From 1996 to 2002, Cloonan was the senior case agent assigned to the "Bin Laden Squad" in the New York Office of the FBI. The Bin Laden Squad was charged with the responsibility of building a prosecutable case against Usama Bin Laden, Ayman Al-Zawahiri and other high-ranking members of al Qaeda. In that role, Cloonan traveled globally finding members of al Qaeda, gaining their cooperation to assist in the prosecution of those who carried out the deadly attacks on the U.S. Embassies in Nairobi, Kenya and Dar es Salaam, Tanzania. As a result of these activities, Cloonan gained insight into how al Qaeda worked from those "al Qaeda insiders" who agreed to cooperate with the U. S. voluntarily. Cloonan is a consultant on terrorism for ABC News and has participated in many panel discussions held on the efficacy of coercive interrogation techniques on suspected terrorists.