Scott Fenstermaker, a lawyer defending one of the men, told The Associated Press that they won’t deny their role, but will use the opportunity to “explain what happened and why they did it,” and they will provide “their assessment of foreign policy.” Fenstermaker reportedly met with his client, Ammar al Baluchi, a nephew of Khalid Sheikh Mohammed (KSM), at the Guantanamo Bay prison last week. Baluchi told him the men had discussed the trial among themselves.

Critics of the trial have complained, among other things, that KSM — who has boasted that he was the lead planner behind the 9/11 attacks, as well as many others — will use the opportunity to grandstand and spread terrorist propaganda. The alternative, however, would be to not allow them to speak at their own trial, which would hardly showcase the American principles of open government and fair trials that the attorney general presumably wants to highlight.

Justice Department spokesman Dean Boyd told the AP on Sunday that he’s not worried that the men will dominate the trial or be able to use it as a vehicle to win new recruits. “We have full confidence in the ability of the courts and in particular the federal judge who may preside over the trial to ensure that the proceeding is conducted appropriately and with minimal disruption, as federal courts have done in the past,” he said.

The Southern District of New York, where the Justice Department wants to hold the trial, is the most experienced of all U.S. federal courts in handling major international terrorism cases.

So it’s significant that today they’ve released a report calling on the United States to follow its legal obligation to prosecute the leaders in the U.S. government responsible for the “torture, cruel and inhuman treatment” of detainees during its own “war on terror.”

“Investigations and prosecutions should focus on the engineers of official policies that were the basis of illegal abuses, to send a clear signal that the absolute prohibition of torture and the ban on cruel and inhuman treatment will be respected by the United States,” the report said, adding that if the U.S. government fails to initiate prosecutions, then other countries will take up the cause. Italy, for example, recently convicted 23 Americans for their involvement in “extraordinary renditions.”

“Failing to hold accountable the architects and overseers of a policy of abuse undermines the U.S. justice system and the fundamental idea that law provides a check on power,” Alex Boraine, acting president of ICTJ, said in a statement today. “As we have seen in countless examples around the world, abuse of power by allowing torture and cruel treatment can tear down what the law and democracy have built.”

While there’s support among many Democrats for some sort of accountability, whether through criminal prosecutions or an independent truth commission, Republicans vehemently resist any suggestion that the Bush administration even did anything wrong.

Since Attorney General Eric Holder announced on Friday that the Justice Department would try the alleged 9/11 co-conspirators in a U.S. federal court in New York, some Republicans have denounced the move as an illegitimate attempt to put the Bush administration, rather than the terrorists, on trial.

“The government is going to try to put Khalid Sheik Mohammed on trial. Defense lawyers will try and put the government on trial,” former New York City Mayor Rudy Giuliani told Fox News.

Tom Ridge, head of the Department of Homeland Security during the Bush administration, added that any effort to use the 9/11 trial to “delve into a fishing expedition” to go after Bush officials is “wrong and unconscionable.”

Meanwhile, in The Wall Street Journal today, former Deputy Assistant Attorney General John Yoo — a potential target of any future criminal prosecution of Bush officials — attacked the decision to try the 9/11 detainees in federal court as a dangerous mistake. “The treatment of the 9/11 attacks as a criminal matter rather than as an act of war will cripple American efforts to fight terrorism,” Yoo wrote. “It is in effect a declaration that this nation is no longer at war.”

Vice Admirals William McRaven and Robert Harward (navy.mil)

Two senior military officers from the shadowy world of Special Operations are playing a large and previously unreported role in shaping the Obama administration’s Afghanistan and Pakistan strategy, a move that underscores that the internal debate has moved past a rigid choice between expansive missions to provide security for Afghan civilians and narrowly tailored missions to find and kill terrorists.

Image by: Matt Mahurin

Debate about a “purely counterterrorism strategy” advocated by Vice President Joseph Biden was “bounced around at one point, but that has been cast aside,” said a National Security Council staffer who attends the meetings and who asked for anonymity because the debate is still ongoing, “mostly because JSOC has said ‘We’re going to do this anyway.’ And it’s not like they’re going to be in a supporting role.” Biden’s advice, which had practically no support from the armed services, was that the military should shy away from protecting the Afghan people and helping build Afghan governing institutions, and instead focus on the JSOC specialties of going after terrorists directly.

