With just over two months to go until President Obama's deadline for the closure of Guantanamo, the administration has finally woken up to the necessity of actually doing something to facilitate the prison's closure by announcing on Friday that Khalid Sheikh Mohammed and four other prisoners accused of involvement in the terrorist attacks of September 11, 2001, will be brought to New York to face federal court trials.

Despite the fact that the "war on terror" was launched over eight years ago to pursue those responsible for the 9/11 attacks, and despite the fact that Attorney General Eric Holder noted, in a statement announcing the trial, that the opportunity for the relatives of the 9/11 victims "to see the alleged plotters of those attacks held accountable in court" had been "too long delayed," Republican critics immediately leapt on the announcement, with Senate Minority Leader Mitch McConnell describing it as "a step backwards for the security of our country" that "puts Americans unnecessarily at risk."

McConnell, former Vice President Dick Cheney, and others who have spent most of the year shamelessly playing the fear card about bringing Guantanamo prisoners to the US mainland to face trials ought to be ashamed of themselves, as there is no reason to delay justice any longer in the case of these men, and every reason to decry the fact that, instead of being prosecuted shortly after their capture, they were diverted into a lawless program of incommunicado detention and torture that threatened to derail the possibility that they could be brought to justice at all.

In the case of Khalid Sheikh Mohammed, for example, the decision to prosecute him in a federal court comes over six years late. Despite having confessed to his involvement in the 9/11 attacks  to an al-Jazeera reporter before his capture by US forces in March 2003, he was held for three and a half years in secret prisons run by the CIA, where he was subjected to torture (including waterboarding, a form of controlled drowning), in a violent and misguided attempt to secure "actionable intelligence." Instead of achieving its desired result, this vile program appears to have prevented no actual planned terrorist attack, and led only to the generation of countless false leads, which wasted the resources of the intelligence services, and also, of course, led to the creation of a global network of secret prisons in which, distressingly, torture only begat more torture.

Khalid Sheikh Mohammed is the most notorious of the five men, but the others - Ramzi bin al-Shibh, Mustafa al-Hawsawi, Ali Abdul Aziz Ali and Walid bin Attash - were also tortured in secret CIA prisons for up to four years, and, as with KSM, the decision to try them in federal courts is most noteworthy for finally bringing to an end the scandalous flight from justice and the law that led to their secret detention and torture.

The Problems With the Military Commissions

However dismal and compromised this story is, it at least has more to recommend it than the simultaneous announcement that five other prisoners will not face federal court trials, but will, instead, face trials by military commission. This alternative judicial system - for "terror suspects" only - was set up by former Vice President Dick Cheney in in November 2001, and struggled to establish anything resembling legitimacy throughout its seven-year existence, securing only three dubious verdicts, and attracting ferocious opposition from its own government-appointed military defense attorneys and also from a number of prosecutors who resigned, including Lt. Col. Darrel Vandeveld and the former chief prosecutor, Col. Morris Davis, who all recognized that it was rigged to disguise the use of torture and to secure convictions.

Amended by the Obama administration and by Congress, the commissions still lack legitimacy, with gray areas involving the admissibility of coerced confessions and hearsay evidence, and a widespread conviction amongst legal experts that federal courts have a proven track record in dealing with terrorism cases that the commissions can never hope to emulate.

Moreover, although Eric Holder claimed on Friday that the revised commission process "will be fair and that convictions obtained will be secure," he neglected to mention that, this summer, senior administration officials conceded that the proposed charge of material support for terrorism - a longtime mainstay of the commissions from 2006 onwards, when they were revived by Congress after being ruled illegal by the Supreme Court - may well be subject to successful court appeals. What makes the decision to proceed with the commissions even more ludicrous is that the government also admits that no such problems exist with prosecuting material support for terrorism in federal courts.

In addition, the very existence of a two-tier judicial system should be enough to set alarm bells ringing, as it suggests - quite correctly, I believe - that the government is hedging its bets when it comes to justice, proceeding with federal court trials when it believes that it will secure successful prosecutions, and reserving the commissions for other cases in which it fears that it may fail, because the evidence is not only contaminated by the use of torture, but is also weak.

