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.