My cell was 8ft by 6ft, the same size as the detainees’ cages at Guantanamo. Barely a week ago I had received a glowing evaluation for my work as the US army’s Muslim chaplain among the “Gitmo” prisoners. Now I was the one in chains.

It was my turn to be humiliated every time I was taken to have a shower. Naked, I had to run my hands through my hair to show that I was not concealing a weapon in it. Then mouth open, tongue up, down, nothing inside. Right arm up, nothing in my armpit. Left arm up. Lift the right testicle, nothing hidden. Lift the left. Turn around, bend over, spread your buttocks, knowing a camera was displaying my naked image as male and female guards watched.

It didn’t matter that I was an army captain, a graduate of West Point, the elite US military academy. It didn’t matter that my religious beliefs prohibited me from being fully naked in front of strangers. It didn’t matter that I hadn’t been charged with a crime. It didn’t matter that my wife and daughter had no idea where I was. And it certainly didn’t matter that I was a loyal American citizen and, above all, innocent.

I was accused of mutiny and sedition, aiding the enemy and espionage, all of which carried the death penalty. I was regarded as a traitor to the army and my country. This was all blatantly untrue — as would be proved when, after a long fight, all the charges against me were dropped and I won an honourable discharge from the army.

I knew why I had been arrested: it was because I am a Muslim. I was just the latest victim of the hostility born the moment when the planes flew into the twin towers and the Pentagon on September 11, 2001.

My real “crime” had been that I had tried to ensure that the suspected Taliban and Al-Qaeda fighters detained in the Gitmo cages were given every opportunity to practise their religion freely, one of the most fundamental of American ideals.

I had monitored the atrocious treatment meted out by the guards. And I had come to suspect that my appointment as the prisoners’ chaplain was simply a piece of political theatre.

When reporters came to Guantanamo on the media tour, everyone had always wanted to talk to the Muslim chaplain. I had told them the things that the command expected me to say. We give the detainees a Koran. We announce the prayer five times a day. We serve halal food. Everything I said had been true. But it certainly wasn’t the full story.

I HAVE NOT always been a Muslim. I am a third-generation American — my grandparents left China in the 1920s — and as a child in New Jersey I grudgingly attended Lutheran church services with my mother.

On holiday after graduating from West Point, however, I met a young woman who was intrigued by Islam. I began to read about it and eventually converted. Then, after the US army sent me to Saudi Arabia and allowed me to visit Mecca, I wondered why there were no Muslim chaplains in the US military.

My father had taught me as a boy that America promises all people an opportunity to lead an extraordinary life. By becoming a Muslim chaplain in the summer of 2000, after four years’ study in Damascus, I saw myself fulfilling this opportunity. I had no idea what I was letting myself in for.

Six months after the September 11 attacks I was asked if I would like to work at Camp X-Ray, the new detention centre at Guantanamo Bay. I said that it would be difficult: Huda, my Syrian wife, was still adjusting to life in America and Sarah, our daughter, was in the throes of the “terrible twos”. It turned out, however, that I had no choice.

By the time I got to Guantanamo, Camp X-Ray was too small for the number of prisoners coming in. When I saw its remains I couldn’t believe that humans were once held here. It looked like a cattle yard. There were hundreds of cages in rows. The only protection from the blistering sun was a tin roof. Dozens of enormous rodents crawled throughout the camp. I was told that these were banana rats and would attack if provoked.

The new prison, Camp Delta, consisted of 19 blocks, each holding 48 detainees in individual open-air cells with steel mesh walls. Like other military personnel, I was briefed that the detainees were among the most dangerous terrorists in the world. We were told that many of the prisoners were responsible for the attacks of September 11 and would strike again if given the opportunity.

I expected to come face-to-face with hundreds of Osama Bin Ladens, but most prisoners were friendly. There were approximately 660 from dozens of countries, including Britain.

An English-speaking Saudi detainee named Shaker was eating a military “Meal Ready to Eat” or MRE when I first met him. MREs often led to constipation. “Chaplain,” Shaker called out. “You know what we call this lunch we eat every day? Meals that Refuse to Exit.”

Shaker said that he had settled in London after marrying a British woman. They had three children and his wife had given birth to his fourth child after he was captured. “My youngest son, we named him Faris, I’ve never seen,” he told me. “My wife doesn’t know anything about what happened to me and I’m so worried about her.”

