JUAN GONZALEZ: Here in New York, opening statements were heard yesterday in the case of Ahmed Khalfan Ghailani, the first Guantánamo Bay detainee to face a civilian trial. Ghailani appeared in a New York courtroom Tuesday on charges he was involved in the US embassy bombings in Tanzania and Kenya in 1998, which killed 224 people.

The case is being closely followed by many in the legal community, as it could help determine how the government decides to try prisoners still being held at Guantánamo.

AMY GOODMAN: Meanwhile, the investigative news website ProPublica has revealed shocking details about another court case involving a Guantánamo prisoner. Earlier this year, a federal judge, Henry Kennedy, Jr., ordered the release of a Yemeni man named Uthman Abdul Rahim Mohammed Uthman. ProPublica reports, a day after Kennedy’s March 16th order was filed on the court’s electronic docket, Kennedy’s opinion vanished. Weeks later, a new ruling appeared in its place. While it reached the same conclusion, eight pages of material had been removed, including key passages in which Kennedy dismantled the government’s case against Uthman.

To talk more about this story, we’re joined by Dafna Linzer. She’s a senior reporter at ProPublica.

Dafna, explain this in detail. This is unprecedented?

DAFNA LINZER: I believe it is. And classification experts, legal ethicists, people who study secrecy and government secrecy, have never seen anything like this before. We have a situation in which we have two opinions. The first one comes out. The judge goes through the evidence offered by the government, really dismantles the weaknesses in the government’s own case, and that takes a look very, very deeply at the different kinds of evidence offered by the government to hold a detainee, really — and this is somebody who’s been held almost nine years, without charge or trial. The opinion vanishes. And suddenly a new one appears five weeks later. Huge elements — whole sentences are rewritten, footnotes vanished. The weakest elements of the government’s case are removed from the decision.

JUAN GONZALEZ: And the original opinion by Judge Kennedy was filed in February, was it?

DAFNA LINZER: He wrote in late February. It went off for —

JUAN GONZALEZ: And it disappeared the following day, right?

DAFNA LINZER: It disappeared — it went off for classification review. It was posted March 16th. And twenty-five hours later it vanished. Simply vanished from the public docket.

AMY GOODMAN: Well, you’ve analyzed this. Talk about what he did say in the original decision that was pulled off the web.

DAFNA LINZER: Sure. And what’s very interesting, too, is sort of the change — you know, how the wording in his original opinion changed in the second opinion and how that alters the public’s perception of who the detainee is and the threat that he poses, which is a central question here in sort of Obama’s detention strategy and policies going forward.

So, in this case, this detainee was arrested in Pakistan on December 15th, 2001. This was in the middle of a five-day battle between US forces and Osama bin Laden’s fighters in Tora Bora, in a cave complex in Afghanistan, not in Pakistan, where Uthman was arrested. You know, in the original opinion, Kennedy noted that. He said it was, you know, unrebutted; both sides agreed. Both the government and the detainee himself acknowledged that he was detained by Pakistani authorities in Pakistan. The opinion vanishes. The new one comes out. All of a sudden, the judge writes that the detainee acknowledges — he, himself, admits that he was arrested in late December 2001 near Tora Bora. He has moved the location of the detainee’s arrest, the date of his arrest, to a different country, weeks later, moving him closer, really, to where bin Laden was believed to have been and where he was believed to have been fleeing. So, in the opinion that the public sees, he suddenly looks far more threatening, far more like an al-Qaeda fighter, like a bin Laden bodyguard, and far less the appearance that the judge originally claimed him to have been, which is somebody who had turned himself in to authorities in Pakistan weeks earlier.

JUAN GONZALEZ: Now, you’ve spent considerable time trying to piece together what happened to make the judge issue this new and altered, really altered, opinion. What have you concluded in terms of what happened behind the scenes? Because obviously a lot of this is because of national security issues, the judge can’t talk about it, and very few prosecutors can talk publicly about it. What have you learned?

DAFNA LINZER: Right. In the habeas litigation in which the detainees are challenging the lawfulness of their detention at Guantánamo, the government holds a lot of cards here, because of secrecy, because of national security reasons that the government claims — you know, they determine themselves that much of the proceedings are classified. That makes it difficult for people to talk. And some aspects of this case still remain a mystery, because people would not speak on the record. People feared speaking on the record. They’re not allowed to speak on the record on these cases. Both defense attorneys, judges, prosecutors, everyone’s kind of in on a secret here as far as the detainees go.

And here, in this case, what we learned was, privately, secretly, again, the Justice Department acknowledged to the judge that they had erred in the original publication of his opinion, that they hadn’t properly redacted it before they allowed its release. They had it removed. They resealed the decision. They gave the judge new guidelines, new redactions, and he issued the new opinion.

