An FBI special agent from 1977 to 2002, Cloonan started working Al Qaeda cases in the mid-1990s. In this interview, he explains why he believes the FBI's method of interrogation is successful. He describes how the FBI cultivated former Al Qaeda operatives Jamal al-Fadl and Ali Mohammed as cooperative sources in the years before 9/11. Cloonan also recounts the FBI's battle with the CIA over custody of Ibn al-Sheikh al-Libi, who ran an Al Qaeda training camp in Afghanistan and who was one of the highest-ranking Al Qaeda operatives captured in the first months of the war in Afghanistan. Cloonan says al-Libi was revealing information that could have been useful in the prosecutions of Richard Reid and Zacarias Moussaoui, before he was transferred to CIA custody, duct-taped, put in the back of a truck, and sent to Egypt for more aggressive interrogation. Cloonan also discusses the FBI's role at Guantanamo and why he believes little good intelligence came out of there. This is the edited transcript of an interview conducted on July 13, 2005.

When 9/11 happens, what was your history with Al Qaeda? ...

I had been seconded to a special team that had been established as a result of President Clinton signing a presidential finding, an intelligence finding, in early January of 1996. And in that finding, he basically declared war on bin Laden, and he directed all U.S. intelligence assets, including the FBI, to go after bin Laden, Ayman al-Zawahiri and the Al Qaeda network. So the follow from that was that we were directed -- that is, the Justice Department, through the attorney general to [former U.S. Attorney for the Southern District of New York] Mary Jo White ... -- to put together a prosecutable case against Osama bin Laden…

Mike Scheuer -- otherwise known as "Anonymous" ... -- put together this team. And we had people from the New York office of the FBI there, from our office in Washington. There was a fusion cell put together to look at information, so on and so forth. That's the background to it.

As a result of that, a person by the name of Jamal al-Fadl, who later earns the nickname of Junior, shops himself around at various U.S. embassies overseas with kind of a wild story about who he is, what he's doing. He even shops himself around to the Saudis, who spurn him altogether. It turns out that Jamal walks into the U.S. Embassy in Eritrea, and he has the good fortune to come across a regional security officer who's pretty well grounded and ... summons the chief of station from the agency. They do an assessment. They think this guy's probably for real [and] call us. And Pat Fitzgerald, who was the U.S. attorney, now in Chicago, flies over with Danny Coleman, my partner, and they do an initial assessment. And lo and behold, this guy is for real.

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.

So we, Pat Fitzgerald and others, convinced Jamal to come to the United States voluntarily. ... Our position was, with Jamal, was that he was going to be treated like any other defendant would be, so that when he's sitting in Eritrea, subsequently moves to Germany, then comes to the United States, he is paroled into the custody of the FBI through the authorization of the attorney general. And we make no agreements with him, no promises, except that he can come to the United States, he's going to be paroled in our custody, and we will talk to him. He agrees to do that.

So he voluntarily comes to the United States, and no one knows about it. We put him in a safe house, and we watch him and live with him, essentially, for three years, 24 hours a day, seven days a week. And what he begins to tell us is -- I hate to use the expression, but it literally did lift the veil, if you will, on what Al Qaeda was.

[He was] enormously entertaining, fun to be with. He did some despicable things, but over the course of time, he was literally seduced by our legal system and by the people that dealt with him, because his expression to us was, "I don't know why I'm talking to you" -- I'm sort of ad libbing here for a moment -- "because you are ... people that I was taught to hate. Yet I don't understand your system. But you're treating me with fairness. I have an attorney, and I can do all the things that any other defendant in your country can do." And we said yes.

Now, were there expectations that we had? He clearly knew that. He went from a man that was very reticent, nervous about talking to a man who saw it as his destiny to confront Sheikh bin Laden in a trial. That was his vision. He wanted to see bin Laden in an orange jumpsuit that said "Metropolitan Correction Center" on it. He talked about it with us, and he literally fantasized about it. And he went through the most incredible highs and lows that you can ever imagine, because we became his surrogate father, his marriage counselor, his financial adviser -- you name it.