I got to know three men from Britain particularly well: Rhuhel Ahmed, Asif Iqbal and Shafiq Rasul. Ahmed, the most talkative, told me that they had grown up together in Tipton, near Birmingham. Their families were close and the men were like cousins. All three told me they had never committed a crime and that their arrests had been a serious mistake.

The man in overall charge was Major General Geoffrey Miller, a slight but self-confident Texan in his late fifties. He was later sent to Iraq to make recommendations on improving intelligence collection at Abu Ghraib prison in the months before it became infamous for the maltreatment of its inmates.

If there was trouble with the prisoners, guards were supposed to restore order calmly. But Miller said when visiting Camp Delta or whenever seeing troopers around the base: “The fight is on!” This was a subtle way of saying that rules were relaxed and infractions were easily overlooked.

Miller was a devout Christian. In one of the first private conversations that he and I had, he invited me for a stroll under the watchtowers and told me that several of his friends and colleagues had been killed in the 9/11 attack on the Pentagon.

He had felt a deep anger towards “those Muslims” who attacked the World Trade Center and the Pentagon — such anger, he explained, that he had sought counselling with a chaplain. I appreciated his candour but I sensed there was a subtle warning behind his words.

THE WORST punishment for prisoners was a “forced cell extraction” by a group of six to eight guards called the Initial Response Force. The troopers called it IRFing.

I witnessed my first IRFing after a military policeman had performed the “credit card swipe” — pressing his fingers inside a detainee’s buttock crack to look for a weapon. This type of physical contact is not acceptable under Islamic law and the detainee had pushed the guard away. But prisoners were not allowed to touch an MP and immediately eight guards were summoned.

They put on riot protection gear — helmets, heavy gloves, shin guards and chest protectors — before forming a huddle and chanting in unison, getting themselves pumped up. Still chanting, they rushed the block, their heavy boots sounding like a stampede on the steel floor. Detainees throughout Camp Delta started to yell and shake their cage doors.

When the IRF team reached the offending detainee, the team leader drenched him with pepper spray and opened the door to his cell. The others charged in. He was no match for eight men in riot gear. The guards used their shields and bodies to force him to the floor. With his wrists and ankles tied, he was dragged down the corridor to solitary confinement.

When it was over the guards high-fived each other and slammed their chests together like professional basketball players — an odd victory celebration for eight men who took down one prisoner.

IRFing was used with extraordinary frequency. Seemingly harmless behaviour could bring it on: not responding when a guard spoke or having two plastic cups in a cage instead of the regulation one. Invasive body searches occurred daily and were a constant source of tension leading to IRFing. I came to believe that the searches were done solely to rile the detainees. The prisoners had been locked in cages for several months in a remote area of Cuba. What could they possibly be hiding?

Violent episodes were increasing. In one incident a guard had to be hauled off a handcuffed detainee whom he was beating on the head with a handheld radio. By the time I arrived the detainee had been taken to the hospital, but his blood was fresh on the ground and what appeared to be large pieces of flesh were soaking in it.

Bad as this violence was, many soldiers discovered a weapon far more powerful than fists: Islam. Because religion was the most important issue for nearly all the prisoners in Camp Delta, it became the most important weapon used against them.

Guards mocked the call to prayer and rattled doors, threw stones against the cages and played loud rock’n’roll music as the prisoners prayed.

Knowing that physical contact between unrelated men and women is not allowed under Islamic law, female guards would be exceptionally inappropriate in how they patted down the prisoners or touched them on the way to the showers or recreation. Detainees often resisted and were IRFed.

The guards knew that Muslims believe that the Koran contains the actual words of God and is to be treated with the utmost respect. I never heard of an incident where a detainee hid anything dangerous in the Koran; doing so would be considered an insult. Yet the guards shook the prisoners’ Korans violently, broke bindings, ripped pages and dropped the book on the floor, all on the pretext of searching them.

Some of the worst complaints that I received were about what was happening inside the interrogation rooms. Some of the translators — Muslim military personnel like me — told stories about female interrogators who would take off their clothes during the sessions. One would pretend to masturbate in front of detainees. She was also known to touch them in a sexual way and make them rub her breasts and genitalia. A translator who had witnessed this woman’s behaviour told me that her supervisor had told her to tone down the tactics but had not disciplined her.

