In the course of these investigations, he became one of the world's top experts on Osama Bin Laden and Al Qaeda, determined to hunt Bin Laden and his followers down and bring them to justice. Those who worked with him said he 'lived, breathed and ate terrorism.' A scrappy, stubborn Irishman with a quick temper, a fondness for the ladies, and a reputation for being brutally blunt on some occasions, and pushy on others, O'Neill was often frustrated by the button-down boundaries of the modern FBI. But he was one of the best sleuths the agency had ' as anyone who worked with him would be quick to acknowledge. U.S. attorney Mary Jo White says this of O'Neill: "John went at it comprehensively, yielding things from people in London or people in Yemen we never otherwise would have gotten." Another admirer, former FBI director Louis Freeh remembers O'Neill as ' the paramount, most knowledgeable agent we had in the FBI, probably in the government, with respect to counterintelligence matters."
In August 2001, FBI Deputy Director John O'Neill resigned from his post over George W. Bush's policy on terrorism and Osama bin Laden. Specifically, O'Neill's department was told to "back off" their bin Laden and Al Qaeda investigations while the Bush administration negotiated with the Taliban. O'Neill became the security chief of the World Trade Center - where he died during the events of 9/11.