On Sunday’s "60 Minutes" on CBS, anchor Scott Pelley interviewed Murat Kurnaz, a german-born Muslim man who was released from Guantanamo Bay after five years, having been found innocent of terrorist activity, and as Pelley declared: "At the age of 19, Murat Kurnaz vanished into America's shadow prison system in the war on terror...The story Kurnaz told us is a rare look inside that clandestine system of justice, where the government's own secret files reveal that an innocent man lost his liberty, his dignity, his identity, and ultimately, five years of his life."

Pelley went on to describe Kurnaz’s claims of being tortured by the U.S. military:

Kurnaz claims his interrogations at Kandahar turned to torture. He told us that American troops held his head underwater...Kurnaz says the Americans used a device to shock him with electricity that made his body go numb. And he says he was hoisted up on chains, suspended by his arms from the ceiling of an aircraft hangar for five days.

After Kurnaz described how a doctor would monitor his health during such torture, Pelley asked: "The point of the doctor's visit was not to treat you; it was to see if you could take another six hours hanging from the ceiling?"

Pelley then said to Kurnaz: "I suspect that you know that the military will deny that this happened. The US military will deny that you were shocked. It will deny that your head was held in a bucket of water. It will deny that you hung from a ceiling for days at a time." Kurnaz replied: "It doesn't matter whatever they will say. The truth -- the truth will not change."

Pelley went on to claim that Kurnaz’s case was one of many, a "pattern" of torture:

Kurnaz isn't alone in these allegations. Other freed prisoners have described electric shocks at Kandahar. And even US troops have admitted beating prisoners who were hanging by their arms. Kurnaz's story fits a pattern...The Pentagon labeled the prisoners "unlawful enemy combatants." They didn't have the rights of prisoners of war and were beyond the reach of any court. At Guantanamo, Kurnaz says he endured endless months of interrogations, beatings at the hands of soldiers in riot gear and physical cruelty, which included going without sleep for weeks and solitary confinement for up to a month in cells that were sealed without ventilation or were set up to punish him with extreme conditions.

Pelley then talked to Kurnaz’s American attorney, Baher Azmy, a constitutional law professor from Seton Hall Law School, who has worked with the left-wing Center for Constitutional Rights while representing Kurnaz. In its mission statement, the Center for Constitutional Rights exclaims: "We are dedicated to restoring the fundamental right to habeas corpus and will continue to combat the illegal expansion of executive power and the American torture programs that have undermined fundamental rights in the name of the so-called "war on terror."

At one point, Pelley asked Azmy: "Have you ever in your legal career run across anything like this?" Azmy responded: "In my legal career, no. But in Guantanamo, no detainee has ever been able to genuinely present evidence before a neutral judge. And so, as absurd as Murat Kurnaz's case is, I assure you there are many, many dozens just as tenuous."

Pelley’s only effort to present the other side came in a brief statement near the end of the segment:

We asked the Department of Defense to talk to us about Kurnaz. Instead, they sent us a statement, calling his allegations "unsubstantiated" and "outlandish," adding that claims that the US military "engaged in regular and systematic torture of detainees cannot withstand even the slightest scrutiny." The statement did not address why Kurnaz was held for five years.

Here is the full transcript of the segment:

7:23PM TEASER:

SCOTT PELLEY: At the age of 19, Murat Kurnaz vanished into America's shadow prison system in the war on terror.

MURAT KURNAZ: They used to beat me when my head is underwater. They beat me, they -- into my stomach and everything.

PELLEY: They were hitting you in the stomach while your head was under water...

KURNAZ: Yes, so...

PELLEY: ...So that you'd have to take a breath?

KURNAZ: Right.

PELLEY: What Kurnaz told us is a rare look into the clandestine system of justice where the government's own secret files reveal that an innocent man lost his liberty, his dignity, his identity, and ultimately five years of his life.

7:28PM SEGMENT:

SCOTT PELLEY: At the age of 19, Murat Kurnaz vanished into America's shadow prison system in the war on terror. He was from Germany, traveling in Pakistan and was picked up three months after 9/11. But there seemed to be ample evidence that Kurnaz was an innocent man with no connection to terrorism. The FBI thought so; US intelligence thought so. German intelligence agreed. But once he was picked up, Kurnaz found himself in a prison system that required no evidence and answered to no one. The story Kurnaz told us is a rare look inside that clandestine system of justice, where the government's own secret files reveal that an innocent man lost his liberty, his dignity, his identity, and ultimately, five years of his life. We found Murat Kurnaz in Bremen, Germany, where he was born and raised. His parents emigrated here from Turkey. His father works in the Mercedes factory. Kurnaz wasn't particularly religious growing up, but in 2001 he was marrying a Turkish girl who was, and he decided to learn more about Islam.

