During the three years after 9/11 that he wore his chains and orange jumpsuit, the most wretched moment for Moazzam Begg came after his first interrogation at Bagram in Afghanistan. Hooded, his arms and legs chained behind him so that his spine arched backwards, he received a visit from the men who had just told him he would never see his children again.

They kicked him in the head.

Thirteen years on, after his latest period of incarceration, Begg says that it was not difficult to comprehend why this was happening. “I understood where the Americans were coming from, at Bagram and Guantánamo,” he says. “I understood that they were reacting to 9/11.”

What is not so easy to fathom, he says in an interview with the Guardian, is why he has spent the last seven months in a cell in Belmarsh high-security prison in south London, facing first two terrorism charges, and then five more, arising from two trips to Syria – only to see the case evaporate when prosecutors announced on Wednesday that they were offering no evidence against him.

The CPS declined to explain its decision, other than to say it had “recently become aware of relevant material” that led it to realise that the chances of a jury finding Begg guilty were highly remote.

It has since emerged that MI5 had neglected to hand over to police and prosecutors its minutes of meetings it had requested with Begg. He had explained that he was planning to visit the war-ravaged country – in part to investigate the agency’s links with the Assad regime – and was assured he would not be hindered.

It has also emerged in court that not long after that meeting with MI5, Begg’s car was bugged. The listening device remained in place for more than a year.

Begg says it is inevitable that he will be bringing civil proceedings against MI5 and the government.

Facebook Twitter Pinterest Moazzam Begg leaves Belmarsh prison after prosecutors dropped terrorism charges against him. Photograph: Lefteris Pitarakis/AP

At his family home in Hall Green, a suburb of Birmingham, Begg uses words such as malicious, and vindictive, when asked to explain what he believes may have been behind his arrest last February.

He also says he feels cheated by the prosecutors’ decision to abandon the case against him. “I wanted my day in court; I was spoiling for the fight. I wanted to challenge every allegation in the case against me. I believe that if I had put my case before a jury I would have been acquitted.”

Begg’s case is that far from being a terrorist, his first trip to the country was undertaken in order to investigate MI5’s alleged role in the rendition of a Libyan man from Syria to one of Muammar Gaddafi’s prisons. The second, he says, was to help to run a training camp in the countryside near Idlib, north-west Syria, where opponents of the regime could undergo physical exercise and acquire the rudiments of first aid and military training, with fake wooden guns.

This, Begg insists, was not an act of terrorism, but an attempt to help people defend themselves against a murderous regime, war criminals who were gassing their own people. “I was never afraid to go to court. Any right-minded person on a jury would have seen very early on that I am not the terrorist here,” he says.

Begg, 46, is by far the best known of the Britons who were picked up in Afghanistan and Pakistan after 9/11, and consigned to Guantánamo by government ministers who were apprehensive of the way in which an enraged US administration would react if the men were allowed to return to the UK, where it was far from clear that they could be prosecuted.

Since Begg’s release in January 2005, he has been the leading light of Cage, a London-based pressure group that campaigns for terrorism suspects denied legal rights.

Begg is a small man, his face is scarred from the beatings he received at Bagram, and he has received treatment for post-traumatic stress disorder. But he insists he will remain uncowed.

Begg says he is bewildered that so many British Muslims have faced arrest and imprisonment after returning from Syria just as Isis was gaining ground in the region. Some, he says, spent no more than a couple of weeks in Syria, during which many were deeply disturbed by what they saw of the brutality of Isis. “People returned specifically because they did not want to be part of that … they wanted to come back.

“In Denmark and Germany they are not arresting returnees from Syria. We need to find another way. Not to take young men, some as young as 19, and put them away for 15 years because they made a misjudgment about the way the British government would view them.”

At the end of last year, when he had been back from Syria for almost a year, Begg realised that he too was about to face problems, when his passport was confiscated on his return from a trip to South Africa. A few weeks later, he was arrested and charged with terrorism offences, as a result of his work at the training camp and an attempt to send a Honda generator to a friend who was fighting in Syria.He was refused bail and, for seven months, was held on remand on a spur at house block four at Belmarsh. There were 74 other men on the same spur, some of them convicted murderers, yet he was one of only two who were being held as Category A prisoners – the highest security category. As a result of this, he says, it was three months before his wife and four children were granted permission to see him. “It was very difficult. I had once again, as I had to do in Guantánamo, say to myself that I am not a father, I am not a son, I am just a number.”

His cell at Belmarsh was larger than the one in which he was detained at Guantánamo. And although he was locked in his cell for up to 22 hours a day, conditions were far easier: so much so that he was initially bewildered when another inmate on the spur attempted to take his own life. “It was hard to understand, because I kept on making the comparison with Guantánamo, which was much worse. I had to remind myself that I was in England, and that I had to compare England with England, and not with Guantánamo.”

Begg was released from Belmarsh a few hours after crown prosecutors told an Old Bailey judge on Wednesday that they were not proceeding with the case against him.

Before long, it became clear that West Midlands police officers were furious that MI5 had withheld the minutes of its meetings with Begg for so long. There were suggestions that police had always been reluctant to arrest a man who had spent three years in Guantánamo without charge, but that MI5 had been insistent. The CPS, meanwhile, issued a terse statement that said: “If we had been made aware of all of this information at the time of charging, we would not have charged.”

Despite not being sure why he was arrested and charged, Begg says he suspects the explanation probably embraces incompetence, Islamophobia, maliciousness and fear. “I think we will know the answer one day and it will be very embarrassing.”

He says it cannot be because he wishes to see young Muslims become radicalised – “to be a fifth column in this country” – because he does not. “I am saying that we have a stake in this country and don’t let our voice be silenced.”

One possibility, he says, is that there are some within the British state who simply wish to silence dissent “from those parts of the population [where] they would expect weakness and fear and apprehension”: British Muslims.