In his announcement about the trials, Eric Holder stated that the "decision as to whether to proceed in federal courts or military commissions was based on a protocol that the Departments of Justice and Defense developed and that was announced in July," adding that the protocol "sets forth a number of factors - including the nature of the offense, the location in which the offense occurred, the identity of the victims, and the manner in which the case was investigated - that must be considered." The process has, therefore, been presented as being based on clear-cut decisions - whether the alleged offenses took place on the US mainland (federal court trials) or elsewhere (military commissions) - but, in reality, Holder let slip that the decisions would be based on whether or not the government thinks it will secure victory. The key is that phrase, "the manner in which the case was investigated"; in other words, how the supposed evidence was gathered.

I've been railing against the proposed revival of the commissions since May, when President Obama first announced them in a major speech on national security, and I remain as confused and depressed about the proposals as I did back then. Glenn Greenwald has also been implacably opposed to the proposals, and on Friday he succinctly summed up the significance of the government's failure to hold only federal court trials as follows: "A system of justice which accords you varying levels of due process based on the certainty that you'll get just enough to be convicted isn't a justice system at all. It's a rigged game of show trials."

The government has not yet announced how many of the remaining 215 Guantanamo prisoners will be put forward for trials - either in federal court or by military commission - but ProPublica reported on Friday that, although "Justice Department officials said the cases of 40 detainees have been referred to government prosecutors for possible prosecution," another administration official conceded that "it was unlikely that charges would be brought against more than 30." This figure of a maximum of 40 prisoners is somewhat encouraging, as it corresponds with the numbers quoted in intelligence reports over the years, but the government is not off to an encouraging start, because, beyond the five men put forward for the 9/11 trial, the choice of the five other men put forward for trials by military commission - all of whom were previously charged under the Bush administration - is disheartening, to say the least.

The Five Prisoners Put Forward for Trial by Military Commission

One is Omar Khadr, the Canadian who was just 15 years old when he was seized after a firefight in Afghanistan in July 2002. Khadr should have been treated as a juvenile prisoner, and rehabilitated rather than punished, but he was subjected to appalling brutality, even though, to this day, the evidence suggests that he was not responsible for the crime for which he will be charged - the killing of a US soldier with a grenade - as, at the time, he was face down and unconscious  under a pile of rubble. In addition, it remains as doubtful as it always has that there was anything extraordinary about the context of his capture (as part of a group of men engaged in combat in a war zone), and that attempts to imbue it with anything related to terrorism are simply misguided.

Khadr's case is undoubtedly the most disappointing of the five, but the other four cases are also troubling, firstly because there appears to be no justifiable basis for not pursuing them in federal courts, and, in some cases, because the very basis for prosecution seems to be in doubt.

In the case of Abdul Rahim al-Nashiri, a "high-value detainee" seized in the United Arab Emirates in November 2002, and held in secret CIA prisons for nearly four years, the main problem is that he, along with Khalid Sheikh Mohammed and Abu Zubaydah, was waterboarded in US custody, and claimed, in his tribunal at Guantanamo in 2007, that he had made false allegations because he was tortured. He said that he made up stories tying him to the bombing of the USS Cole and confessed to involvement in several other plots - the attack on the USS Limburg, other plans to bomb American ships in the Gulf, a plan to hijack a plane and crash it into a ship and claims that Osama bin Laden had a nuclear bomb - in order to get his captors to stop torturing him. "From the time I was arrested five years ago," he said, "they have been torturing me. It happened during interviews. One time they tortured me one way, and another time they tortured me in a different way. I just said those things to make the people happy. They were very happy when I told them those things."

Moreover, as his attorney, Nancy Hollander, explained on Friday (as reported on Daily Kos ), "his case was first investigated as a criminal case, and the only reason to try him in a military commission is that they do not have the evidence to go to a legitimate court."

The other three are not even accused of involvement in specific attacks. Ibrahim al-Qosi, a Sudanese prisoner who was charged in the commissions' first incarnation in 2004 and again in 2007, was only finally arraigned on November 19, 2008, when the major claim against him - that he was responsible for al-Qaeda's payroll in Khartoum, before Osama bin Laden and his entourage moved back to Afghanistan in 1996 - was dropped by the government, and all that remained were claims that he worked at an al-Qaeda compound from 1996 to 1998, that he fought "as an al-Qaeda mortar man near Kabul from 1998 to 2001" and that he sometimes worked as a driver and bodyguard for bin Laden.