MURAT KURNAZ: I didn't know how to pray. I didn't know anything. So I had to study more about Islam so I could go to the mosque and pray.

PELLEY: In Bremen, he met Islamic missionaries who urged him to go to Pakistan for study. As he was planning the trip, 9/11 happened.

KURNAZ: It was horrible. It was...

PELLEY: He told us he was horrified by the attacks, had never heard of Al-Qaeda and he decided to go ahead with his trip anyway. Did you begin to think that that wasn't a great idea?

KURNAZ: Today, I know it wasn't a great idea.

PELLEY: Kurnaz told us his story using the English that he learned from his American guards. If he seems a little distant, reserved, you'll understand why as his story unfolds. It begins in 2001, when he was at the end of that trip to Pakistan. He was headed to the airport to fly home to Germany when his bus was stopped at a routine checkpoint.

KURNAZ: They stopped the bus, and because of my color, I am--I'm much more different than the Pakistani guys, so...

PELLEY: You're lighter skinned.

KURNAZ: Right. He looked in the -- he looked into the bus, he came to me to my window, and knocked on my window.

PELLEY: He was a Pakistani cop who's pulled Kurnaz off the bus. The reason Kurnaz was singled out may always be a mystery, but at the time, the US was paying bounties for suspicious foreigners. Kurnaz, who'd been rambling across Pakistan with Islamic pilgrims, seemed to fit the bill. Kurnaz says that he was told that US intelligence had paid $3,000 for him. He ended up bound and shackled on an American military plane.

KURNAZ: I was sure, as soon as they would find out I'm not a terrorist, they will -- they will apologize for it and let me go back home.

PELLEY: But the plane flew him out of Pakistan and to a US base in Kandahar, Afghanistan, where he was mixed with prisoners fresh off the battlefield. The military took this picture, as Murat Kurnaz disappeared into the system for terrorists. His new identity was "number 53." He was kept in an outdoor pen in subfreezing weather and interrogated daily.

KURNAZ: They asked me where is Osama Bin Laden, and if I am from Al-Qaeda or from Taliban, questions like that. And I told them I don't know where is Osama Bin Laden, I never saw him. And I don't know anything about Al-Qaeda, I don't know what it is. That I spent all my time in Pakistan.

PELLEY: What happened next?

KURNAZ: I told them just they can -- they can call Germany and ask who I am, and they can ask anybody in Germany who I am.

PELLEY: Back in Germany, Bremen police were investigating, and what they were hearing made matters worse. Kurnaz's worried mother told them that her son had recently become more religious, had grown a beard, and was attending a new mosque. Schoolmates said that Kurnaz might have been headed to Afghanistan.

BERNHARD DOCKE: It was just guessing, just a fear, no more. But the fear turned into a fact.

PELLEY: Attorney Bernhard Docke was hired by Kurnaz's mother. He says there was no reason to suspect Kurnaz knew anything about Al-Qaeda. But this was weeks after 9/11 and some of the hijackers had been living in Hamburg.

DOCKE: And so close after 9/11 and close after Germany realized that 9/11 started with the Hamburg cell in Germany, everybody in the secret services got crazy.

PELLEY: Docke says the police report was sent to the Americans, and Kurnaz claims his interrogations at Kandahar turned to torture. He told us that American troops held his head underwater.

KURNAZ: They used to beat me when my head is underwater. They beat me into my stomach and...

PELLEY: They were hitting you in the stomach while your head was underwater?

KURNAZ: Yes, so...

PELLEY: So that you'd have to take a breath?

KURNAZ: Right. I had to drink, I had to -- how you say...

PELLEY: Inhale. Inhale the water.

KURNAZ: I had to inhale the water, right.

PELLEY: Kurnaz says the Americans used a device to shock him with electricity that made his body go numb. And he says he was hoisted up on chains, suspended by his arms from the ceiling of an aircraft hangar for five days.

KURNAZ: Every five or six hours, they came and pulled me back down. And the doctor came to watch if I can still survive or not. He looked into my eyes, he checked my heart. And then he said, `OK.' Then they put me back up.

PELLEY: The point of the doctor's visit was not to treat you; it was to see if you could take another six hours hanging from the ceiling?

KURNAZ: Right.

PELLEY: I suspect that you know that the military will deny that this happened. The US military will deny that you were shocked. It will deny that your head was held in a bucket of water. It will deny that you hung from a ceiling for days at a time.

KURNAZ: It doesn't matter whatever they will say. The truth -- the truth will not change.

PELLEY: And you're telling me in this interview that this is the truth?

KURNAZ: This is the truth.

