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ROBERT SIEGEL, host:

From NPR News, this is ALL THINGS CONSIDERED. I'm Robert Siegel.

MICHELE NORRIS, host:

And I'm Michele Norris.

James Yee is the former Army chaplain at Guantanamo Bay. He was wrongfully accused of aiding al-Qaeda; now he's published a memoir. The book provides a rare look inside the detention camp. Hundreds of what the Pentagon calls suspected terrorists are locked away indefinitely, most without charges filed against them. Captain Yee, a West Point graduate, advised Army commanders at Guantanamo pertaining to Islam, and he was a spiritual adviser and confidant to the detainees.

Then in 2003, Yee was arrested under suspicion of espionage and helping the enemy. He spent 76 days in solitary confinement in conditions not unlike what he saw at Guantanamo. The allegations were later dropped. Yee talked with us today, telling us his side of the story. For one thing, he says anti-Muslim sentiments ran high in the Army at Guantanamo, and religion often was used to control or manipulate prisoners.

Captain JAMES YEE (Former Army Chaplain at Guantanamo Bay): I saw the Korans with the bindings literally torn and ripped from the guards who had inspected them. Initially when I got down there, guards were allowed to search all the cells as you would expect, and that included the actual holy texts itself. They were treated like they were any other object, and this is why it resulted in torn and ripped bindings, ripped pages. And this all happened in front of the prisoners, who took offense from that.

And I was very much a part of trying to find solutions because when the prisoners got upset over the disrespect of the Koran, it led to protests, it led to riots within the cell blocks. And when that happened, then the prisoners would have to get punished. So these tensions led to forceful extractions of the prisoners. It was a violent process to get that prisoner--transfer that prisoner to another cell, and that happened over and over and over again.

NORRIS: You weren't present during the interrogations, but you would talk to the detainees. And from what I understand in reading your book that they'd actually confide to you about some of the things that happened in that process. What would they tell you?

Capt. YEE: Well, they would talk about some of the things that happened to them in the interrogations, because they trusted me that I would address these to the command to try and stop some of these things that were going on. Some of those complaints revolved around abuse of the Koran; some of them revolved around abuse of the detainees themselves. In one particular incident, prisoners complained that a Koran was actually kicked on the floor. And interestingly enough, a translator also did come to me with that concern to inform me that he was disturbed that an interrogator had done this. And this caused riots and led to disturbances within the camp to the extent that I believe even the intelligence section of the operation felt that that incident had disrupted the entire interrogation process.

NORRIS: Newsweek reported that the Koran was actually flushed down the toilet and that it was pasted with offensive material. Now you talked about guards searching the Koran and tearing the binding and sometimes dropping them on the ground. Did you have any knowledge of the Koran actually being flushed down the toilet?

Capt. YEE: My knowledge of that incident, you know, I can't speak directly on. One particular conversation I had with a prisoner did refer to his time at Camp X-Ray, which was prior to Camp Delta and prior to my deployment, in which they had, at the time, in this makeshift prison, buckets which the prisoners had to use for a toilet. And what--prisoners had told me that the Korans had ended up in the toilet buckets back in Camp X-Ray. But again, this was before my arrival.

NORRIS: The nation is repeatedly reminded by the White House that the US is at war against terrorism and terrorists. And some would argue that it's legitimate to use every tool the US has, within reason, to combat terrorism. What would you say to that?

Capt. YEE: I think fighting terrorism is important, and I think national security is a priority. We do need to be safe and secure within our own country. But we also have to look at the freedoms that this country stands for and why we uphold certain values, like religious freedom and diversity. When you take away those freedoms, you are actually underminding the strength of what makes this nation great.

NORRIS: So when detainees had concerns, complaints, when there were allegations of abuse, you brought those to your command. Were you concerned at all that you were perhaps being used by those who were housed at Guantanamo?

Capt. YEE: Initially, before I even went down there, I had no idea what my role was going to be in terms of specifics. However, I was very unsure on how I was going to be used, or if I was really even going to be seriously used in the operation, but rather just as a showpiece to be down there so that the command or the administration can say, `Yes, we do have a military chaplain down there; therefore, we are being very sensitive to the religious needs of the prisoners.'

NORRIS: What about the prisoners? Were you concerned that at some point you were being used or manipulated by the detainees?

Capt. YEE: One of the things that I did make clear to the detainees was I would listen to their concerns and address them to the command, and that it wasn't within my capacity as the chaplain to make those command decisions. There's a balance that has to be made there, and I was someone who was effectively able to balance both the unique religious paradigm of the operation as well as the security concerns that is necessary, especially in detention operations, anywhere.

NORRIS: Now there are some who might dismiss your book as payback toward the Pentagon after charges were filed against you and later dismissed, because you only wrote about these things after you were ill-treated. Is there an element of payback here?

Capt. YEE: So you're suggesting some people may say that I wrote this book to--as payback?

NORRIS: Well, that you may have been motivated by anger or hurt.

Capt. YEE: What I've really been motivated by in writing this book was by writing this book, I can help others and ensure that, you know, what happened to me doesn't happen to anyone else. What happened to me--of course, it was clearly a gross miscarriage of justice and, you know, I suffered through a very difficult, trying ordeal. But by writing this book, my motivation is that if this helps prevent what happened to me from happening to anyone else, then I've made a huge contribution. It's a lesson about why the values of diversity and religious freedom and justice are very important to everyone.

NORRIS: You have an honorable discharge, a commendation medal. You also wanted an apology. Did you ever get it?

Capt. YEE: I have not gotten an apology, and I hope that one day I'll get that apology. So I bring up this note that, yes, after my ordeal, the Department of Defense inspector general did agree to investigate my case as to how it was that me, Chaplain James Yee, Captain James Yee, landed in prison for 76 days and why did it all happen. Was it my faith that was scrutinized or part of the reason why I was thrown in prison? Did the military follow the proper procedures or treat me properly as an officer? That investigation is ongoing. Perhaps that will lead to what I believe is a very deserving apology.

NORRIS: James Yee, thank you for talking to us.

Capt. YEE: Oh, it's been a pleasure. Thank you.

NORRIS: James Yee is the author of "For God and Country: Faith and Patriotism Under Fire." Yee is the former US Army Muslim chaplain at Guantanamo Bay.

SIEGEL: And we asked the Army for a response to James Yee's allegations, and spokesman Paul Boyce told us--and we quote--"The US Army has thoroughly examined the allegations associated with Chaplain Yee."

You're listening to ALL THINGS CONSIDERED from NPR News.

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