Emanuel’s back-room dealings with Graham represent a little-noticed element of President Barack Obama’s gradual retreat from promises to rely on traditional civilian and military courts as the best way to bring alleged terrorists to justice and to close the Guantanamo Bay prison.

Though Emanuel’s defenders insist that he has been loyal to the administration’s decisions once they’ve been made, some evidence suggests that he continued to encourage Graham to resist politically sensitive judgments, such as Attorney General Eric Holder’s decision to try five alleged 9/11 plotters in civilian court rather than before military commissions.

For instance, the Washington Post reported that after losing out to Holder on the internal debate last fall, Emanuel tried to keep tabs on the process through Graham and apparently used profane language to suggest that the South Carolina Republican drive home to the White House how much damage Holder’s decision had caused.

Graham told the Post that Emanuel would "say: 'How's it going? Did you tell them they were going to lose you?' And in terms a sailor could understand."

The seeds of the Emanuel-Graham collaboration and Obama’s policy reversals can be traced back to the weeks after Obama’s election when the President-elect met with Graham and Sen. John McCain, Obama’s defeated presidential rival, at the transition headquarters in Chicago in December 2008. The goal was a bipartisan approach to the dilemma of Guantanamo detainees.

Obama told Graham, a former judge advocate general in the military reserves, that he needed his help in closing Guantanamo and put him in touch with Emanuel about working on a bipartisan plan to turn that vision into a reality, the Post reported.

Emanuel and Graham did speak, and Emanuel, known as a hard-charging political dealmaker, soon realized that winning Graham's support as well as the support of other Republicans to shutter Guantanamo would not be possible unless self-professed 9/11 mastermind Khalid Sheikh Mohammed (KSM) was prosecuted before a military commission.

However, in his first days in office, President Obama focused on fulfilling his campaign promise to overturn many of Bush’s “war on terror” policies.

Obama ruled out abusive interrogations and struck down some of Bush’s secrecy edicts. Obama also issued an executive order halting the military commissions at Guantanamo, while setting up a task force and ordering a review of the more than 200 cases there to determine which detainees should face criminal prosecution as part of a larger effort to permanently close the facility by January 2010.

In April 2009, Obama also overruled CIA Director Leon Panetta and sided with Attorney General Holder in releasing the contents of the Bush administration’s memos that had justified the use of torture against alleged terrorists.

The Pressure Mounts

Soon, however, Obama was coming under fierce attack from former Vice President Dick Cheney and other Republicans who claimed that the new President was putting the nation at greater risk of terrorist attack while also putting into legal jeopardy CIA and Justice Department personnel who had been following orders in implementing the interrogation policies.

Obama reacted to these broadsides by shifting direction. Under pressure from Graham and other members of Congress, Obama flip-flopped on an agreement to disclose photographs depicting U.S. soldiers abusing prisoners in Iraq and Afghanistan.

Then, on May 15, 2009, after what three sources described as months of pressure from Defense Department officials – as well as from Graham and the Republicans – Obama announced that his administration would resurrect the Bush-era military commissions.

''Military commissions have a long tradition in the United States,” Obama said. “They are appropriate for trying enemies who violate the laws of war, provided that they are properly structured and administered."

The White House promised that Obama would first get Congress to include more legal safeguards, such as prohibitions on evidence gleaned through torture or via hearsay, and providing detainees with more freedom in choosing their own military lawyers.

Graham praised this move as a step in the right direction – and renewed Emanuel’s hopes of closer cooperation with the Republicans on Guantanamo.

''I continue to believe it is in our own national security interests to separate ourselves from the past problems of Guantanamo,'' Graham said at the time. "I agree with the President and our military commanders that now is the time to start over and strengthen our detention policies. I applaud the President's actions today.''

However, civil liberties groups and legal scholars denounced Obama’s decision as Bush-lite.

Zachary Katznelson, legal director of Reprieve, a legal charity based in London that represents more than two dozen Guantanamo prisoners, said, as a constitutional scholar, "Obama must know that he can put lipstick on this pig - but it will always be a pig."

Constitutional law professor Jonathan Turley said no amount of spin from the White House could change the fact that Obama was politicizing the law.

"It is clear that Obama has determined that these men stood a chance of being released if they were given full legal protections and procedures," Turley wrote on his blog. "Thus, he has discovered the value of extrajudicial punishment with indefinite detentions and tribunals. The tribunal system is run on rules written by the Bush administration to ensure convictions.”

Civilian Trials

Yet, while resurrecting the military tribunals, Obama granted Attorney General Holder the principal say over where and how to try which Guantanamo detainees, including KSM and the four other accused 9/11 plotters.

Sensitive to Graham’s feelings, Emanuel opposed using the civilian courts. However, Holder prevailed and – on Nov. 13, 2009 – announced that the trial for the five would be held in federal court in lower Manhattan.

Holder did agree to send other Guantanamo detainees who were involved in overseas attacks, such as the bombing of the USS Cole in 2000, to stand trial before military commissions.

Though praised by civil libertarians and initially endorsed by New York City Mayor Michael Bloomberg, the 9/11 trial decision infuriated the Right, which said the alleged plotters didn’t deserve the protections of the U.S. Constitution, an argument that seemed to resonate with many rank-and-file Americans.

"During this whole civilian-trial debate, Rahm's gut instincts knew that taking KSM to New York for civilian trials was going to be a misstep," Graham told the Washington Post. "He has a better ear for domestic politics on this issue than anybody in the administration, quite frankly."

Though Emanuel declined to be interviewed by the Post for its story (which generally praised his political pragmatism), Graham’s remarks suggest that Emanuel continued a rearguard action against Holder’s decision, signaling to Graham that he shouldn’t let up on the political pressure.

Last month, Jane Mayer of The New Yorker reported that Emanuel also disdained the Guantanamo legal philosophizing that absorbed Holder and White House counsel Greg Craig. “When Guantánamo walked in the door, Rahm walked out,” one informed source told Mayer.

Worried about alienating the U.S. intelligence community, Emanuel also opposed other decisions by Holder, such as an expansion of special counsel John Durham’s investigation into abuses in the CIA’s interrogation program, Mayer wrote.

Noting that the United Nations Convention Against Torture requires any nation where there are serious torture allegations to investigate the facts, Holder maintained that he was obligated, as the chief U.S. law enforcement officer, to do something.

“Emanuel couldn’t complain directly to Holder without violating strictures against political interference in prosecutorial decisions,” Mayer wrote. “But he conveyed his unhappiness to Holder indirectly, two sources said. Emanuel demanded [about Holder], ‘Didn’t he get the memo that we’re not re-litigating the past?’”

‘A Lot of Drama’

Mayer reported, too, that Emanuel took Sen. Graham’s side in battling Holder over the 9/11 cases.

“There was a lot of drama,” Mayer’s informed source said. “Rahm felt very, very strongly that it was a mistake to prosecute the 9/11 people in the federal courts, and that it was picking an unnecessary fight with the military-commission people. …

“Rahm had a good relationship with Graham, and believed Graham when he said that if you don’t prosecute these people in military commissions I won’t support the closing of Guantánamo. …

“Rahm said, ‘If we don’t have Graham, we can’t close Guantánamo, and it’s on Eric!’”

Emanuel got Holder to speak with Graham several times, according to Mayer, who quoted Graham as saying, “It was a nonstarter for me. There’s a place for the courts, but not for the mastermind of 9/11.”

Graham has vowed to do all he can to derail Holder’s decision on civilian trials. “The President’s advisers have served him poorly here,” Graham told Mayer. “I like Eric, but at the end of the day Eric made the decision.”

However, some elected officials welcomed Holder’s decision to bring the alleged 9/11 plotters to New York City to stand trial.

Rep. Jerrold Nadler, D-New York, who had chaired the House Judiciary subcommittee hearing about the deep-seated legal problems with the military commissions system, said "it is fitting" to prosecute KSM and the four other alleged 9/11 co-conspirators in New York.

"New York has waited far too long for the opportunity to hold these terrorists responsible," Nadler said. "We have handled terrorist trials before, and we welcome this opportunity to do so again. Any suggestion that our prosecutors and our law enforcement personnel are not up to the task of safely holding and successfully prosecuting terrorists on American soil is insulting and untrue.”

Then Christmas happened.

The Underwear Bomber

On Dec. 25, Nigerian Umar Farouk Abdulmutallab allegedly attempted to blow up a Northwest Airlines jet that he had boarded in Amsterdam as the plane was landing in Detroit. He had concealed the bomb in his underwear.

Republicans soon were blasting the Obama administration for turning this al-Qaeda sympathizer over to the FBI for questioning, a decision that Holder ultimately made after consulting the FBI, the Pentagon and the CIA.

Republicans issued statements saying Abdulmutallab should have been treated as an "enemy belligerent" and pressed for actionable intelligence. They accused the administration of treating al-Qaeda’s actions as a criminal issue rather than as a “war,” as Bush had framed the conflict.

The Christmas Day incident became a rallying cry for Republicans who cast Democrats as weak on national security. Republicans also reprised their complaint about the planned civilian trial of KSM and his four co-defendants.

Scott Brown, the Republican Senate candidate in Massachusetts, touched a raw nerve with the voters when he argued that taxpayers’ money should be spent on weapons to kill terrorists, “not on lawyers to defend them.” Brown’s surprising victory on Jan. 19 suggested that many voters agreed that constitutional protections should not be afforded alleged Islamic terrorists.

Over the following weeks, the drive to push the Obama administration into fully embracing military commissions for Guantanamo detainees took off.

On Jan. 27, Mayor Bloomberg withdrew his support for holding the trial in New York, citing costs. The next day, the White House ordered the Justice Department to find a new venue, while still insisting that the trial would be held in a civilian setting. News reports suggested that Obama would personally be involved in choosing a new venue for the trial.

Then, with Graham leading the charge, a bipartisan group of senators introduced legislation prohibiting federal funds from being used to prosecute KSM and other alleged 9/11 plotters in federal court. Holder and Defense Secretary Robert Gates opposed the move, noting that "the exercise of prosecutorial discretion has always been and should remain an Executive Branch function."

But news reports began to surface disclosing that Emanuel, as a Graham ally, had clashed with Holder over the decision to prosecute KSM in federal court. It seemed the Justice Department was being politicized once again.

Pushing for a Reversal

Emanuel essentially confirmed his role in an interview  with The New York Times last month. "You can't close Guantanamo without Senator Graham, and KSM was a link in that deal," Emanuel said.

By publicly stating his own position on the KSM trial, Emanuel seemed to be suggesting that the White House no longer supported Holder's decision. For his part, Graham told the Times that the trial issue "is the one that could bring the presidency down."

Democrats for the most part remained silent while Republicans spent months attacking the decision to prosecute KSM in federal court.

On Feb. 11, however, Senate Judiciary Chairman Patrick Leahy and Senate Intelligence Committee Chairwoman Dianne Feinstein sent Obama a letter saying they believe that whether the 9/11 trial is held in New York City or another location, “these men should be brought to justice in a federal court."

Holder also continued to lobby for civilian trials. On Feb. 22, federal prosecutors secured a guilty plea in New York against Najibullah Zazi, a native of Afghanistan and a U.S. permanent legal resident who admitted he was recruited by al-Qaeda to plan an attack on New York City's subway system.

At a news conference following the announcement of Zazi's agreement to plead guilty to three criminal charges, which included providing material support to al-Qaeda, Holder said the case "demonstrates that our federal civilian criminal justice system has the ability to incapacitate terrorists, has the ability to gain intelligence from those terrorists and is a valuable tool in our fight against terrorism.

"To take this tool out of our hands, to denigrate the use of this tool flies in the face of the facts, in the face of the history of the use of that tool and is more about politics than it is about facts," Holder said.

But the writing was already on the wall. Or so it seemed.

It would appear that the half dozen or so news reports published over the past two months that detailed the infighting and disagreements between Emanuel and Holder over the 9/11 trial were coordinated by the Obama administration as a way of softening the blow for what lay ahead.

Last Friday, the Washington Post, citing unnamed sources, said Obama's "advisers" are close to recommending that KSM be prosecuted before a military commission.

"The President's advisers feel increasingly hemmed in by bipartisan opposition to a federal trial in New York and demands, mainly from Republicans, that Mohammed and his accused co-conspirators remain under military jurisdiction, officials said," according to the Post.

"If Obama accepts the likely recommendation of his advisers, the White House may be able to secure from Congress the funding and legal authority it needs to close the U.S. military prison at Guantanamo Bay, Cuba, and replace it with a facility within the United States."

Justice Department spokesman Dan Boyd told me that the "case is under review. There hasn't been a final decision made, and I can't speculate on what the department might or might not do until that happens."

Pushing Back

Civil liberties groups, however, wasted no time condemning the anticipated move.

"If this stunning reversal comes to pass, President Obama will deal a death blow to his own Justice Department, not to mention American values," said Anthony Romero, executive director of the ACLU.

"If the President flip-flops and retreats to the Bush military commissions, he will betray his campaign promise to restore the rule of law, demonstrate that his principles are up for grabs and lose all credibility with Americans who care about justice and the rule of law.

"Even with recent improvements, the military commissions system is incapable of handling complicated terrorism cases and achieving reliable results. President Obama must not cave in to political pressure and fear-mongering. He should hold firm and keep these prosecutions in federal court, where they belong."

Human Rights First arranged a conference call for reporters with three retired military officials who warned the Obama administration about caving in to political pressure and embracing a system of justice that is rife with flaws.

"I think it's sad and a mistake that we should politicize these decisions and get Congress involved in what is clearly the constitutional responsibility of the President," said U.S. Navy Rear Adm. John D. Hutson, a retired judge advocate general.

"The President has to push back and say, this is the right thing to do and I'm going to do it that way. I'm not going to succumb to the political pressure of people who are trying to undermine the administration."

Maj. Gen. William L. Nash of the U.S. Army said if Obama reversed Holder, it "would give aid to our enemies, it would lessen our reputation with our allies who have been extremely happy with the reverse course that we've taken. This is not the time to be scared. …

“This is not the time to accommodate those who have led this country under an aura of fear for eight years. And it's time to do the right thing and persevere through."

On Sunday, the ACLU ratcheted up the pressure, delivering a blunt message to Obama in the form of a full-page ad in The New York Times, which posed the question: "What will it be Mr. President? Change or more of the same?"

The ad showed a picture of Obama morphing into Bush across four panels.

Sen. Graham, in an appearance Sunday  on CBS News' "Face the Nation," responded to the ACLU's ad, saying it shows how Obama is getting "unholy grief from the Left."

Graham then put his offer on the table, the same one that Emanuel received 15 months earlier during his meeting with Graham at the transition headquarters in Chicago, the same one Emanuel has been publicly lobbying for over the past few months.

Graham said he told the White House that if KSM is prosecuted before a military commission, "I will help you in getting the Republican votes that are needed to close Guantanamo."

A decision is expected to be announced before Obama leaves for Indonesia on March 18.  

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