And to this day there is a bond, whether we want to accept it or not, those of us that dealt with him, that is unmistakable. It is something that you can't imagine -- that you would sit across the table from somebody who, by the way, walked into a sealed courtroom in the 7th District [Court] of New York before the great jurist Judge Leonard Sand, who sits on top of the Embassy bombing trial, and pleads guilty to conspiracy to kill U.S. nationals abroad. The sentencing guidelines on that are from zero to life. Jamal al-Fadl, since 1996 to this present day, has not been sentenced. He is living in the Witness Protection Program. He has been moved seven, maybe as many as 14 times since he's been in the Witness Protection Program.

And he has been a valuable resource, because throughout all of this that's happened, he is a person that you could go to and [who could] tell us whether we were on the right track or not. He also led us to a number of other people. His debriefings, including how he was recruited, what it means to be a suicide bomber, how do you assess a target, led us to other people that we subsequently found in other parts of the world. ...

Ultimately, we ended up talking to bin Laden's first trainer, Ali Mohammed, Ali Abdul Saud Mohammed, who is currently in jail. He taught bin Laden. In one of the first training classes that Ali Mohammed conducted was Sheikh bin Laden; Ayman al-Zawahiri; Abd al-Rahim al-Nashiri, who's chief of military operations at the time; Saif al-Adel, who's still one of the 22 most wanted fugitives, and others. ... What he tells us and what he did would make the hair on the back of your head stand up. This is the type of stuff, again, that we dealt with in the usual setting that the bureau found themselves in, in ... a regular interview, because each one of these defendants, if you will, had legal representation.

And those lawyers played a very vital role in gaining their subjects' cooperation with the United States government. Each one of them was seduced by our legal system that many people poke fun at, thinks cumbersome. If you could listen to these guys, and they'll tell you -- I'm referring to Al Qaeda members -- "You mean to tell me that the United States government will give me the legal representation?" "Correct." "You mean to tell me that if I cooperate with you, that you will at least possibly protect me against retaliation?" "Yes." "You mean that you could unite me with my family?" "Yes."

In one instance, we smuggled over 20 members of a family out. We did everything that we could possibly do within the law to make this work. ...

9/11 happens, and fairly quickly it becomes apparent that there will be a battlefield, and people will start to be taken off that field and interrogated, debriefed; that information will be both necessary, both tactical and strategic. ... Where are you at that moment, and what do you think is going to happen, and what do you think should happen, in that immediate aftermath?

Well, on the morning of 9/11, I was on a secure line. I was in Sana, Yemen, talking to my office in New York when the person on the other end said, "Jack, I'm sorry, I can't speak to you because we think the Trade Center has been bombed." And the phone went dead. ...

I didn't know what to make of it at the time, but I was sick to my stomach. And of course, then we saw the second plane, and we're all sitting there just absolutely dumbfounded. We pretty much knew at that point what it was, and it took us a long time to get out of the embassy and all that other stuff. I flew back finally, and I went to the Trade Center, because [Special Agent] Lenny Hatton, who was a friend of mine, had been killed. And John O'Neill had been killed, who I worked for. So I had to see it. ...

We understood at that time that there was going to be a change, and it was really apparent to us, certainly, when the boots went on the ground in Afghanistan, because what the CWs, as we refer to them -- cooperative witnesses -- had told us was that bin Laden really feasted on the fact that the United States would never, ever put boots on the ground in Afghanistan. It was his sanctuary; it was the caliphate of greater Afghanistan that he referred to it as, and that we did not have the collective will to do that. He prided himself on that. He believed in it, and so did everybody else.

We actually brought the chief HUMINT [human intelligence] officer from Delta Force -- I did -- from Fort Bragg, [N.C.], brought him up to the Metropolitan Correction Center prior to them going into Afghanistan. ... You have to see this scene in the MCC. You've got a young, full colonel from Delta who's got 2 percent body fat, and his neck comes out of his shoulders someplace. And I'm walking him into the MCC, and we're going up to see Ali Mohammed, who's an ops guy; he's a special ops guy. ...