The question here is — and it remains a little bit of a mystery — is how much pressure did the judge feel? Was he able to challenge some of the classification issues? The judges have very little say in what the government decides can be withheld from their opinions. So everybody was in a little bit of a bind here. But it seems like the judge was basically offered a difficult choice: we either hold on to your opinion, in which nobody knows what your reasoning is, in your order to release this detainee, or you come up with a new one that doesn’t have anything we don’t want in it.

AMY GOODMAN: Can you tell us about the Saudi man, Bukhari, who was held for five years?

DAFNA LINZER: Absolutely. This is another interesting element of this very layered story, which is the witnesses that the government used against this detainee. They use statements in almost every single habeas litigation. They use statements from some detainees against other detainees. In this case, the government offered evidence from a detainee, a Saudi, whose name you said, who was in custody for five years in Guantánamo, who was diagnosed by a US military psychiatrist as becoming psychotic as a result of his interrogations and detention at Guantánamo. That detainee’s statements were used against Uthman. They were dismissed by the judge, in large measure because of his mental health. The fact that his —- that he had this diagnosis was completely removed from the public opinion. So, again, when the public -—

JUAN GONZALEZ: From the second. From the second opinion.

DAFNA LINZER: From the second opinion. From the only opinion that the public was allowed to see. So, when the public reads Kennedy’s reasoning, they have no idea why he has dismissed the testimony of this witness. It almost seems as if Kennedy either doesn’t understand or is not capable of understanding the evidence against this detainee and perhaps erred in ordering his release. But unless you know the truth — and the truth is, you know, that Kennedy dismissed this witness because he is psychotic. And this was not sort of, you know, defense attorneys saying this detainee doesn’t seem like a good guy; this is US military psychiatrists diagnosing him and offering psychiatric evaluations that he is psychotic.

Another witness that they offered against Uthman was a detainee who committed suicide in Guantánamo three years ago after months of hunger strikes. This is a detainee who walked into Guantánamo weighing 150 pounds, at death weighed about eighty pounds. And not only that, but the testimony that they offered on behalf of this detainee was flawed. He came up with an alias after having seen a photo of Uthman, claiming that Uthman must have been somebody that he had seen in Kabul named Yasser Al-Madani. That would infer that the detainee was from the city of Medina in Saudi Arabia, and that’s not where Uthman is from. In English, it would be like saying this guy is from Boston, but meaning he’s from Austin. If you speak English, it makes a big difference.

JUAN GONZALEZ: And what you’ve done on the ProPublica website is you’ve taken both decisions, the original one that was pulled within a day and then the new one, and done a line-by-line analysis of the changes in the — in the enormous changes in what the judge wrote?

DAFNA LINZER: Right. We want the public to be able to see what was missing and what was removed. You can go line by line through the opinion and click and see every single change, alteration, deletion, omission, rewritten sentence, removed footnote, every single contention, so that people can see what the judge saw and what the real evidence against this detainee is.

What we learned through our reporting is that this particular detainee is one of forty-eight, a handful, on a secret list written by the Obama administration of detainees they plan to hold indefinitely, long after Guantánamo closes, if it does. This is a group of detainees that they have no intention of ever prosecuting or ever releasing. So this is the first time there really is an opportunity to really —

JUAN GONZALEZ: And the reason for that, they’re contending, is that they can’t try them or release them?

DAFNA LINZER: Can’t try them, can’t release them, right. Too dangerous to release, too difficult to try. The too difficult to try thing, I think, is really obvious after you look at what they’ve offered in the habeas litigation.

AMY GOODMAN: So, overall, your observation on what this means and how much you know about how the Obama administration weighed in here, which is what’s most significant?

DAFNA LINZER: Right. Well, this is the Obama Justice Department at work here. This is not — this is not, you know, just a legacy issue where they’re just going to federal court or arguing old cases or keeping up with arguments that they — you know, that were handed to them. This is the Obama Justice Department, its own civil division, that is making the choices to use this kind of evidence in court against these detainees. And it’s the Obama administration’s decision to keep its list of detainees it plans to hold indefinitely secret. And I think when we see that judges are ordering the release of detainees they plan to hold indefinitely, it becomes more obvious why they want hold — why they want to keep the list secret.

JUAN GONZALEZ: But now what happens with Uthman, since the judge’s final decision was that he should be released, right? What happens now?

DAFNA LINZER: Right. Well, the Obama administration appealed, and they’re waiting — you know, they’re waiting for — you know, to go ahead with an appeals process. That said, they are facing a court order to release a detainee they claim that they have no intention of releasing. So, you know, we have a dilemma here. And the Justice Department, interestingly enough, I thought, wouldn’t say on the record, wouldn’t say at all, what they plan to do, should they lose on appeal. They wouldn’t say whether or not they would abide by a court order to release him.

AMY GOODMAN: Well, we’re going to leave it there. I want to thank you very much for being with us, Dafna Linzer, senior reporter at ProPublica. And we will certainly link to all your work there.