Yet the fact that JSOC veterans like McRaven, Harward and McChrystal favor an overall counterinsurgency strategy with a counterterrorism component demonstrates that the military no longer believes distinguishing between the two is tenable in the Afghanistan war. “Special Operations Forces that were traditionally used for counterterrorism better understand how their capabilities fit into a counterinsurgency campaign than perhaps they did when the wars in Iraq and Afghanistan began,” said Andrew Exum, a veteran of both wars and a fellow at the Center for a New American Security who over the summer advised McChrystal in a review of Afghanistan strategy.

More directly, McRaven and Harward share a professional fraternity with McChrystal. Before McRaven took over JSOC — an entity that operates almost entirely in secret — McChrystal ran it for five years, supervising stealthy teams in Afghanistan and Iraq that tracked down and killed senior terrorists like al-Qaeda in Iraq leader Abu Musab al-Zarqawi. One of McChrystal’s deputies during that period was Harward, and the bonds between the officers remain strong. “General McChrystal and Vice Admirals McRaven and Harward have established relationships through the special operations community,” said McChrystal’s spokesman, Air Force Lt. Col. Tadd Sholtis.

In his Afghanistan review, McChrystal said that a key goal for him would be to increase coordination between his NATO command and the independent command of JSOC, which suggested that the dichotomy between using Special Operations Forces for counterterrorism and conventional forces for counterinsurgency was eroding. “One of General McChrystal’s priorities is seeking greater unity of effort across all military activities in Afghanistan, which includes regular interaction with ISAF Joint Command, regional, and task force commanders,” Sholtis said, using the acronym for NATO’s military command in Afghanistan.

As a result, McChrystal is turning to McRaven and Harward for critical tasks in Afghanistan. McRaven runs a secretive detachment of Special Forces known as Task Force 714 — once commanded by McChrystal himself — that the NSC staffer described as “direct-action” units conducting “high-intensity hits.” In an email, Sholtis said that because Task Force 714 was a “special ops organization” he “can’t go into much detail on authorities, etc.” But the NSC staffer — who called McRaven “McChrystal Squared” — said Task Force 714 was organized into “small groups of Rangers going wherever the hell they want to go” in Afghanistan and operating under legal authority granted at the end of the Bush administration that President Obama has not revoked.

In a move signaling his own importance to McChrystal, Harward will arrive in Afghanistan later this month to command a new task force, known as Task Force 435, that will take charge of detention facilities in Afghanistan, “primarily the new one at Bagram that will open this month,” Sholtis said. In his famous August strategy review, McChrystal wrote that detention operations are “critical to successful counterinsurgency operations” and need to work toward “the long-term goal of getting the U.S. out of the detention business” through transition to Afghan control — a counterinsurgency task not traditionally given to a Special Operations veteran like Harward. McChrystal’s strategy recommended creating a new command, which Harward will now lead, of “approximately 120 personnel” focused on “defeat[ing] the insurgency through intelligence collection and analysis,” prisoner de-radicalization, and working with the Afghan corrections apparatus to “employ best correctional practices [and] comply with Afghan laws.”

Last month, McChrystal delivered a request for additional troops to the Obama administration for the Afghanistan war. The request, structured as a palette of options from which the president could choose, included so-called “high-risk” options of numbers as low as 10,000 new combat troops and a so-called “low-risk” option of an 85,000-troop reinforcement. Participants in the discussions have said on background that they viewed the 85,000-troop request as an unserious option meant to clear the way for Obama to approve a middle course of around 40,000 new troops.

But while the media has typically discussed a counterterrorism approach in Afghanistan as a low-troop option, the two counterterrorism-experienced admirals are both said to favor “as many troops as we can muster,” according to the NSC staffer, who specified that McRaven and Harward were pushing for McChrystal’s largest resource option of 85,000 new troops. A senior administration official who requested anonymity said that the Obama administration was not considering a troop escalation of more than 40,000 combat troops. (It is possible that support and logistical units could increase any troop number that the administration cites as the total estimate, as happened when President Bush announced a troop surge to Iraq of about 20,000 troops in January 2007 but about 28,000 new troops actually deployed.) On Saturday, McClatchy Newspapers reported that Obama is leaning toward an increase of 34,000 troops. An announcement is expected shortly after Obama returns from a trip to Asia on Nov. 20.