They talked about what we're going to do on the ground for the Delta operators. The first word out of Ali's mouth: "You own the night. Anything that moves at night, you shoot; you kill." And they planned. Ali took them through all the training camps he had been in in Afghanistan, and he told them what they should be looking for. He said: "If you find a camp, and you find free weights in the camp, that's an Al Qaeda camp. You see jungle; you see" -- whatever those things are, parallel bars or something -- "that's an Al Qaeda camp. The Taliban, they don't care about that stuff; Al Qaeda does, though."

And it's interesting, because about a day later, we saw something on television -- the video you've seen many times, when people are on the parallel bars or whatever they are -- and I thought that was hysterical. But it was relevant in that it took older information but still made it relevant. ...

So that's kind of the context in which all of this took place. And then we knew that the critics were going to come out, that maybe the way we were doing things was probably not to different liking. This was a terrible event; we had to respond. And we did, but it was pretty evident once our guys got to Afghanistan that the dynamic had changed. It was a military operation; we were certainly poor cousins. The agency was essentially operating independently, certainly in [Bagram Air Base, Afghanistan]. ...

What do you mean, independently?

They've got their own air force, and they've got their own chain of command.

And they're what, cherry-picking the high-visibility guys, right?

Yeah, they've got HVT targets, high-value targets, and then the bureau is following the chain of command. We're really -- when I say poor cousins, I don't necessarily mean that we weren't effective, but it became apparent that what had to be created was to take whatever expertise we had developed vis-à-vis Al Qaeda primarily, give it to the people that were doing the initial debriefs, because who was doing the initial debriefs? These were by and large National Guardsmen who were in an intelligence unit. And where were they from? They were cops.

So you've got FBI agents, a couple of New York City detectives on the ground in Bagram, creating a fusion cell that's very effective. And I'm not saying that the agency wasn't effective. I have a great deal of admiration for what they do, because some of them find themselves in the god-awfulest, worst situations you can imagine. But for us and our culture is that we approach everybody humanely; that we are officers of the court. There are repercussions that come our way if we do something wrong. We know that. And nobody in my position ever wanted to run the risk of running afoul of the law or have to explain in a courtroom why you did such-and-such. ...

But the dynamic in change, we knew that the agency was operating independently in Bagram, and we were going to do our level best to help the military with the initial triage. ... It's a new day, and the gloves are off. And what we had been doing was considered passé, so we just had to do what we can traditionally do, hope for the best, try to be as effective as we can.

What does "the gloves off" mean?

To me it's very obvious. Look, the last thing that anybody wanted was to have U.S. law enforcement involved in dealing with these guys, because that sets off a whole train of events, doesn't it? ... Did I like the fact that somebody was taken from our custody and rendered to another country? No.

This is Ibn al-Sheikh al-Libi you're talking about, right? So tell me the al-Libi story from when you enter it, from when you get out.

I'm not on the ground in Bagram, I'm talking to the people who are there.

You're in the New York office.

I'm in New York, I'm talking to the two people. And look, what we're getting out of this is, al-Libi is identified as a pretty good target, because he's an Emir, a leader of a training camp. I don't recall which training camp he might have been the leader of, but my memory's pretty good on a couple of key points, and one of them was that he was giving information on Zacarias Moussaoui and Richard Reid. Now, the Richard Reid end of the thing was one thing, because he was in custody and everything, but this case on Zacarias Moussaoui was not a slam dunk, as most people thought it was.

So my instructions to a young agent and to a veteran New York City detective was as follows -- and I'm telling you almost verbatim what I told them in one critical conversation, because they were complaining to me about all the stuff that was going on by the agency. And I'm not saying the agency's doing anything wrong -- they were just complaining because they're in there pitching, too; they want to win; they want to hit a home run. And so I said: "Look, guys, I want you to conduct yourselves just the way you would if that person was sitting right here in New York City. ... Listen, please. I want you to give him his advice of rights. I don't want you to promise him anything. I want you to provide the translation. I want you to do it. You've got all the documents in Arabic, blah, blah, blah." ...

