O’Neill oversaw many sensitive operations during his time in New York, including deterring suspected plots ahead of the 2000 ball drop in Times Square. He was active in the New York Joint Terrorism Task Force and was in attendance when the task force marked its 20th anniversary atop the North Tower at Windows on the World in September 2000.
But after being passed over for promotions, and amid internal tensions at the bureau, O’Neill retired from the FBI on August 22, 2001. The next day he started a new job—chief of security at the World Trade Center. He was recruited to the role by New York–based security firm Kroll Associates, which had advised that security at the towers be revamped after the 1993 truck bombing.
In late August, just days before the attacks, O’Neill spoke with a friend, ABC News producer Chris Isham, about his new World Trade Center security job and the threats posed by terrorists to New York. Isham remembered jokingly telling O’Neill that “at least they’re not going to bomb it again,” to which O’Neill replied: “They’ll probably try to finish the job.”
Just two weeks into his new job, O’Neill was in his office on the 34th floor of the South Tower when a plane struck the North Tower.