The advice of McRaven and Harward to the White House strategy review, the staffer said, was to push for a “heavy, heavy, heavy COIN [counterinsurgency] presence” in select population centers like the capitol city of Kabul, while relying on new or expanded counterterrorism units like Task Force 714 for hunting and killing terrorists outside of those population centers — particularly in areas like the porous border between Afghanistan and Pakistan, a key transit point for Taliban and al-Qaeda-affiliated insurgents.

“They’re focusing on the main population centers that they think they can save with manpower on the ground, and everything else will be crossborder,” the NSC staffer said. An executive order signed by George W. Bush in mid-2008 and not revoked by Obama authorized special forces to, in some cases, cross the Afghan border into Pakistan in pursuit of top insurgent targets. “JSOC is already ramping up for that. … These are what they call kinetic, direct-action task forces,” military terminology to describe intense fighting with small units. The prospect of crossborder raids by U.S. military forces has been greeted in Pakistan as an offensive violation of Pakistani sovereignty.

The two admirals are also said to be influential with Jim Jones, Obama’s national security adviser. McRaven, at least, worked with Jones in a previous assignment, commanding Special Operations Forces in Europe in 2006 while Jones was ending his tour of duty as NATO commander. “A lot of people think Jones is not taking military counsel, that he’s anti-surge, he’s this, he’s that,” said the NSC staffer. “In reality, he’s taking counsel from pretty much a purely military palette of people, including McRaven.”

Asked about McRaven’s role in the strategy debates, Ken McGraw, a spokesman for the U.S. Special Operations Command, which oversees JSOC, said, “It would not be appropriate for us to comment on who may or may not be involved in discussions at the White House or what may or may not have been the substance of conversations at the White House.” A spokesman for the Joint Forces Command did not return repeated phone and email messages seeking comment about Harward. A spokesman for the National Security Council did not respond to a request for comment about Jones’ interactions with Harward and McRaven.

The bonds between McChrystal and the two admirals may not have been widely known because of the secrecy surrounding almost all aspects of JSOC, but the Obama administration is getting a sense of their strength. “Harward and McChrystal were running JSOC,” said the NSC staffer, “and all three of them [have been] in the nether regions forever.”

The Justice Department has said it will not appeal the Sept. 17 order of Judge Judge Colleen Kollar-Kotelly, who granted Al Rabiah’s petition for release in a scathing ruling that criticized the U.S. government and described how interrogators used coercion and abuse to extract false confessions from him. Al Rabiah’s lawyer, David Cynamon, has demanded an investigation from the Senate Armed Services Committee and the inspectors general of the Defense and Justice departments, as well as from Attorney General Eric Holder. He has not received a response.

The situation sounds reminiscent of the case of Mohammed Jawad, an Afghan teenager who a military commission judge had similarly ruled was “tortured” and coerced into confessing to throwing a grenade at U.S. soldiers. The bulk of his case was based on his coerced statements, and was eventually thrown out by the military commissions and dropped by the Justice Department.

Jawad’s military lawyer, David Frakt, complained repeatedly to senior Defense Department officials that he believed U.S. military personnel had committed war crimes in connection with his client. As TWI documented in September, Frakt never received a response, and the matter appears never to have been investigated.

Jawad is now back in Afghanistan. Al Rabiah’s future, however, remains in doubt. Although the Justice Department has said it won’t appeal his order of release, a military commission case is still pending against him.

“Some have opposed the closing of Guantanamo because they believe there is no viable alternative approach to handling terrorist suspects,” said Thomas Pickering, former Undersecretary of State for Political Affairs and former U.S. Ambassador and Representative to the United Nations, in a statement released yesterday. “This declaration presents a careful plan for finally bringing terrorists to justice in full keeping with our Constitution, as well as for protecting our nation’s values, security, and commitment to our international obligations.”