Translators with the Joint Intelligence Group (JIG) also confirmed that some prisoners were forced to prostrate themselves in the centre of a satanic circle lit with candles. Interrogators shouted at them, “Satan is your God, not Allah! Repeat that after me!”

I came to believe that the hostile environment and animosity towards Islam were so ingrained in the operation that Miller and the other camp leaders had lost sight of the moral harm we were doing.

I began to keep a record of the atrocities that I was hearing about. But the more time I spent on the blocks the more aggressive many of the guards became towards me. I was authorised to have unescorted access and to speak with detainees in privacy. But guards eavesdropped on my conversations, standing very close and attempting to intimidate me. Most refused to move away.

“I’ve been told to stay within one arm’s length of you at all times,” one guard told me.

When an administrative assistant in the navy chaplain’s office showed me a slanderous and hatefilled diatribe against Muslims that was to be inserted into a weekly newsletter to hundreds of Christian military personnel on the base, I decided it was time for action.

It began, “Egyptian Muslim Mohammad Farouk hated Christians . . . in an attempt to obey the Koran and please Allah, Mohammad and his friends began to assault and harass Christians in their village . . .” It claimed that the Koran instructs Muslims to espouse violence and hatred, the opposite of the truth.

Yet Vincent Salamoni, a Catholic priest who worked as the naval command chaplain, only grudgingly complied with the advice from the Christian chief chaplain on the base not to distribute this material. Salamoni said that he felt it was necessary first to find out if the Koran did instruct Muslims to kill Christians.

In briefings to newcomers to the base, given with the express support of the operations staff, I tried to dispel the principal myth that all Muslims are terrorists. Little did I understand that by trying to educate my colleagues about the need for religious tolerance, I was encouraging them to suspect me.

Although I had been ordered to prepare the presentation by the command, the fact that I talked knowledgeably about Islam was enough to lead some of them to question my loyalty.

Captain Jason Orlich, an army reservist who had taught in a Catholic school before arriving in Guantanamo to take charge of intelligence and security for detention operations, sat in my briefing on his first day and asked: “Is he on our side or is he on the enemy’s side?” As I was to discover much later from court documents, he made it his mission to keep an eye on me. Nor was I the only one under suspicion: Muslim colleagues — all loyal Americans — were spied on and bugged.

When I got together with other Muslim personnel on the base, our conversation routinely turned to what appeared to be open religious hostility.

Ahmad al-Halabi, a young airman who helped me with the detainees’ library of religious books, told me that he had been given a copy of a CD widely circulated by the troopers. Among the images on it was a phoney Playboy cover showing Muslim women in provocative dress and poses, and another depicting Muslim men engaged in anal sex during prayer. He suspected that the disc had originated in the security section headed by Orlich, who appeared in several photographs on the disc.

All of us on the base knew that, like the detainees, we were likely to be under surveillance wherever we were. Watch what you’re saying, soldiers would joke, because the “secret squirrels” are listening. We never knew exactly who they were, but the government agencies represented on the island included the FBI, Naval Criminal Investigative Service, Army Counterintelligence and the CIA. Nothing was off limits. Our e-mails were read, our telephone calls were monitored and everything we said had the potential of being overheard.

I had a feeling that our Muslim Friday prayers, attended by about 40 in a small room at the chapel complex of the camp, were under surveillance. Men in khakis and polo shirts — the common uniform of the FBI and CIA — would stand just outside, watching to see who came and went. I sometimes asked if they wanted to join us but they always declined, offering no explanation of their presence. A translator confirmed that a man sitting outside was an FBI agent he had worked with in interrogations.

WHEN I was given a larger apartment to live in, I called some of the guys to come over and share evening prayers in my spare bedroom. Afterwards we hung around in my living room and had sodas and snacks. Before long, evening prayers at my house became a frequent occasion and word spread among the Muslim personnel that anyone who wanted to join us was welcome. People started turning up with tasty Middle Eastern food. I did not realise what the repercussions would be.

Many months later I learnt the facts from court documents.

