A convicted “sleeper terrorist” linked to the 9/11 planners has spoken for the first time about his treatment in detention, claiming he was tortured and abused during 13 years of incarceration on American soil.

Three years after his release, Ali al-Marri claims he is innocent and wants his FBI interrogators brought to account.

Al-Marri was arrested after the 2001 attacks and later declared an “enemy combatant” by George W Bush. Held in solitary confinement without charge for six years at a naval brig in South Carolina, he was the only non-US citizen detained outside Guantánamo.

Al-Marri’s allegations of torture are supported by detention logs which are set to reignite the controversy over the US handling of al-Qaida suspects before the impending appointment as CIA director of Gina Haspel, a woman accused of presiding over “enhanced interrogation techniques”.

Al-Marri, a Qatari, arrived in Chicago on 10 September 2001 with his wife and five children. In their hotel room, as the kids searched for the cartoon channel, images of 9/11 appeared on the screen.

“I had a sense. I rang the airline immediately – could we get home? But everything was grounded. I didn’t think al-Qaida could do it. In my hotel people were yelling at me. it was clear what was happening.”

When he went to collect a trunk shipped from home, the FBI were alerted. Al-Marri was arrested on 9 December. It would be 13 years before he saw his family again.

FBI officers found an encyclopaedia bookmarked at US waterways, internet searches for toxic chemicals, and printouts of hundreds of American credit card numbers. His claim to have come to the US to study was in doubt, as he had arrived two weeks late for the start of his course and 10 years after completing his first degree in the country.

Threatening to sodomise me, threatening to rape my wife, threatening to bring in my kids – that’s torture Ali al-Marri

FBI agents said he wanted to poison lakes with cyanide and disrupt the US banking system. They claimed he had visited al-Qaida training camps in Pakistan, and was in contact with Khalid Sheikh Mohammed, mastermind of the 9/11 attacks.

Al-Marri has never answered the allegations. In 2009, he pleaded guilty in a civilian court to conspiracy to provide material support to al-Qaida and was jailed for 15 years, a sentence that took into account his previous captivity.

Now, backed by UK advocacy group Cage, he wants “the American government to bring their case against me to neutral ground. I challenge them this.”

Al-Marri claims his encyclopaedia was bookmarked by his wife when she tidied his desk – “I was reading about the biggest lake, the longest river, I like these kind of facts” – and says the chemical research was because he was considering importing chemicals from his brother-in-law’s Qatar company.

“It was not just cyanide, it was 200, 300 different chemicals,” he said.

The credit card numbers, said Al-Marri, were down to idle research on algorithms, while the trips to Pakistan were on business.

What is undisputed is that from 2003 Al-Marri was held in a deliberately chilled cell with periods of enforced nudity. His head and beard were shaved, and he was given a metal rack to lie on. He was subjected to sleep deprivation, interrogation and isolation while being monitored by surveillance cameras.

He alleges that on 11 March 2004 he was “dry-boarded” – socks stuffed down his throat and tape wrapped round his head as he sat shackled to the floor. “I was choking, I was dying,” he said. “The suffering, you taste the pain, you taste it. Threatening to sodomise me, threatening to rape my wife, threatening to bring in my kids, that’s torture. Threatening to send me to a black site, to become a military lab rat, choking me to near death. This is torture.”

The brig log from 11 March says his interrogators, frustrated with his chanting of verses from the Qur’an, had taped his mouth.

“I knew I had no rights, I was down the rabbit hole. It was dark times. My cell was six steps one way and, to lay down the other way, I’d have to bend my knees. I cannot see if it’s day or night. I felt as though I was buried in a concrete grave. I know the Americans were angry, but that gave them no right to treat me like that. In times of test your morals and values should not change. Unfortunately, at that time you were guilty until proven innocent – all the bragging about American justice and American constitution, all this goes out of the window. My thought was they will shoot me, hang me.

“Yes I was scared, I was afraid of death, I was homesick for my kids, I wanted to smell the air. But I didn’t want to let that show, I was non-compliant from day one.

“I was treated the worst of any inmate in America. I had no mattress, no blanket, no pillow, no Qur’an or prayer rug. I had no idea which way is Mecca, so I prayed each way each time.”

I was planning a master’s degree and maybe a PhD. I ended up with a PhD in American hospitality Ali al-Marri

By 2009 his conditions had improved, but al-Marri claims he pleaded guilty to get home. “Everything in that plea bargain that has to do with al-Qaida and terror is 100% false,” he said.

“My battery was at 1%, I’m done. From seven years of isolation, I missed my kids, my wife. To kiss my mum before she died outweighed my need to show innocence. In the military jail there’s no light at the end of the tunnel.

“My best time was getting my sentence: 18 January 2015. Finite, out.”

On his return to Qatar, al-Marri received a hero’s welcome. The prime minister telephoned him and celebrations were held. “People were stopping me in the street, taking selfies,” he said. “What were they celebrating? An inmate who has spent his time in jail and got out?

“They do not believe I am a terrorist. Terrorist is a relative term; one man’s terrorist is another’s hero. America’s founding father George Washington was a terrorist to the British. To the west, yes, I am a terrorist, but to the Arabs I’m not, I’m a hero. So Osama bin Laden is a hero? When they call me terrorist, or they call me hero, I don’t see that.

“I was planning a master’s degree and maybe a PhD. I ended up with a PhD in American hospitality,” he said. “Nobody has been held accountable. There are people who admit they have done this and people who deny it. I do not need apologies, I need accountability. What they said and did to me was torture.”

In a statement, the FBI told the Guardian they would not comment on the case but that “the FBI does not engage in torture and we maintain that rapport-building techniques are the most effective means of obtaining accurate information in an interrogation”.