By Stephen Grey (author of Ghost Plane) in the New Statesman

More than 7,000 prisoners have been captured in America’s war on terror. Just 700 ended up in Guantanamo Bay. Between extraordinary rendition to foreign jails and disappearance into the CIA’s “black sites”, what happened to the rest?

Sana’a, Yemen. By the gates of the Old City, Muhammad Bashmilah was walking, talking, and laughing in the crowd – behaving like a man without a care in the world. Bargaining with the spice traders and joking with passers-by; at last he was free.

A 33-year-old businessman, Bashmilah has an impish sense of humour; his eyes sparkled as he chatted about his country and the khat leaves that all the young men were chewing. But when I began my interview by asking for the story of his past three years, his mood shifted. His face narrowed, his eyes calmed, and he stared beyond me – as if looking directly into the nether world from which he had so recently emerged.

For 11 months, Bashmilah was held in one of the CIA’s most secret prisons – its so-called “black sites” – so secret that he had no idea in which country, or even on which continent, he was being held. He was flown there, in chains and wearing a blindfold, from another jail in Afghanistan; his guards wore masks; and he was held in a 10ft by 13ft cell with two video cameras that watched his every move. He was shackled to the floor with a chain of 110 links.

From the times of evening prayer given to him by the guards, the cold winter temperatures, and the number of hours spent flying to this secret jail, he suspected that he was held somewhere in eastern Europe – but he could not be sure.

When he arrived at the prison, said Bashmilah, he was greeted by an interrogator with the words: “Welcome to your new home.” He implied that Bashmilah would never be released. “I had gone there without any reason, without any proof, without any accusation,” he said. His mental state collapsed and he went on hunger strike for ten days – until he was force-fed food through his nostrils. Finally released after months in detention without being charged with any crime, Bashmilah was one of the first prisoners to provide an inside account of the most secret part of the CIA’s detention system.

On 6 September, President George W Bush finally confirmed the existence of secret CIA jails such as the one that held Bashmilah. He added something chilling – a declaration that there were now “no terrorists in the CIA programme”, that the many prisoners held with Bashmilah were all gone. It was a statement that hinted at something very dark – that the United States has “disappeared” hundreds of prisoners to an uncertain fate.

Let’s examine the arithmetic of this systematic disappearance. In the first years after the attacks of 11 September, thousands of Taliban or suspected terrorist suspects were captured. Just in Afghanistan, the US admitted processing more than 6,000 prisoners. Pakistan has said it handed over around 500 captives to the US; Iran said it sent 1,000 across the border to Afghanistan. Of all these, some were released and just over 700 ended up in Guantanamo, Cuba. But the simple act of subtraction shows that thousands are missing. More than five years after 9/11, where are they all? We know that many were rendered to foreign jails, both by the CIA and directly by the US military. But how many precisely? The answer is still classified. No audit of the fate of all these souls has ever been published.

Bush’s next big scandal

Since the publications of photographs from Abu Ghraib, the Bush administration has faced a string of scandals concerning its conduct of the war on terror: from abuses of prisoners by the US military, to the rendition of terrorist suspects to jails in places such as Egypt and Syria, where torture is routine, a process first described in the New Statesman in May 2004. International outrage, inquiries launched against CIA activities by prosecutors in Europe, as well as clear instructions from the US Supreme Court that, in its reaction to 9/11, Congress had not issued the president with a “blank cheque”, have all challenged the administration’s venture into what vice-president Dick Cheney called “the dark side” of warfare.

But if Bush hoped to appease his critics with his public acknowledgement of the CIA’s secret programmes, and his promise to bring some of America’s most important captives to an open military trial at Guantanamo, then he will be disappointed. After last week’s midterm elections, the administration will face legislators more emboldened to probe its conduct. And the issue of disappearances – of the fate of the missing prisoners held by the CIA and the Pentagon – threatens to become the next big scandal.

It was in early 2002, when the camp at Guantanamo Bay was opening up, that I heard from a source close to the CIA that most of the media were missing the point. As cameras showed images of chained prisoners being wheeled across the base on trolleys, there was predictable outrage. But the source described these images as “the press release”.