We were overruled. We were getting 302s [formal written statements] that were going from the general in charge of the 10th Mountain Division or the Special Forces. [Whoever] was in charge of bargains at the time was getting a look at this. So was the military, and so was the director, our director, because this is a critical thing, to the point where the director argues for the bureau to get Ibn al-Sheikh al-Libi; that we want him in our custody; that this is what we intend to do. The director fought long and hard, but he was overruled, and the agency took him.

Fought with who?

He made his representation to the Department of Justice, ultimately from the attorney general to the White House. Now, I was nowhere. [It] was way above my pay grade. But look, what happens is a decision is made that the last thing we want to do is get involved in this legal process again, because we really don't. That's not what we want. And the agency had been given the mandate, and so they took him. They duct-taped him. They denied putting him in a box in the back of a truck. My guys that were there saw what they did.

What do you mean? They just kind of show up and knock on the door and say, "He's ours"?

Well, they had seen him; they had talked to him; they said he was alive. I know the agency officer that was doing it. I was his supervisor in there. He was a language specialist in the FBI some years ago. I was his supervisor. I know him, and I know who the chief of station was.

Look, who can make this happen? The director of Central Intelligence, or on orders to the White House, it's a rendition. This is not a program that's new. It's been going on in earnest since 1995 at least. So our guys are there. They're there the day he gets taken. ... They don't only see it; they take pictures. And so when Ibn al-Sheikh al-Libi goes to go to be taken, they're there. ...

But look, they knew where the guy was going: He's going to Egypt. And so you tell the guy: "Listen, you know where you're going. Before you get there, I'm going to do something to your mother." So it's amateur night; it's not stuff we do. We didn't feel good about it; they didn't feel good about it; they lost. So he goes off to Egypt.

I'm willing to believe that when some of these people are rendered that there's no doubt in my mind that they got information. There's no doubt in my mind. It just meant that for us, we're trying to build a case against a guy that's the only person that's been arrested in the attacks on 9/11. Do you think I want to make sure that I can probably put together some evidence that's untainted, that will stand up to scrutiny in court, that will be transparent, that 12 citizens or whatever will sit there and look at this -- and that not only will they look at it, but so will the world? And there's going to be a living document that can be reviewed for years to come as to what the United States government did. And to me, that speaks volumes. ...

What happened to al-Libi?

He went back. He went to Egypt, I was told. They claimed that he wasn't tortured, and he came back, and he's back in U.S. custody. He was considered a high-value target -- HVT, to use the military expression. And he went over and was questioned by EGIS [Egyptian General Intelligence Service], and let me [explain], if I can just go on for something, why I'm concerned about the Egyptian end of things. When we were dealing with Ali Mohammed, he would talk to us about Egyptian services, and how the Muslim [Brotherhood] had penetrated Egyptian services.

And they knew that the United States government would periodically go into a certain prison outside of Cairo -- I don't remember the exact name of it. He had a name for it, called the "Scorpion Prison." That's what he called it because it was where the political prisoners went. Somehow the United States government would participate in the questioning -- not actively, but I can tell you from personal experience that we did. But we never saw anybody and nor would we ever condone anybody being brutalized. But we certainly had information that I think is extremely credible, aside from looking at a body, that things are done pretty aggressively over there. ...

When guys are starting to be sent to Guantanamo, what's the FBI's role there? What is happening? What is your role? What do you prepare?

Well, the FBI's role again is a secondary role in that obviously it's a military installation, a military-run operation. So we get to the subjects after they have been spoken to by the military, and as you probably know, as a result of the ACLU FOIA [Freedom of Information Act] request, there's been some concern. And it started very early on.

As I said to you, we go back to our basic protocol, how we approach subjects. ... The bureau lives and dies by paper. We don't have a great computer system, as you know, but we have a lot of paper. ... And people will document -- if somebody comes into the room and they're going to be interviewed, they will take a look at them physically, and they'll make notes about what they see. One of the things that people should understand is that the bureau doesn't editorialize when it takes a statement from somebody. In other words, they don't give you personal opinions [as] to whether or not we think this person is providing false information or not. We just record what it is, and it's a document that stands on its own.

