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We now know what the Supreme Court ruled about a detention center at Guantanamo Bay, Cuba. Detainees can challenge their detentions in federal courts. We're still learning what the Bush administration will do about it.

Today, the president's top lawyer suggested that ruling makes only limited difference. Yet the administration has now suffered three defeats in the Supreme Court. This latest ruling even struck down an administration plan that had been approved by Congress. And the majority opinion suggests impatience with the detention center that has held some prisoners for more than six years.

We have more this morning from NPR legal affairs correspondent Nina Totenberg.

NINA TOTENBERG: After the Supreme Court told the Bush administration it could not on its own make up a set of rules for Guantanamo, Congress took just three weeks to essentially ratify what the administration had previously been doing. That was less than two years ago. Now the Supreme Court has struck down that law, too, declaring that it strips the detainees of their constitutional right to challenge their detentions in court.

It matters not, the court said, that the detainees are aliens. They still have rights not to be wrongly imprisoned by the U.S. government.

Writing for the court majority, Justice Anthony Kennedy said the system set up for screening Guantanamo detainees is fraught with risk of error. The prisoner has no lawyer, no chance to see or rebut evidence against him, and may not even know what the critical allegations against him are. If there's a mistake, the court said, a detainee may find himself in prison for a generation or more.

And the system set up by the Bush administration and approved by Congress does not give a detainee any opportunity to correct errors or any chance to present new exculpatory evidence. Instead, the Military Commissions Act gives review to a single court that's instructed to give the benefit of the doubt to the government and to rely on the record of the flawed Guantanamo review tribunal.

That, the Supreme Court said, simply violates the requirements of the Constitution. In essence, the court said to the Bush administration, you can continue with these flawed proceedings at Guantanamo, but when they're reviewed by the courts, the prisoners will have a full range of legal tools to challenge their detentions, and the burden of proof will be on the government.

Professor NEIL KATYAL (Georgetown University): I think that the decision today is the end of Guantanamo as we know it.

TOTENBERG: That's Georgetown Law Professor Neil Katyal, who represents one of the detainees. Administration allies, with great pain, agree. Andrew McBride wrote a brief on behalf of former GOP attorneys general siding with the administration. He calls yesterday's court decision a stinging rebuke for the Bush administration and a watershed decision.

Mr. ANDREW MCBRIDE (Attorney): For the first time in history, it does inject judicial supervision into the conduct of war.

TOTENBERG: Georgetown Law Professor Martin Lederman puts it another way.

Professor MARTIN LEDERMAN (Georgetown University): The court has decided that the Constitution does protect alien detainees being held by the United States and that there is no legal black hole.

TOTENBERG: Reaction to the decision was swift. President Bush in Rome had this to say.

President GEORGE W. BUSH: We'll abide by the court's decision. That doesn't mean I have to agree with it.

TOTENBERG: And in Washington, the chief judge of the federal district court, where some 200 cases are currently pending, called a meeting of the judges likely to hear the cases. There are still many questions unresolved, questions that will have to be sorted out first by the district court and perhaps eventually by the Supreme Court.

What's the standard of proof the government's required to meet? How long do detainees have to wait before they can challenge their detentions in court? What procedures will there be to protect intelligence sources and methods? How long will the government be given to produce the evidence against the detainees?

Basically, the 275 detainees fall into three categories. The government has said roughly a third of them are not dangerous and have been approved for release to their home countries. But those countries don't want them, nor does any other country seem to want these people whom the U.S. once characterized as the worst of the worse.

What will the courts do with them? Again, here's Georgetown's professor Katyal.

Prof. KATYAL: That is precisely the question the administration should have asked years ago instead of holding people for years in conditions in which undoubtedly some of them had to become radicalized against the United States even if they weren't to start. And it is an extremely difficult problem. Having said that, the United States does have the full range of diplomatic tools available to it to entice other countries to take individuals.

TOTENBERG: Andrew McBride contends that if no solution can be found, some of these men might be released into the United States. The courts, he argues, don't have the expertise to decide such questions.

Mr. MCBRIDE: A wrong decision could be devastating to this country in terms of terrorist attacks.

TOTENBERG: The same questions apply to some of the second group of detainees, the third of the detainees that the government wants to keep indefinitely behind bars because they're viewed as dangerous. But some of these detainees may well prevail when they challenge their detentions and once again, the question will be where and how they're released.

A third group, about 80 detainees, are expected to face war crimes charges. The administration finally, after nearly seven years, got some of these cases under way last week, and the Justice Department said yesterday these trials would continue.

But even the administration's legal allies don't believe that. Here, for example, again, is Andrew McBride.

Mr. MCBRIDE: Today's ruling probably means that there has to be a different system and greater protections in the context of military tribunals as well as in the initial evaluation of whether or not someone is an enemy combatant.

TOTENBERG: Most of the current and former top legal officers from the Army, Navy and Air Force have testified that the Uniform Code of Military Justice could provide the framework for trying accused war criminals. But former Bush administration Assistant Attorney General Jack Goldsmith questions whether that's really workable.

Mr. JACK GOLDSMITH (Former Assistant Attorney General): The question is whether you can try them consistent with the demands of classified information and the demands of collecting evidence on the battlefield. You need to use rules that would loosen hearsay rules.

TOTENBERG: Thomas Romig, who served as judge advocate general for the Army until 2005, counters that classified information can be dealt with under the Code of Military Justice.

Mr. THOMAS ROMIG (Former Judge Advocate General, Army): It's a bit of a red herring because military courts-marshal have a process for dealing with classified information, and there have been a number of trials in the past where there was classified information provided as evidence, and the court dealt with it.

TOTENBERG: Romig says another problem is that some of the information used against detainees is the result of physical or mental coercion, even torture. None of that can be used under the Military Code of Justice, he observes, and even a bragging confession in open court is not enough without some corroborative evidence.

Former Navy Judge Advocate General John Hudson says there are ways in most cases to deal with problems of classified information, chain of custody and hearsay. These have worked well in the past, he says, but he adds there may be a few cases where detainees are acquitted.

Mr. JOHN HUDSON (Former Judge Advocate General, Navy): If the United States can't create a system in which the judicial rights considered to be indispensable by all civilized people, then we shouldn't be prosecuting the guy. I mean, you simply can't permit a prosecution in which the court says we have a guy - we can't tell you who - who gave us some evidence - we can't tell you what - that leads us to believe you're guilty - we can't tell you why.

TOTENBERG: In his opinion for the court majority yesterday, Justice Kennedy put it another way. Security subsists, he said, in fidelity to freedom's first principles. Chief among these is freedom from arbitrary imprisonment.

Nina Totenberg, NPR News, Washington.

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