The bipartisan declaration, coordinated by Human Rights First and the bipartisan Constitution Project, opposes indefinite detention without charge and supports the trial of all terrorism suspects in federal courts.

Yesterday, Jonathan Hafetz, the American Civil Liberties Union lawyer who represented Al-Marri in his challenge to military detention, told The New York Times that the sentence by a federal judge was “a powerful reminder that America’s civilian courts can deliver justice even in the most challenging circumstances.” But David Rivkin, a former Reagan-era Justice Department official and strong supporter of military commissions to try suspected terrorists had a different take. Criminal courts are “ill-suited” to terror cases because the sentences are “a crap-shoot,” he said, adding that military commissions “arrive at a better judgment, being comprised of warriors, as to what level of danger the person poses.”

Al-Marri, a legal U.S. resident living in Peoria, Ill., before his arrest in late 2001, spent almost six years in a U.S. Navy brig in South Carolina without charge, mostly in isolation. Shortly before his case questioning the legality of his indefinite detention on U.S. soil was set to reach the Supreme Court,  the Obama administration transferred him to civilian custody, incarcerated him in a federal prison and prepared for his trial in federal court. But prosecutors agreed to accept a plea bargain, in which Al-Marri admitted that he’d been ordered by al-Qaeda official Khalid Shaikh Mohammed to move to the United States from his native Qatar and await instructions. Al-Marri moved his wife and five children to Peoria and he enrolled at Bradley University, where he had studied earlier. He admitted in his plea that he “researched online information related to various cyanide compounds” and communicated with other al-Qaeda operatives.

When al-Marri was arrested in December 2001 on charges of financial fraud, he hadn’t carried out any terrorist acts. But 18 months after his arrest, the government dropped the criminal charges and named al-Marri an “enemy combatant,” which in the Bush administration’s view, gave the government the right to hold him indefinitely in military custody. He remained at the Navy big, without charge or trial, until February.

Whether it’s legal for the United States to imprison indefinitely a lawful U.S. resident in a military prison on U.S. soil remains an open question, largely because the Obama administration did not give the Supreme Court an opportunity to rule on it. That may have been a strategic move designed to leave open the possibility of using that power again, particularly since President Obama promised to close the Guantanamo Bay prison by January 2010, but hasn’t yet decided what to do with many of the detainees imprisoned there.

For Al-Marri, however, it means he will now serve another eight years in prison. (He faced up to 15 years, but the judge agreed to consider the time he’d already served.) Al-Marri yesterday tearfully apologized for helping al-Qaeda and said he no longer wants to harm the American people.

Notwithstanding Rivkin’s criticism of the federal court’s sentence, it’s worth noting that in the two contested cases where terror suspects were sentenced by military commissions for similarly assisting al-Qaeda, both received lighter sentences. Salim Hamdan, for example, Osama bin Laden’s driver, was sentenced by a military jury of “warriors” to just five and a half years in prison, and given credit for time served. He’s already back home in Yemen. In the other case, Australian David Hicks pleaded guilty to providing material support for terrorism and was sentenced to only nine months in prison. A former kangaroo-skinner, Hicks is now home.

At the time, the report didn’t get a huge amount of attention. But the Justice Department got defensive, and shortly before TRAC posted the report on its Website, the department, which had received an early copy of the report from TRAC, sent out a public attack on the organization. DOJ said it could not verify TRAC’s data or conclusions because “they routinely differ from other data and statistics reflected in Justice Department reports, U.S. Sentencing Commission data or U.S. Courts Data. Furthermore, TRAC has had a pattern of omitting certain statistics, resulting in misleading information regarding prosecutions.”

Now, TRAC has shot back, demanding a retraction — and re-issuing the critical report on terror prosecutions, along with its latest press release about DOJ’s complaints.

“All of the reports and data we post on our web sites are based on very detailed material we obtain from government itself, generally under the Freedom of Information Act,” reads the letter, signed by TRAC’s directors. “Among others, TRAC’s data sources include various Justice Department divisions and agencies, the Office of Personnel Management, the Department of Homeland Security, the Internal Revenue Service, the Administrative Office of the United States Courts.” What’s more, they wrote, the Government’s own General Accountability Office in a recent report favorably cited TRAC’s report on the immigration courts. And “[v]arious inspector general offices, the OMB, the Supreme Court and other government bodies subscribe to our data services.”

