2008. "According to the mythmakers, a battle ensued between a cop obsessed with tracking down Osama bin Laden and a bureaucrat more concerned with the feelings of the host government than the fate of Americans and the realities of terrorism....I am not here to either defend or attack O'Neill. He was a complex man. But what happened after Al Qaeda's attack on the U.S. destroyer Cole was a complex story."
Concerned over both threats to the investigators and lack of cooperation by Bodine and the Yemenis, he requested the team, now composed of the FBI and the Naval Criminal Investigation Service, to be withdrawn. Freeh agreed on 27 October 2000.
O'Neill formally ordered the FBI to leave Yemen on 16 June 2001. Osama bin Laden released a videotape a few days later, of a form that O'Neill considered an indicator of a major attack in the near term. By then, however, he had decided to retire.
Jack Cloonan took over the New York anti-terrorism squad. Maggie Gillespie, an FBI analyst at the Counterterrorism Center, had earlier asked that Khaled al-Mihdhar and Nawaf al-Hazmi, both of whom were 9-11 hijackers, on a watchlist. She passed this to Dina Corsi, another intelligence analyst at FBI headquarters, since Mindhar had reentered the United States. Corsi alerted Cloonan's squad, and Cloonan asked that he be able to use FBI criminal agents since there was an existing indictment against bin Laden; the criminal side of the New York office had far more resources. Corsi emailed back, "If al-Mindhar is located the interview must be intended by an intel agent. A criminal agent CANNOT be present at the interview...If at such time intformation is developed indicating the existence of a substantial federal crime, that information will be passed over the wall according to the proper procedures and turned over for follow-up investigation." 
A Salon.com critic also questions the ABC miniseries as taking liberties with reality, being overly critical of the Clinton Administration, suggesting Clarke and O'Neill had given specific warnings, yet ignoring the President's Daily Brief warning of 6 August 2001. While the television show suggested Condoleeza Rice said the President wanted to take action as a result of that warning, the 9/11 Commission indicates no action was taken. 
After he started in the World Trade Center security position, he did meet with a former New York Police Department colleague, Raymond Powers, on September 10. Powers recalls that O'Neill expected the Twin Towers to be targeted again, saying "It's going to happen, and it looks like something big is brewing."
- Murray Weiss (2003), The Man Who Warned America: the life and death of John O'Neill, the FBI's couterterror warrior, Harpercolllins, ISBN 0060508221, pp. 351-353}}
- Lawrence Wright (14 January 2002), "The counter-terrorist; John O'Neil was an F.B.I. agent with an obsession: the growing threat of Al Qaeda.", The New Yorker
- Kelli Arena (19 August 2001), "FBI probing top counter-terrorism agent", CNN
- Weiss, pp. 57-59
- Weiss, pp. 92-94
- Weiss, pp. 96-103
- Lawrence Wright (2006), The Looming Tower: Al-Qaeda and the Road to 9/11, Alfred A. Knopf, ISBN 037541486X, pp. 237-239
- "Transcript of "The Man Who Knew"", PBS
- "9/11 Miniseries Is Bunk: Former ambassador to Yemen says ABC traded fact for drama in portraying events after the 2000 bombing of the destroyer Cole.", Los Angeles Times, 8 September 2008
- Weiss, pp. 317-318
- Weiss, pp. 331-335
- Wright, pp. 352-354
- Joe Conason (8 September 2006), "The Sept. 11 that never was", Salon.com
- Weiss, p. 360