So I think when the bureau finds itself in a position where they realize from talking to one inmate after another that some things might be going on that are a little bit shady, they're going to make it a matter of record. And I think that's clearly what happened in this instance. ...

I'm thinking about the allegations about Korans and all that other stuff being misused and disabused, whatever. So this was a clash that was inevitable. The military culture and its intelligence needs don't necessarily mesh with what the bureau wants. Their way of going about things is not consistent with the way we do things. ...

[Describe the interrogation methods in that first year at Guantanamo.]

Well, I think you had a lot of inexperienced people who didn't have a knowledge base. They were not subject experts by any means. So they get what they got at their indoctrination at Fort Huachuca, or some other place, and they go in and they try to use it to the subject. And it was ad hoc; it was sort of making it up on the go, and it wasn't very effective. [Everything] that I was told was that there was nothing coming out of there of any value, nothing. Now, that could obviously have changed, and of course it depends on what you mean by what's value, what's good intelligence, what's actionable. But anybody that I knew that went there thought it was a complete waste of time. They got some good sun, they tried to do some bone fishing or something, and it was a nuisance. ...

[What happens when Gen. (Geoffrey D.) Miller takes charge of Guantanamo?]

Well, again, I don't presume to know. What I've heard is simply what I've tried to tell you, and that is that the people that I knew that were there and that have talked to me said it wasn't effective.

Remember, there's an element to all this, too, that there's an intelligence operation that's going on down there. This is not just bringing these guys into a room and sweating them and trying to get some information out of them. There's another reason. Some of those guys that are down there obviously have cooperated, and they're finks; they're informants.

So to the extent that you're going to find out ... a lot of critical stuff about what Al Qaeda is doing, the chances of that happening are minimal. They're almost nonexistent, because if you understood how Al Qaeda operated, its cell structure, how many people were involved in it, you'd know that most of these people were just fodder, because they're not the brains. The people that go into Al Qaeda in a lot of instances are not what you think. Thirty-five to 40 percent of them have advanced degrees. This is a middle-class phenomenon. This is not what's down in Gitmo.

The secretary of defense [Donald Rumsfeld] said many times that "This is the worst of the worst."

Listen, I don't doubt for a moment that these are bad guys and that they, given the opportunity, would shoot or kill you and I; that they were out in the battlefield. I don't discount that. I don't really know, but I assume that that's right. But are those the people that we ought to be looking at as going to do damage in the United States? No. ...

This question that haunts everybody now -- that is, who are the detainees, and how did they get there? You read Time magazine about Mohammed al-Qahtani, and you read about what was done to him and how they accidentally discovered him or whatever it was, all that stuff. What's your read on him and that story and the way that it's told?

Well, in that particular story and some of the others, you've got kind of a combination of things. You've got sort of the efficacy of the watch list, you have the information from liaison services, and you have the whole issue of rendition. So if you're wrong on any of those fronts, there's a price to be paid. So that's what I think in a situation like [his] and some of the others, where we have been wrong. I mean, do you know how many people in the watch list have been named Ahmed al-Masri, Ahmed the Egyptian? There are hundreds.

The person who put together the bombs for the attacks on the U.S. Embassy in Nairobi and Dar-es-Salaam was named Ahmed al-Masri, and I can't tell you how many Ahmed al-Masris there are in Al Qaeda or the Egyptian Islamic Jihad. So we just don't get it right in some instances, so I would hope that we don't engage in situations, in cases like that again, because when they get repatriated, what do we say to everybody? ...

What do you make of this? Once Gen. Miller gets [to Guantanamo], supposedly things toughen up. Supposedly medical records are shared. Supposedly there's the Behavioral Science Consultation Teams (BSCTs). What's your take on all of that?

Well, that concept of using the behavioral sciences and specialists to assess and interview a victim is certainly not new. We used it effectively all the time, and with very good results. I'll give you a classic case in point: [American "dirty bomb" suspect] Jose Padilla. He's down in the Navy brig. Agents go down from New York; they're going to talk to him. Our behavioral science people are down there, and they do an assessment and listen to a little bit of it. And of course we're walled off; we're not allowed to talk to him. Behavioral science said, "You know what he needs?" They said, "He needs a father figure."