People initially became suspicious of me because of the presentation that I gave during the newcomers’ briefing. Stories quietly began to circulate about me and my fellow Muslim personnel. We were too sympathetic to the plight of the detainees and too critical of how the MPs treated the prisoners. We prayed together on Friday afternoons. Orlich even noted that Ahmad was seen to be “shadow boxing” as he left the chapel. “I found that to be odd,” Orlich told a military investigator.

The accusations were retold and exaggerated in back yards and on the beaches during the hot Cuban evenings, fuelled by boredom and discount vodka. Some troopers adopted names for us: “the Muslim clique” and, far more disturbing, Hamas, after the Palestinian organisation.

Did these soldiers truly believe the things they were saying about us and were they truly threatened by the fact that we practised our religion? Or were they just caught up in the pervasive anti-Muslim hostility that defined the mission? I believe that those who accused us of being “radical Islamists” were unable to see that someone can be a Muslim and not be a terrorist.

Most of the Christian soldiers at Guantanamo practised their religion regularly and attended weekly services. Miller was rarely missing from the front row of the chief chaplain’s service, which gave it an unstated command emphasis.

Three Christian chaplains hosted weekly Bible studies where soldiers met to discuss their faith. I am sure that they believed this made them better people and better soldiers and helped to ease the tremendous strain of life at Guantanamo. Why couldn’t they see that we were simply doing the same?

For months Orlich watched me and the other Muslims who regularly attended my religious services. He was particularly concerned with Ahmad whose “case” was assigned to Lance Wega, a young civilian agent from the Air Force Office of Special Investigations.

Investigators twice surreptitiously entered Ahmad’s living quarters. They took photographs of the house, copied his telephone records and mirrored the hard drive on his computer.

Microsoft was instructed to store Ahmad’s e-mails and records of his internet activity without his knowledge.

“You are requested to not disclose the existence of this request to the subscriber or any other person,” the letter to Microsoft stated. “Any such disclosure could subject you to criminal liability for obstruction of justice.”

Many Muslim personnel came to me to share concerns that things just didn’t feel right. Staff Sergeant Mohammad Tabassum, a no-nonsense type of guy in his mid-forties, told me that he had been cleaning out a cupboard in his house on the base and discovered a listening device hidden inside.

Ahmad then told me that his security clearance had been suspended. He was the last person I thought would come under suspicion; he was a loyal American and an exceptional soldier, the best translator in the camp.

When Ahmad’s tour of duty came to an end, he left with great excitement, heading for Syria to be married. He and his fiancée had been forced to postpone the wedding when his deployment at Guantanamo was extended. His mother, who had recently recovered from cancer, was to meet Ahmad at the airport in London and then fly with him to Damascus.

A few days after Ahmad left, however, we heard that he had been arrested in Jacksonville, Florida, when he got off the plane from Guantanamo. Nobody knew why or what had happened to him.

After a few weeks news arrived that Tariq Hashim, an air force captain who had been on the same plane, had also been arrested. The FBI had taken both of them. Then we had heard that another member of our prayer group, Petty Officer Samir Hejab, a navy cook, had been arrested as he left Guantanamo at the end of his deployment.

Suddenly it seemed as if every Muslim at Guantanamo was being detained on reaching American soil. Were we all going to be arrested and jailed without explanation?

In the midst of this confusion, I decided that it was time for me to take a break from Guantanamo. Every trooper was allowed a short vacation and by late August I was ready for mine. I felt overjoyed at the idea of seeing my family again. But I also was growing more concerned by the day that something suspicious was happening behind the scenes.

“Have you heard anything about Muslim personnel being arrested recently?” I asked Orlich.

He looked me in the eye. “Nothing,” he told me.

“The situation is strange,” I said to him. “There’s a lot of rumours and I’m wondering if I’m next.”

Orlich smiled and put his hand on my shoulder, “Now why would anyone want to arrest you, chaplain?”

I persisted: “Because I am the Muslim chaplain and the one who leads these three missing Muslims in prayer.”

Orlich just laughed off my concerns.

My wife said she had my gun in one hand and two rounds in the other

I still don’t understand how the misguided suspicions of a few inexperienced soldiers led to the ordeal that changed my life, tore apart my family and destroyed my career.

While my plane headed home to the US on September 10, 2003, representatives of at least five government agencies awaited me at the Jacksonville air station: FBI, Naval Criminal Investigative Service, US Bureau of Immigration and Customs Enforcement, US Customs and Border Protection and Army Counterintelligence.

