He was a special agent for the Bureau’s Osama bin Laden unit from 1996 to 2002, which was part of an interagency team assembled by Michael Scheuer. It had been created when Bill Clinton signed a Presidential Finding, in January 1996, directing the United States intelligence community to pursue bin Laden, Ayman al-Zawahiri and the Al Qaeda network. The FBI, as part of the U.S. Department of Justice, also intended to put together a case that could be prosecuted, under [former U.S. Attorney for the Southern District of New York] Mary Jo White.
The first significant interrogation results came from Jamal al-Fadl in the spring of 1996, is the first window we have into Al Qaeda. He's a member; he raised his right hand and swore ... his allegiance to Sheikh bin Laden, recruited in Brooklyn. And he's got blood on his hands. He has blood on his hands, because he tells us about things that he has done for Al Qaeda and that he is essentially on the run, because he's taken some unauthorized commissions from Sheikh bin Laden. And there's nothing like a person who's on the run and is frightened about what might happen.
He was a lead interrogator, using noncoercive methods, for one of the major sources on the 1998 bombings of U.S. Embassies in Africa, L'Houssaine Kherchtou.  Before Jose Padilla was transferred to military custody, he was the primary interrogator.
Cloonan said there was a major change after the 9/11 Attacks, as the process as being taken out of the judicial system "...by design, because we have declared a war, have we not? "  The FBI has been criticized as too focused on the law enforcement process to work effectively on counterterrorism, since agents have been conditioned to use interrogation techniques that can be described in court without causing evidence to be rejected. Cloonan said this could even apply to a military tribunal.
To Cloonan, "breaking" a terrorist doesn't mean torture, but interrogating "the right way: by being intelligent and humane."a conference, by interrogation experts from intelligence and law enforcement, sponsored by Human Rights First.
He worked with several suspects in the embassy bombings. While Kherchtou was basically cooperative, Ali Mohammed was implicated, and had expected to be tortured. "Instead, we assured him that we wouldn’t harm him, and we offered to protect his family. Within weeks, we had opened a gold mine of information about al-Qaeda’s operations. Ali Mohamed wasn’t unique. We gave our word to every detainee that no harm would come to him or his family. This invariably stunned them, and they would feel more obligated to cooperate. Also, because all information led to more information, detainees were astonished to find out how much we already knew about them—their networks."
- The Torture Question: Interview, Jack Cloonan, Public Broadcasting Service
- Jason Vest (June 19, 2005), "Pray and Tell: Jack Cloonan has done his share of terrorism interrogations. Instead of torture, he recommends prayer rugs and figs. Yes, figs.", The American Prospect
- Top Interrogators Declare Torture Ineffective in Intelligence Gathering, Human Rights First, June 24, 2008
- "No Torture, No Exceptions", Washington Monthly, January/February/March, 2008