Fredrik Laurin, a Swedish journalist who worked on The Broken Promise, extensively researched the leased Gulfstream jet that was used to take Zery and Agiza to Cairo. Laurin told me that he was able to track the aircraft to landings in Pakistan, Kuwait, Egypt, Germany, England, Ireland Morocco, as well as the Washington DC area. It also made visits to Guantánamo. The company told Laurin that the plane was leased almost exclusively to the US government. Significantly, the records obtained by Laurin indicate that the Gulfstream apparently halted its overseas trips from May 5 2004 - the week after the Abu Ghraib scandal broke - until July 7, when it flew from Dulles Airport in suburban Washington to Cairo.
After the Abu Ghraib abuses were revealed, a former senior intelligence official with direct information about the SAP gave me an account of how and why the top-secret programme had begun. As the American-led hunt for al-Qaida and Osama bin Laden began to stall, he said, it was clear that the American intelligence operatives in the field were failing to get useful intelligence in a timely manner. With the pressure mounting, some information was being delivered via the CIA by friendly liaison intelligence services - allies of the United States in the Middle East and south-east Asia - who were not afraid to get rough with prisoners. The tough tactics appealed to Rumsfeld and his senior civilian aides.
Rumsfeld then authorised the establishment of the highly secret programme, which was given blanket advance approval to kill or capture and, if possible, interrogate high-value targets. The SAP - subject to the defence department's most stringent level of security - was set up, with an office in a secure area of the Pentagon. The people assigned to the programme recruited, after careful screening, highly trained commandos and operatives from US elite forces - navy seals, the army's delta force, and the CIA's paramilitary experts.
"Rumsfeld's goal was to get a capability in place to take on a high-value target - a stand-up group to hit quickly," the former senior intelligence official told me. The operation had across-the-board approval from Rumsfeld and from Condoleezza Rice. Fewer than 200 operatives and officials, including Rumsfeld and General Myers [Chairman of the US Joint Chiefs of Staff], were "completely read into the programme", the former intelligence official said. "The rules are 'Grab whom you must. Do what you want.'"
One Pentagon official who was deeply involved in the programme was Stephen Cambone, the undersecretary of defence for intelligence. Cambone had worked closely with Rumsfeld in a number of Pentagon jobs since the beginning of the administration, but this office, to which he was named in March 2003, was new; it was created as part of Rumsfeld's reorganisation of the Pentagon. Known for his closeness to Rumsfeld, Cambone was a strong advocate for war against Iraq. He chafed, as did Rumsfeld, at the CIA's inability before the Iraq war to state conclusively that Saddam Hussein harboured weapons of mass destruction.
Early in his tenure, Cambone provoked a bureaucratic battle within the Pentagon by insisting that he be given control of all special-access programmes that were relevant to the war on terror. In mid-2003, the SAP was regarded, at least in the Pentagon, as one of the success stories of the war on terror.
"It was an active programme," the former senior intelligence official told me. "As this monster begins to take life, there's joy in the world. The monster is doing well - real well" - at least from the perspective of those involved who, according to the former officer, began to see themselves as "masters of the universe in terms of intelligence".
I was initially told of the SAP's existence by members of the intelligence community who were troubled by the programme's prima facie violation of the Geneva convention; their concern was that such activities, if exposed, would eviscerate the moral standing of the United States and expose American soldiers to retaliation. In May 2004, a ranking member of Congress confirmed its existence and further told me that President Bush had signed the mandated finding officially notifying Congress of the SAP.
The legislator added that he had none the less been told very little about the programme. Only a few members of the House and Senate leadership were authorised by statute to be informed of it, and, even then, the legislators were provided with little more than basic budget information. It's not clear that the Senate and House members understood that the United States was poised to enter the business of "disappearing" people.
The Pentagon may have judged the SAP a success, but by August 2003, the war in Iraq was going badly and there was, once again, little significant intelligence being generated in the many prisons in Iraq. The president and his national security team turned for guidance to General Miller, the "Gitmo" [Guantánamo] commander. Recounting that decision, one of the White House officials who had supported General Gordon's ill-fated effort to change prisoner policy asked me, rhetorically, "Why do I take a failed approach at Guantánamo and move it to Iraq?"
By the autumn of 2003, a military analyst told me, the extent of the Pentagon's political and military misjudgments in Iraq was clear. The solution, endorsed by Rumsfeld and carried out by Cambone, was to get tough with the Iraqi men and women in detention - to treat them behind prison walls as if they had been captured on the battlefields of Afghanistan. General Miller was summoned to Baghdad in late August to review prison interrogation procedures.
Rumsfeld and Cambone went a step beyond "Gitmoizing", however: they expanded the scope of the SAP, bringing its unconventional methods to Abu Ghraib. The commandos were to operate in Iraq as they had in Afghanistan. The male prisoners could be treated roughly and exposed to sexual humiliation.
"They weren't getting anything substantive from the detainees in Iraq," the former intelligence official told me. "No names. Nothing that they could hang their hat on. Cambone says, I've got to crack this thing and I'm tired of working through the normal chain of command. I've got this apparatus set up - the black special-access programme - and I'm going in hot.
"So he pulls the switch, and the electricity begins flowing last summer. And it's working. We're getting a picture of the insurgency in Iraq and the intelligence is flowing into the white world. We're getting good stuff."
Cambone then made another crucial decision, the former intelligence official told me: not only would he bring the SAP's rules into the prisons, he would bring some of the army military intelligence officers working inside the Iraqi prisons under the SAP's auspices.