This was what Washington wanted the world to see. Beyond Cuba was a concealed network of prisons around the globe that were becoming home to thousands more prisoners. The CIA had its own secret facilities, but many more were held in jails run by foreign allies. There are some good operational reasons for keeping the arrest of suspected terrorists secret. Sometimes, in the short term, deception makes good tactical sense; staying quiet about an arrest may keep the enemy guessing. Sometimes it can be for diplomatic reasons: secrecy may help to persuade countries such as Egypt to accept a prisoner.

But why is it so sensitive to confirm what happened to these prisoners, to detail how many were transferred where and when? Why should a country receiving prisoners be so embarrassed? And why – when countries such as Egypt have come clean and said “yes, we received 70 to 80 prisoners rendered by the United States” – will the United States itself not confirm what it did? Despite admitting, in general, that the CIA carries out renditions, the US has yet to own up to a single specific case of transferring a prisoner to foreign custody.

The explanation for the secrecy is one that most of the CIA officers involved in rendition will quite freely admit – a transfer to places such as Egypt or Uzbekistan (a country known for boiling prisoners alive) will inevitably involve torture. And knowingly sending a prisoner to face torture is, under both US and international law, an illegal act. Revealing the fate of the missing prisoners may be just too politically embarrassing.

Justifying war with torture

One of those “disappeared”, for example, is the former al- Qaeda camp commander Ibn-al Shaykh al-Libi, who was captured in late 2001. Al-Libi was first interrogated by the FBI but, according to those involved, he was then snatched by the CIA and rendered to Cairo. It was while he was under Egyptian interrogation that al-Libi provided an important piece of “testimony”: that Saddam Hussein had an operational relationship with al-Qaeda. It was an erroneous claim, since formally withdrawn by the CIA, but was used as part of the justification for the war in Iraq. Al-Libi’s anonymous testimony was cited by Colin Powell before the United Nations. But no one mentioned where the intelligence came from.

After his interrogation in Egypt, al-Libi was sent back to US custody in Afghanistan. But now he has disappeared. Perhaps he has been sent to Libya? He is certainly a more important prisoner than the vast majority at Guantanamo. Yet sending al-Libi to the Cuban camp, put ting him on public trial and allowing him to tell his story would be a political disaster. So he remains hidden.

Other key prisoners are missing too – others whose stories would shock the public conscience. The US, for example, has never acknowledged what it did with German citizen Mohammed Haydar Zammar. He was captured in December 2001, one of the first in custody who was connected to the Hamburg cell that carried out the 9/11 attacks. And, again, instead of being held in US hands, he was rendered in secret to Damascus. He has never been brought to a public trial or had any chance to reveal how he was treated.

The cases of al-Libi and Zammar, who according to fellow prisoners in Syria was brutally tortured, illustrate the corrosive effect of the policy of disappearance. While the secrecy may protect the US from legal jeopardy and from political embarrassment, it also makes the threat of torture self-fulfilling. If you send a prisoner to Damascus, Tripoli or Tashkent, how can you hope to protect that prisoner – to ensure a fair trial or see that he stays alive – if you keep that rendition quiet? Secrecy protects the torturer; and it denies those innocent, those wrongly accused of crimes of terrorism and caught up in these renditions, any chance of justice.

Last month, Bush signed into law his new Military Commissions Act, which provides for the trial at Guantanamo of top al-Qaeda leaders. The act grants fewer rights to defendants than the Nazis got at Nuremberg. And yet, in this strange world, the rights now granted to men such as Khalid Sheikh Mohammed, the man who devised the 9/11 attack and who will now be brought to trial, still rank far higher than the rights of the small fry, those much less significant players behind bars in foreign jails. In this new justice, the big terrorists are granted privileges, and the other missing prisoners, subtracted from the public record, are disappeared off the face of the earth. That’s the mathematics of torture.

Stephen Grey is the author of “Ghost Plane: the inside story of the CIA’s secret rendition programme” published by C Hurst & Co (?16.95)