After my arrest I was sure that General Miller would order my release. He ran a tight ship and he was a tough leader, but he was a general and he would therefore be fair. But when I was at last arraigned at a pre-trial hearing, I was presented with a memorandum signed by Miller that stated: “Chaplain Yee is known to have associated with known terrorist sympathisers.”

He added: “Yee is suspected of several extremely serious crimes, including espionage, which potentially carries the death penalty.”

I was too cut off from the world to know that the news of my arrest had broken and that the government was slandering me in the press. There were reports that I had contact with Syrian government officials, that I was affiliated with Al-Qaeda and the Taliban, and that I had been found with maps of Guantanamo and names of the detainees and interrogators.

Sometimes I wondered if I would go crazy trying to deal with the situation and being locked in solitary confinement for what turned out to be 76 days. If it were not for my military training and my religion, perhaps I would have.

After a month I learnt that I was not going to be charged with spying, sedition or aiding the enemy after all but with the “slap on the wrist” charges of taking classified information to my housing quarters and of transporting classified material without the proper container. But my hopes quickly vanished when my lawyer told me that the army was saying that more serious charges might still be brought.

I discovered that I was in the same prison as Yasser Hamdi, an American-born Saudi who was allegedly captured fighting US forces in Afghanistan, and Jose Padilla, who was arrested in Chicago on suspicion of belonging to Al-Qaeda and participating in a plot to detonate a dirty bomb in the United States. Both were deemed enemy combatants. Did this mean I was, too?

At another pre-trial hearing, investigators claimed I was part of a spy ring. The press repeated false information from anonymous government sources that it was one of the most dangerous spy rings to be discovered in the US military since the cold war.

The army was doing far more harm to me privately. Martha Brewer, an agent with the Department of Defence Criminal Investigative Service, went to my apartment near Seattle and told Huda, my wife: “Your husband is not the person you think he is. He’s having an affair with three women.”

She produced photographs of me with female colleagues on social occasions at Guantanamo in what was clearly a desperate attempt to turn Huda against me. Although these photographs would have been acceptable to most people, Brewer clearly understood that given her traditions, Huda would be particularly upset to see me photographed with women. Huda later told me she was so distressed that some days she couldn’t get out of bed and all she could do was cry.

On November 25, with no serious charges in sight, I was suddenly released from custody. But the same day news bulletins announced that I was being charged with adultery (a criminal offence in the military) and with downloading pornography on a government computer. By revealing the new charges on the day of my release from prison, the army had captured the story.

I called Huda and had one of the most difficult experiences of my entire ordeal. She told me that when she had learnt of the new accusations, she had searched out my Smith & Wesson .38 special handgun, which I kept on the top shelf in my cupboard, hidden from view.

“I’m holding it in one hand,” she told me, “and two rounds in the other.”

“Put it down,” I said firmly, fear rising inside of me.

“Tell me how to use it,” she whispered. She said that she couldn’t deal with this any longer and wanted to be free from everything — the media, the scrutiny, the idea that the United States government could be doing this to our family. It was not the first time that Huda had suggested a desire to die since my arrest, but it had never gone this far.

I didn’t know what to do. She hung up and when I called back several times, she didn’t answer. Finally I called the local police department. They sent officers to our apartment, who took Huda to a nearby hospital against her will. She was released after several hours, but the police kept the gun. I could not be with her. I was forbidden to leave my military base.

In February last year my lawyers reached a deal with the army that the criminal charges would be dismissed and I would resign my commission with a recommendation for an honourable discharge from Miller and other senior officers. Even so, the military continued to whisper that I was indeed a threat to the nation but it was somehow in the interest of security to drop the case against me. Miller found me guilty of adultery and possessing pornography and formally reprimanded me. Two months later — by which time my case had become a cause celebre — I won an appeal against his decision.

After the charges against me were dropped and it became obvious that the government had erred, many newspaper editorials were written to demand that the military issue an apology.

Of course I want an apology, but it will not restore my marriage which has suffered irreparable damage from the vindictive claims that the military made. Nor will it give me back my job as a Muslim chaplain in the army — a job that allowed me to fulfil my dream of serving both God and country.