"So here are fundamentally good soldiers - military intelligence guys - being told that no rules apply," the former official said.
In a separate interview, a Pentagon consultant, who spent much of his career directly involved with special-access programmes, spread the blame. "The White House subcontracted this to the Pentagon, and the Pentagon subcontracted it to Cambone," he said. "This is Cambone's deal, but Rumsfeld and Myers approved the programme." When it came to the interrogation operation at Abu Ghraib, he said, Rumsfeld left the details to Cambone. Rumsfeld may not be personally culpable, the consultant added, "but he's responsible for the checks and balances. The issue is that, since 9/11 we've changed the rules on how we deal with terrorism and created conditions where the ends justify the means."
According to interviews with several past and present American intelligence officials, the Pentagon's operation - aspects of which were known inside the intelligence community by several code words, including Copper Green - encouraged physical coercion and sexual humiliation of Iraqi prisoners in an effort to generate more intelligence about the insurgency. A senior CIA official confirmed the details of this account and said that the operation stemmed from Rumsfeld's long-standing desire to wrest control of clandestine and paramilitary operations from the CIA.
Who was in charge of Abu Ghraib - whether military police or military intelligence - was no longer the only question that mattered. Hard-core special operatives, some of them with aliases, were working in the prison. The military police assigned to guard the prisoners wore uniforms, but many others - military intelligence officers, contract interpreters, CIA officers, and the men from the SAP - wore civilian clothes. It was not clear who was who, even to General Karpinski, then the commander of the 800 military police brigade. "I thought most of the civilians there were interpreters, but there were some civilians that I didn't know," Karpinski told me. "I called them the disappearing ghosts. I'd seen them once in a while at Abu Ghraib and then I'd see them months later." The mysterious civilians, she said, were "always bringing in somebody for interrogation or waiting to collect somebody going out". Karpinski added that she had no idea who was operating in her prison syste m.
Military intelligence personnel assigned to Abu Ghraib repeatedly wore "sterile", or unmarked, uniforms or civilian clothes while on duty. "You couldn't tell them apart," a source familiar with the investigation said. The blurring of identities and organisations meant that it was impossible for the prisoners, or, significantly, the military policemen on duty, to know who was doing what to whom and who had the authority to give orders.
By last autumn, according to the former intelligence official, the senior leadership of the CIA had had enough. "They said, 'No way. We signed up for the core programme in Afghanistan - pre-approved for operations against high-value terrorist targets. And now you want to use it for cab drivers, brothers-in-law, and people pulled off the streets.'" The CIA balked, the former intelligence official said: "The agency checks with their lawyers and pulls out," ending those of its activities in Abu Ghraib that related to the SAP. (In a later conversation, a senior CIA official confirmed this account.)
The CIA's complaints were echoed throughout the intelligence community. There was fear the situation at Abu Ghraib would lead to the exposure of the secret SAP, and thereby bring an end to what had been, before Iraq, a valued covert operation. "This was stupidity," a government consultant told me. "You're taking a programme that was operating in the chaos of Afghanistan against al-Qaida, a stateless terror group, and bringing it into a structured, traditional war zone. Sooner or later, the commandos would bump into the legal and moral procedures of a conventional war with an army of 135,000 soldiers."
In mid 2003, Rumsfeld's apparent disregard for the requirements of the Geneva convention while carrying out the war on terror had led a group of senior military legal officers from the Judge Advocate General's (JAG) Corps to pay two surprise visits within five months to Scott Horton, who was then chairman of the New York City Bar Association's Committee on International Human Rights. "They wanted us to challenge the Bush administration about its standards for detentions and interrogation," Horton told me in May 2004. "They were urging us to get involved and speak in a very loud voice. [ ... ] The message was that conditions are ripe for abuse, and it's going to occur." The military officials were most alarmed about the growing use of civilian contractors in the interrogation process, Horton recalled. The JAG officers told him that, with the war on terror, a 50-year history of exemplary application of the Geneva convention had come to an end.
In July 2004, I again spoke to Scott Horton, who has maintained contact with a network of JAG lawyers. He told me that Rumsfeld and his civilian deputies had pressured the army to conclude the pending investigations by late August, before the Republican convention in New York. Horton added that the politics were blatant.
Pentagon investigations, he said, "have a reputation for tending to whitewash, but even taking this into account, the current investigations seem to be setting new standards". Rumsfeld's office had circumscribed the investigators' charge and also placed tight controls on the documents to be made available. In other words, Horton said, "Rumsfeld has completely rigged the investigations. My friends say we should expect something much akin to the army inspector general's report - 'just a few rotten apples'."
But General Taguba's highly critical internal investigation into military prisons in Iraq - which, together with the shocking photographs of prisoner abuse, sparked the Abu Ghraib scandal in April - amounted to an unsparing study of collective wrongdoing and the failure of army leadership at the highest levels. The picture Taguba drew of Abu Ghraib was one in which army regulations and the Geneva convention were routinely violated, and in which much of the day-to-day management of the prisoners was abdicated to army military intelligence units and civilian contract employees.
Rumsfeld's most fateful decision, endorsed by the White House, came at a time of crisis in August 2003 when the defence secretary expanded the highly secret SAP into the prisons of Iraq. The roots of the Abu Ghraib scandal therefore lie not in the criminal inclinations of a few army reservists, but in the reliance of George Bush and Donald Rumsfeld on secret operations and the use of coercion - and eye-for-an-eye retribution - in fighting terrorism.
· This is an edited extract from Chain of Command: The Road from 9/11 to Abu Ghraib, by Seymour M Hersh, published today by Penguin Press.