So they look around the squad: Who's the oldest guy on the squad? So I'm the father. I'm going to go in and hear Jose Padilla's confession. But be that as it may, as simple as it sounds, there is a lot of things that you can do with that. And it's the same stuff that you see on Law & Order. It's not that complicated. But there is a little bit of that.

Where the thing goes south for me is that when you have people who are either psychiatrists -- or psychologists, rather -- who get into this gray world of what can you inflict upon somebody that might elicit information. That, to me, is where you cross the line. Laying hands on somebody or engaging in sleep deprivation, other sensory deprivation-type things, is borderline to me.

But clearly you've made the decision that this is never going to go into a court of law. And maybe even under a military tribunal, you'd have some problems, because the conscience of the court would be shocked. But what has happened is that they've taken this, and they've put it into a purely military context. ... So we've taken it from the usual legal process that we are accustomed [to] under our laws, and we've put it into that framework, and that gives you much more flexibility. And it clearly was done by design, because we have declared a war, have we not? And that's the context in which all of that takes place.

Now, how effective are these techniques? If you listen, if you go back and talk to the Soviets, who are really good at this stuff, and you talk to some of the Vietnam detainees, captives for a long, long time, they will tell you, of course you give up information.

The question is, what do you give up, the quality of it, and can you spin a tale? And you can. In Al Qaeda's training manual, there's a part on interrogation. And it says that any brother subjected to strong physical torture is only obligated to keep to the truth for 72 hours, because nobody can withstand physical torture after that, generally. So they took no revenge against you for being an apostate, for collaborating with the enemy. So I don't think you had to inflict a lot of pain on somebody to get information.

I think what they found themselves in was a conundrum, and it was timing. They had to get this right away. That's what I think led them to some of these more robust interrogation techniques. Generally speaking, it doesn't work. You will get some information, though. Listen, if somebody's going to sleep-deprive me, or if somebody's going to beat me in my midsection or suffocate me or make me do whatever, I think it would take 10 minutes, because I know that I can spin a pretty good story and probably give up some information that they would consider vital. But in point of fact, once I leave the group, everything that I have, everything that I know is obsolete. It's only got a shelf life for a very short period of time, and I go back to my prior statement: Consider the consequences. ...

Do you believe that it's as bad as we hear or even have read in the FBI e-mails and memos? How bad was it?

I think that any agent who walked into a room and saw a subject as has been described -- crawled up in the fetal position, either deprived of water or subjected to unusually warm temperatures, pulling his hair out, people on hunger strikes, and so on -- understands that that person is no good to you from an intelligence perspective. They've collapsed; they're not coherent. So what good is it? What you want to do is you want to sit across the table from them -- "Would you like some tea? How about some figs? How's the wife? How's this? How's this?" Sit there and talk, because people have a natural yearning to talk. They're proud of what they do.

So why did it happen? Why were guys laying on the floor with their hair pulled out?

I think the chain of command -- clearly the orders were a little bit different. We were operating, again, in this context, as I described earlier, [of] what's permissible. If you can tell me what the pain associated with organ failure is, I'll feel that I've been really enlightened, because that's what we know having been talked about in the so-called torture memo. I don't know what we thought we were going to get, what we were accomplishing. Water boarding, sleep deprivation, probably some drugs, probably creating a parallel universe for some of these guys -- I'm sure that all happened. In worst cases, we know that people have been beaten, and the agency's got I think three murder investigations on the way, if not more. That's not good.

Is this making it up as they go, ad hoc, amateur night?

I think you had very young kids, by and large, maybe the first time they've confronted a subject like this, very little life experience, told to go in there and get a job done, have pressure on them. They've gotten some advice, so-called professional advice, and then it went downhill. It probably wasn't that effective. So I don't know who was overseeing it, I don't know what the orders of the day were, but clearly they at least initially weren't very well defined, and probably made some very serious mistakes -- stiffened the resolve, got a lot of bad information, probably wasted a lot of time. ...