The letter goes on to describe the range of multi-level data checks and double-checks the organization uses, and noted that its report on the Justice Department’s botched efforts to categorize and prosecute terrorism was based completely on data obtained from the government itself.

Given that the government is the original source for all of the data presented in our reports and the extensive and varied efforts to check and double check the material before it is passed along to the public, we were astonished by the statement your Public Affairs Office provided reporters several days before the posting our latest report on September 27 . In that report we examined and compared data from the U .S. Courts, the National Security Division, and the EOUSA on the government’s record on criminal enforcement of the country’s terrorism laws . (See http ://trac .syr.edu/tracreports/terrorisml215/) TRAC had provided your office early access to our embargoed study to enable the Justice Department to have an informed comment about the questions it raised. Instead, the short statement asserted that the Department “stands by its record” and then went into an ad hominem attack on TRAC. And contrary to the initial claim, the statement provided no concrete information about the department’s record.

Personally, I’ve reviewed and relied on TRAC data myself, as have many other reporters in a broad range of respected news organizations. It’s often not that flattering to the federal government, but then, flattery really isn’t the job of a data analysis and open-government organization. TRAC has been providing an enormous and unmatched service to news organizations, scholars, nonprofits and businesses for years. If the Justice Department is going to publicly attack the group’s efforts, to have any credibility it ought to be able to use the same level of specificity to back up its complaints as TRAC uses to document its data analyses.

Take the nomination of Dawn Johnsen, Obama’s pick to the head the Office of Legal Counsel, which provides critical legal advice to the president. The OLC, of course, is the same office that got into all sorts of trouble under the Bush administration, and several of its former lawyers are the subject of a much-awaited report from the Justice Department’s Office of Professional Responsibility, which reportedly has concluded that the lawyers violated legal ethics in recommending President George W. Bush permit the abuse of detainees and other suspensions of constitutional rights in the so-called “war on terror.” That report, although reportedly drafted last year, is apparently still being reviewed by the very lawyers it apparently censures, and is likely being edited and potentially watered-down as a result.

But even as President Obama says he wants to look forward, not back, he’s not exactly pushing very hard to get a new director for that Office of Legal Counsel confirmed so she can lead his legal department on its forward march. The nomination of Johnsen, a highly-respected law professor who was second-in-command at OLC under President Clinton, was voted out of the Senate Judiciary Committee with full Democratic support in March. She has yet to get a full Senate vote — though back in May, Attorney General Eric Holder called her confirmation “probably my top priority.”

Republicans have made clear that they’ll fight the Johnsen nomination and slow the voting process down, even though it seems clear Democrats have enough votes to confirm her. GOP lawmakers have painted Johnsen as a radical for publicly challenging some of the advice given by the Office of Legal Counsel during the Bush years. And during her confirmation hearings, some Republicans seized on the fact that Johnsen was a lawyer for the National Abortion Rights Action League (NARAL) early in her career, and 20 years ago was one of ten co-authors on a brief in which there was a footnote that some Republicans found objectionable.

With the health care debate ongoing and the president staking much of the success of his first term on its outcome, the Obama administration may not have much interest in pushing the Johnsen nomination just now, since Republicans will likely insist on cloture — and the 30 hours of debate that comes with it — which would detract from the president’s current mission.

As a result, according to the White House and Senate staffers, a vote on the Johnsen nomination isn’t even on the calendar yet.

“Clearly, Al Qaeda is a threat not only to the U.S. homeland and American interests abroad, but it has a murderous agenda,” one senior administration official said in an interview initiated by the White House on Wednesday on the condition of anonymity because the strategy review has not been finished. “We want to destroy its leadership, its infrastructure and its capability.”

The official contrasted that with the Afghan Taliban, which the administration has begun to define as an indigenous group that aspires to reclaim territory and rule the country but does not express ambitions of attacking the United States. “When the two are aligned, it’s mainly on the tactical front,” the official said, noting that Al Qaeda has fewer than 100 fighters in Afghanistan.

