Zebley was an FBI special agent working for the bureau's Counterterrorism Division for seven years. As an FBI agent, Zebley investigated al-Qaeda's bombings of U.S. embassies in east Africa in 1998, and after the September 11 attacks was assigned to the FBI's PENTTBOM team, which investigated the terrorists responsible for the attacks. Zebley was on the arrest team that captured one of the embassy bombers, Khalfan Khamis Mohamed, in October 1999 in Cape Town, South Africa. Zebley was one of the investigators who built the case against Zacarias Moussaoui, who was ultimately sentenced to life imprisonment. Zebley was a summary witness in Moussaoui's penalty proceeding, testifying to the ways in which Moussaoui's confession in 2005 could have helped track down the September 11 hijacks in the month before the attacks had he provided truthful information when first arrested.