At the arraignment, al-Qosi's civilian lawyer, Lawrence Martin, declared that his client, "far from being a war criminal, was a cook," adding, "He was not even a cook for bin Laden, but a cook for a compound where bin Laden was sometimes a visitor." This position is also maintained by his military defense lawyers, including Maj. Todd Pierce, who visited Sudan over the summer to meet al-Qosi's family, and it seems, therefore, to cast al-Qosi in a similar role to that of Salim Hamdan, a Yemeni who was one of bin Laden's drivers in Afghanistan. Hamdan received a meager sentence after his trial by military commission in August 2008, when the military jury threw out the conspiracy charge against him, accepting that he knew nothing about the workings of al-Qaeda.

Ahmed al-Darbi, a Saudi who was seized on arrival in Azerbaijan in June 2002 and "rendered" to US custody in Afghanistan two months later, is accused of plotting to attack a ship in the Strait Of Hormuz, meeting Osama bin Laden and attending a training camp in Afghanistan, but in September, at one of the last pre-trial military commission hearings before Friday's announcement, his civilian lawyer, Ramzi Kassem, urged that all of the 119 statements that al-Darbi made to interrogators should be ruled out, because they were obtained through the use of torture and abuse, including beatings, threats of rape, sensory deprivation, sleep deprivation and sexual humiliation, both at Bagram, where al-Darbi was held for eight months, and at Guantanamo (a full statement by al-Darbi is available here ). At the time, the judge in his case, Army Col. James Pohl, reserved judgment on Kassem's request, but it is clear that these unresolved issues will surface at al-Darbi's trial, and it is difficult to see how they can easily be brushed aside.

The last man to be put forward to face a trial by military commission is Noor Uthman Muhammed, also from Sudan. On May 23, 2008, Muhammed was charged with conspiracy and providing material support for terrorism, based on allegations that he served as the deputy emir of the Khaldan training camp in Afghanistan from 1996 to 2000, when the camp was closed, that he served as an instructor at the camp and that he delivered a fax machine to Osama bin Laden at a training camp in 1999.

Noticeably, in his tribunal at Guantanamo in 2004, Muhammed did not deny that he was sometimes involved in the administration of the camp, but he insisted that Khaldan was "a place to get training" that had nothing to do with either al-Qaeda or the Taliban. "People come over to that camp, train for about a month to a month and a half, then they go back to their hometown," he said, adding that what the people did with the training they received was their own business.

Behind the Facade

This may appear to have been an evasive explanation on Muhammed's part, but, in fact, the whole story of Khaldan is dangerously complicated for the government, not merely because these claims have been aired before, and because it appears that the camp was closed in 2000 because its emir, Ibn al-Shaykh al-Libi, refused to cooperate with bin Laden, but also because both al-Libi and Khaldan's gatekeeper, Abu Zubaydah, are people that the government want to keep quiet about.

Al-Libi, perhaps the CIA's most notorious "ghost prisoner," was rendered to Egypt, where, under torture, he produced a false confession about connections between al-Qaeda and Saddam Hussein that was used to justify the invasion of Iraq in March 2003. Returned to Libya in 2006, after spending over four years in a series of proxy prisons or prisons run by the CIA, he died in mysterious circumstances in May of this year.

Zubaydah, who is still in Guantanamo, but has not been put forward for a trial, was the first prisoner to be subjected to the torture techniques - including waterboarding - that were developed for use on the "high-value detainees," and the problem for the government is not that officials have to build a case against him while avoiding all mention of the use of torture, but that his role was massively overstated, and he appears to be too psychologically damaged to be put on trial.

It is, therefore, difficult to see how Noor Uthman Muhammed's trial by military commission can proceed without focusing on the stories of Ibn al-Shaykh al-Libi and Abu Zubaydah, but even if it does prove possible, the very mention of these men points to some dark truths that lie behind Friday's announcement: that other supposedly "high-value detainees," in addition to Abu Zubaydah, have not been put forward for trial, that the question of what to do with Zubaydah, a Palestinian, appears to present an insoluble problem, and that the murky world of proxy prisons and CIA prisons, and the torture regime that involved at least 150 prisoners (and maybe many more) is barely hidden behind Eric Holder's decision to announce the trials of the ten men mentioned above. Even on this limited basis, the pursuit of justice is contaminated, and the question of accountability - deliberately ducked by the Obama administration - seems unlikely to go away.

Perhaps, as some commentators have suggested, the Bush administration will be under the spotlight as much as Khalid Sheikh Mohammed in the forthcoming trials, and it seems probable, therefore, that questions about the Bush administration's responsibility for torture and abuse  will also leak out in the trials by military commission, and will remain, like a guilty secret waiting to be revealed, in the cases of many of the other men at Guantanamo, whose fates have yet to be decided.

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