Another official, who also was authorized to speak but not to be identified, said the different views of Al Qaeda and the Taliban were driving the president’s review. “To the extent that Al Qaeda has been degraded, and it has, and to the extent you believe you need to focus on destroying it going forward, what is required going forward?” the official asked. “And to prevent it from having a safe haven?”

My emphasis. The administration is now considering two alternative propositions that require delicate assessment.

The first is, as the piece reports Richard Holbrooke is arguing, whether the Taliban would allow al-Qaeda back into Afghanistan if it took control. And there, the available evidence appears to support Holbrooke’s contention that it wouldn’t. Taliban elements have free reign in many areas of southern and eastern Afghanistan, yet the administration is contending that there are only an estimated 100 al-Qaeda operatives in Afghanistan.

Now, even a Taliban fulsomely backed by Pakistani intelligence couldn’t take control of the entire country, so it’s unlikely that any Taliban “victory” scenario is going to end up with the Taliban and its affiliates running all of Afghanistan, and accordingly the administration will have to ask whether quantitative gains in Taliban control would lead either al-Qaeda or the Taliban to change the current dynamic. What’s more, it has to ask whether, say, the upcoming Pakistani military offensive in Waziristan would make al-Qaeda’s senior leadership look for safer haven.

The danger for the administration is clear: premising a strategy on an optimistic scenario or a dimunition of danger is both substantively and politically troublesome. That’s not to say it’s necessarily wrong, but it’s what Gen. McChrystal would call a high-risk option.

The second consideration is whether the public will support a war that really does decouple al-Qaeda from the Taliban. So far the polling doesn’t suggest the public will. But there the considerations are actually much easier: if the public doesn’t support such a war and such a decoupling is necessary, then it’s the war that should be scaled down. Any temptation to overstate the relationship between the Taliban and al-Qaeda in order to sustain support for the war will be a disaster. But that’s too often the kind of inertial thinking that takes over Washington at war.

Rajiv Chandrasekaran’s behind-the-scenes account of the Afghanistan-Pakistan debate within the administration, continuing through the present strategy review, exposes the fissures that quote concealed. It’s a masterful piece, and its central question is whether the Obama administration — indeed, whether President Obama — understood the costs entailed by embracing counterinsurgency. Damaging quote number one:

“It was easy to say, ‘Hey, I support COIN,’ because nobody had done the assessment of what it would really take, and nobody had thought through whether we want to do what it takes,” said one senior civilian administration official who participated in the review, using the shorthand for counterinsurgency.

But there was an assessment. That was the white paper, the result of a weeks-long process chaired by Brookings’ Bruce Riedel and co-chaired by Flournoy and special representative Richard Holbrooke, with contributions from many others, including lead skeptic Tony Blinken, Vice President Biden’s longtime foreign policy adviser. That paper’s embrace of a rather fulsome counterinsurgency strategy — fulsome in the sense of its focus on far more than just military measures, but governance and development and communications and regional attitudes as well — led lots of people to believe that the policy was set. Administration officials, that day and for months after, referred the white paper when questions about the strategy got raised.

Someone who read the white paper was Gen. Stanley McChrystal. That’s why to nearly everyone who asked, he portrayed his approach as his take on what would be required to flesh out Obama’s strategy — which he thought was the white paper. As he told Frontline for a forthcoming documentary, “When I hear the president talk about the commitment to Afghanistan as he did in the spring when he announced more forces, I believe that most Americans probably recognize or share his resolve.” And the feeling that the White House might no longer have that commitment, after placing McChrystal in Afghanistan precisely to design and conduct a counterinsurgency campaign, is why some in uniform have been thrown for a loop by this process. I have heard a great deal of frustration from civilians that they are not sure whether, in their day-to-day work, they are actually executing the president’s strategy, as that strategy may change. Damaging quote number two:

“We were operating under the assumption that when they said COIN, that’s what they meant,” said a senior U.S. military official in Afghanistan, “and they were serious about committing the necessary resources.”

It’s one thing to rethink basic assumptions, and to use setbacks as an opportunity to examine whether the entire enterprise is on a secure intellectual footing. But it’s another to adopt that footing without thinking through its implications — while assuring everyone that you had.