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A much anticipated, much debated trial will finally get underway early this year. The defendants are five men accused of helping plan the September 11th attacks. Initially, the alleged 9/11 plotters were going to be tried in a New York federal court, but congressional opposition forced the Obama administration to reverse course. The trial will now be in a military commission at Guantanamo Bay, Cuba. As NPR's Dina Temple-Raston reports, the case has become a litmus test for a new system of justice reserved for suspected terrorists.

DINA TEMPLE-RASTON, BYLINE: The person most associated with pushing to get Khalid Sheikh Mohammed and the other 9/11 plotters into a military courtroom is probably Senator Lindsay Graham of South Carolina.

SENATOR LINDSAY GRAHAM: The reason I want a military commission trial is it balances our national security needs against the rights of the accused better than civilian court.

TEMPLE-RASTON: That's Senator Graham talking to Fox News back in April, when the Obama administration announced that Khalid Sheikh Mohammed would stand trial at Guantanamo.

GRAHAM: We're at war. He did not rob a liquor store, he attacked our country.

TEMPLE-RASTON: You just need to look at the courtroom where the alleged plotters will be tried to understand how important the case has become. The military literally built a courthouse just for the 9/11 trial. The room is enormous, about 50 feet long, with six long conference tables dotted with computer monitors, one table for each defendant and his legal team, with a spare one for any extra lawyers who might attend.

MATTHEW WAXMAN: So, 2012 will be a big year for military commissions.

TEMPLE-RASTON: That's Matthew Waxman. He used to be in charge of detainee affairs during the Bush administration. Now, he's a professor at Columbia Law School.

WAXMAN: The U.S. government has several goals here that they're trying to achieve. Obviously, they want to achieve successful convictions, but they also want to prove that the military commissions system is a legitimate one.

TEMPLE-RASTON: During the Bush administration, military tribunals were criticized as unfair, partly because commission rules seemed stacked against the defendant. Hearsay evidence, for example, was admissible in court. Information obtained through torture could also be used. The perceptions of unfairness got so bad, U.S. allies refused to turn over terrorism suspects if they would stand trial at Guantanamo.

The Obama administration tinkered with the rules and now, the 9/11 case will be one of the first to put those changes to the test.

WAXMAN: This is now the Obama administration taking ownership of military commissions, saying we've improved it, we've corrected the problems of the Bush administration, and we're now going to use this as a tool in combating terrorism.

RAHA WALA: I'm Raha Wala. I'm of the advocacy counsel at Human Rights First.

TEMPLE-RASTON: Wala sees the military commissions a little differently.

WALA: I'd argue that they're already broken, but I think, certainly in the public eye, it's a make-or-break year. We're going to have extreme scrutiny on these processes and we're going to see both the prosecutors and the defense testing these commissions on very basic issues.

TEMPLE-RASTON: Basic issues like attorney-client privilege. That came up just days ago. The prison commander at Guantanamo Bay just issued new rules that essentially allow the prison staff to read the mail between military commission defendants and their lawyers. That means prison authorities would be able to, for example, review drafts of legal motions or evidence that lawyers are trying to share confidentially with their clients. The prison commander said the new rules are necessary for safety and security on the base.

But it seemed like yet another example of how some of the basic rules governing military commissions have still to be worked out. Again, Columbia University's Matthew Waxman.

WAXMAN: There are a lot of doubters out there who see military justice and the military commission system as tainted or illegitimate and the Obama administration wants to turn around that perception.

TEMPLE-RASTON: The charges against Khalid Sheikh Mohammed and the other alleged plotters haven't been finalized yet, but they could be arraigned in a Guantanamo courtroom as early as April. Dina Temple-Raston, NPR News.

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