In 1995, O'Neill began to intensely study the roots of the 1993 World Trade Center bombing after he assisted in the capture of Ramzi Yousef, who was the leader of that plot.

[2]: 199  While there, he established the Fugitive Task Force in an effort to promote inter-agency cooperation and enhance ties between the FBI and local law enforcement.

[1] Intrigued by the case, O'Neill continued to study the 1993 World Trade Center bombing that Yousef had masterminded and other information about Islamic militants.

He was directly involved in the investigation into the June 1996 bombing of the Khobar Towers in Saudi Arabia, which took place during a retreat O'Neill had organized in Quantico for FBI and CIA counter-terrorism agents.

[3] In 1996 and 1997, O'Neill continued to warn of growing threats of terrorism, saying that modern groups are not supported by governments and that there are terrorist cells operating within the United States.

[3] In August 1998, two United States embassies were bombed in quick succession in simultaneous attacks in Nairobi, Kenya, and Dar es Salaam, Tanzania.

O'Neill hoped to be involved in the investigation because he had gained a tremendous knowledge of Osama bin Laden's al-Qaeda terrorist network.

[3] He was a Catholic, married with two children, but separated from his wife; his family continued to live in Atlantic City, and he supported them financially and paid the mortgage on their house.

The two had widely divergent views on how to handle searches of Yemeni property, and interviews with citizens and government officials, and they only grew further apart as time progressed.

[3] In early 2001, Richard A. Clarke, the National Coordinator for Security, Infrastructure Protection, and Counter-terrorism wanted to move to another position; he insisted O'Neill was the best person to replace him.

When O'Neill heard of upcoming leaks to The New York Times about the May 2000 incident in which his briefcase had been stolen, he decided to retire from the bureau and take a higher-paying job in the private sector, as chief of security at the World Trade Center.

The FBI investigation was reported to have concluded that the briefcase had been snatched by local thieves involved in a series of hotel burglaries and that none of the documents inside had been removed or even touched.

[18] O'Neill's counter-terrorism work at the FBI as well as insights into his character and private life have been extensively detailed in books and documentaries about the lead-up to the September 11 attacks, including the following: