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ROBERT SIEGEL, host:

From NPR News, this is ALL THINGS CONSIDERED. I'm Robert Siegel.

Among the questions facing Congress as it returns from summer recess is how to try accused war criminals who are being held at Guantanamo Bay. In a landmark ruling at the beginning of the summer, the Supreme Court struck down the system that was set up by President Bush. That decision has been widely viewed as the most important ruling on executive power in decades.

NPR's Nina Totenberg has put together this anatomy of the case and how it rose from the battlefields of Afghanistan.

NINA TOTENBERG: In the aftermath of 9/11 and the war in Afghanistan, President Bush created a system for trying those captured on the battlefield who were deemed to be war criminals. If convicted, the defendants could be subject to the death penalty.

In 2003, the Pentagon established two offices, one to prosecute and one to defend the accused. Although a handful of detainees were designated as potential targets and moved into isolation, no charges were actually brought for months.

In December 2003, Navy Lieutenant Commander Charles Swift was appointed by letter to represent one of the still uncharged defendants Salim Ahmed Hamdan. Hamdan had served as one of Osama bin Laden's drivers. Commander Swift.

Lieutenant Commander CHARLES SWIFT (United States Navy): The letter said that my access to him was conditioned on us negotiating a plea bargain. If we didn't negotiate one, then my access could be cut off.

TOTENBERG: The letter presented a dilemma for Swift. He thought it was a violation of the code of legal ethics to accept that condition. He picked up the phone and called Georgetown law professor Neil Katyal, who by then was on board as the defense team's civilian lawyer.

The 33-year-old Katyal had volunteered his services and quickly been embraced by the defense. He had worked for two years in the Clinton Justice Department on national security issues so it was easy to renew his security clearance. And because he'd been an early academic critic of the Bush tribunals, he had quickly become the point man for developing a legal strategy aimed ultimately at Supreme Court review.

Now Katyal and Swift were worried that if Swift went to talk to Hamdan about a plea deal and Hamdan didn't want to plead guilty, Swift would never see his client again and would be unable to represent him in court. Professor Katyal.

Professor NEIL KATYAL (Georgetown University): To avoid that, I drafted a legal document that essentially said that Commander Swift would be authorized on behalf of Mr. Hamdan to file a challenge in Commander Swift's name.

TOTENBERG: Swift then went to Guantanamo to meet with his client, telling him -

Commander SWIFT: If we say no, I may not see you again. But understand I will start fighting and keep fighting for you the entire time.

TOTENBERG: Hamdan said he did not want to plead and signed the paper authorizing Swift to file a legal challenge on his behalf.

Swift now took his next step.

Commander SWIFT: I demanded a speedy trial. They said, you don't have the right to a speedy trial. And I said, Okay. And then I filed the lawsuit.

TOTENBERG: The suit was filed in Swift's name in Seattle, Washington, Swift's legal residence because he lived there when he enlisted in the JAG Corps nine years earlier. But neither Swift nor Katyal was licensed to practice law there. And they needed a local lawyer to file the suit.

Coincidentally, one of Katyal's former students called him. The former student now worked at one of Seattle's leading law firms, Perkins Coie. By evening, the managing partner was on the phone pledging major help, including partners who would continue to work on the case for the next three years.

The defense team by then had settled on Hamdan's case as the best one to use to challenge the military tribunals. Commander Swift focused on Hamdan after watching a documentary about the Nuremberg trials in which he noticed that Hitler's driver was not prosecuted as a war criminal.

Commander SWIFT: They didn't prosecute him. They interviewed him. In the law of war, the idea is to charge the principals, not the foot soldiers, unless of course, they are shooting civilians on a battlefield, lining them up.

TOTENBERG: Yes, says Neil Katyal, the defense lawyers knew they would take a PR hit for defending Osama Bin Laden's driver, but -

Professor KATYAL: Hamdan stood out as being the one who had done nothing bad himself besides being the driver to a bad guy. A lot of the other individuals had actually picked up guns, shot people and the like.

TOTENBERG: As the months dragged on though, Hamdan, who remained in solitary confinement, went into a spiral of depression, refusing to eat or drink. Commander Swift.

Commander SWIFT: It wasn't because he was striking. He just wasn't hungry. He was in severe depression. The guards were really worried about him.

TOTENBERG: Swift finally got hold of a picture of Hamdan's children in Yemen and brought it to the prison.

Commander SWIFT: And he broke down, just sobbing. And I said, how do you leave them - see, he's an orphan - how do you leave them the way they were left? And he started drinking water. But it was a tough day, tough day.

TOTENBERG: While all this was going on, the Supreme Court announced it would decide whether the other detainees at Guantanamo - not those charged as war criminals - had a right to challenge their detention in court.

The Hamdan lawyers saw this as an opportunity and they notified their superiors of their intention to file a friend of the court brief in the regular detainees' case unless ordered not to. The letter was CC'ed to their civilian lawyer, Neal Katyal.

Professor KATYAL: Our fear at the time was they could shut this brief down and the world wouldn't know about it and so the CC to me was designed to make sure that there would be some repercussions if they decided to gag the lawyers.

TOTENBERG: According to Bush administration sources, there was a desire to veto the brief. But White House officials finally decided it wasn't worth the hit they would take in the press, and the brief was filed with much accompanying publicity. Commander Swift.

Commander SWIFT: The amicus brief changed the rules forever. We'd been told we would never talk to the press, we would never be seen. We would simply sit there, take it and then it would be over. It was to be a one way show. The amicus brief gave us an opportunity to break out.

TOTENBERG: In June of 2004, the Supreme Court ruled that the detainees could go to federal court to challenge their detention. And for technical reasons, the Hamdan case was moved back to D.C.

Four months later, a federal judge struck down the military tribunals as unconstitutional. The victory for the defense, however, was short lived. A federal appeals court panel that included then Judge John Roberts overturned the decision.

Now the defense was fully focused on persuading the Supreme Court to accept the case for review. Katyal filed a brief contending that the rules the president had established for the tribunals were blatantly unfair.

Professor KATYAL: In response, what the government did was change some of the rules to make them on paper look a bit fairer to Mr. Hamdan and then told the Supreme Court, don't hear this case in legal filing because we've changed the rules now to make them better.

TOTENBERG: Katyal then wrote a reply brief contending that these very changes proved his point that the rules were not rules at all, but an ever moving target, a system completely at the whim of the president.

In November, the Supreme Court announced it would Hamdan's case and three days later, Arizona Senator Jon Kyl introduced and immediately won passage of a bill he had prepared with White House help to strip the courts of jurisdiction in these cases.

Now the defense team led by Katyal went into high gear to get the language in the bill changed to exempt pending cases. Lawyer Tom Goldstein worked on the case.

Mr. TOM GOLDSTEIN (Defense, Hamdan case): What Neil did is he worked tirelessly - as somebody with really no Capitol Hill experience and with none of the influence of the president of the United States - to get that law changed so that Hamdan's case could stay alive.

TOTENBERG: And stay alive it did. In the months that followed, Katyal, who had never argued a Supreme Court case before, would devote thousands of hours to preparation. He made a list of the lawyers across the country who intimidated him the most and flew out to do dry runs in front of them. In all, he did 15 moot courts, working with as many as 1000 other lawyers.

He coordinated some 40 friend of the court briefs filed by retired military officers, diplomats, human-rights groups and conservative as well as liberal legal scholars. And he honed his own arguments, resolving much conflicting advice he got from all over the country.

All the while, as law student Danielle Tarantola(ph) observes, the defense team was in virgin legal territory.

Ms. DANIELLE TARANTOLA (Law student): For every paragraph, it could have been 50 hours of work for someone to do the research to come up with that one paragraph.

TOTENBERG: It all paid off on June 29, when the Supreme Court sided with the defense on almost every point. It was a stunning rebuke to the president, but Katyal doesn't see it that way.

Professor KATYAL: One of the great things about the way the military and the administration has handled this is that they have let me do my job and they have let Commander Swift do his job. You know, in some other country, I'm sure we might have been shot.

TOTENBERG: Nina Totenberg, NPR News. Washington.

SIEGEL: And you can listen to the oral arguments in Hamdan v. Rumsfeld at the Supreme Court at our website, NPR.org.

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