PELLEY: Kurnaz isn't alone in these allegations. Other freed prisoners have described electric shocks at Kandahar. And even US troops have admitted beating prisoners who were hanging by their arms. Kurnaz's story fits a pattern. After six weeks in Afghanistan, Kurnaz was loaded onto another plane, this time bound for Guantanamo. The Pentagon labeled the prisoners "unlawful enemy combatants." They didn't have the rights of prisoners of war and were beyond the reach of any court. At Guantanamo, Kurnaz says he endured endless months of interrogations, beatings at the hands of soldiers in riot gear and physical cruelty, which included going without sleep for weeks and solitary confinement for up to a month in cells that were sealed without ventilation or were set up to punish him with extreme conditions.

KURNAZ: It's dark inside, no lights. And they can punish you in isolation with -- by coldness or by the heat. They have a special air conditioners over there, very strong. They can turn it very, very cold or very hot.

PELLEY: He says it all went on, year after year, always the same questions about Al-Qaeda, and the endless effort to break his will. He heard nothing from the outside and wondered whether anyone knew he was there. Then, in 2004, the US Supreme Court ruled that Guantanamo prisoners did have the right to lawyers, and to his complete surprise, one day Kurnaz was told he had a visitor. It was Baher Azmy, an American lawyer. Tell me about your first meeting with Kurnaz.

BAHER AZMY: He was chained to a bolt in the floor around his ankle, and had an absolutely enormous beard that had marked the years that he was in detention. He looked like someone who had been shipwrecked, which, of course, in a sense, he really was.

PELLEY: Azmy is a professor of constitutional law at the Seton Hall Law School. He dug into Kurnaz's case and found that the military seemed to have invented some of the charges. Military prosecutors had said one of Kurnaz's friends was a suicide bomber, but the friend turned up alive and well in Germany. How could they have gotten that so wrong? I mean, you're either a suicide bomber or you're not; there's no in between.

AZMY: This goes to the utter preposterousness of the government's legal process that they established in Guantanamo, this tribunal system that was supposed to differentiate from enemy combatant and civilian. So, in order to justify that he was an enemy combatant, they simply made up an allegation about someone he was associated with.

PELLEY: But far worse than the false charges was the secret government file that Azmy uncovered. Six months after Kurnaz reached Guantanamo, US military intelligence had written this: "Criminal Investigation Task Force has no definite link or evidence of detainee having an association with Al-Qaeda or making any specific threat toward the US." At the same time, German intelligence agents wrote their government saying "USA considers Murat Kurnaz's innocence to be proven. He is to be released in approximately six to eight weeks." How long was Kurnaz kept at Guantanamo Bay after this memo in 2002?

AZMY: Three and a half years.

PELLEY: They kept him, Kurnaz says, by inventing new charges. In this makeshift courthouse, Kurnaz claims that a military judge charged that Kurnaz had been picked up near Osama Bin Laden's hideout in Afghanistan while fighting for the Taliban. Ironic, since it was the US that flew him to Afghanistan to begin with. Have you ever in your legal career run across anything like this?

AZMY: In my legal career, no. But in Guantanamo, no detainee has ever been able to genuinely present evidence before a neutral judge. And so, as absurd as Murat Kurnaz's case is, I assure you there are many, many dozens just as tenuous.

PELLEY: And a US federal judge agreed. She ruled the Guantanamo military tribunals violated the prisoners' right to a defense. And she singled out Kurnaz's case. We asked the Department of Defense to talk to us about Kurnaz. Instead, they sent us a statement, calling his allegations "unsubstantiated" and "outlandish," adding that claims that the US military "engaged in regular and systematic torture of detainees cannot withstand even the slightest scrutiny." The statement did not address why Kurnaz was held for five years. The break in Kurnaz's case came when the German chancellor asked President Bush for his release. In August 2006, a plane came to take Kurnaz home. On the way out, he told us he was asked to sign a confession that his captors had written for him, saying that he had been Al-Qaeda all along. He refused. On the plane, he was chained and surrounded by soldiers, but by the end of the flight, he was free. There's a picture of you hugging your mother. Tell me about that moment.

KURNAZ: She wouldn't let me go. She wouldn't let me, anymore. She just grabbed me. And, of course, she was so happy, she cried. And I would -- I would go to my father and my brothers, also. But she didn't let me. They had to wait.

PELLEY: He was 19 when he went in, 24 when he got out. His new wife had divorced him. Kurnaz has written a book just translated into English, called "Five Years of My Life." He told us he wanted to visit the United States one day, but he can't because the US still considers him to be an unlawful enemy combatant.

—Kyle Drennen is a news analyst at the Media Research Center.