Update April 25, 2011: On Sunday night, a number of news outlets and WikiLeaks published a trove of classified documents on detainees at Guantanamo Bay. ProPublica has been reporting on Gitmo and the issues surrounding indefinite detention for more than two years. In October 2010, Dafna Linzer revealed how the Obama administration censored one federal judge's Gitmo decision that had questioned the government's evidence against a detainee.

This story was originally published on Oct. 8, 2010 and co-published with The National Law Journal.

When Judge Henry Kennedy Jr. ordered the release of a Guantánamo Bay detainee last spring, the case appeared to be a routine setback for an Obama administration that has lost a string of such cases.

But there turns out to be nothing ordinary about the habeas case brought by Uthman Abdul Rahim Mohammed Uthman, a Yemeni held without charges for nearly eight years. Uthman, accused by two U.S. administrations of being an al-Qaida fighter and bodyguard for Osama bin Laden, is among 48 detainees the Obama administration has deemed too dangerous to release but "not feasible for prosecution."

A day after his March 16 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.

In his first opinion, Kennedy wrote that one government witness against Uthman had been diagnosed by military doctors as "psychotic" with a mental condition that made his allegations against other detainees "unreliable." But the opinion the public sees makes no mention of the man's health and discounts his testimony only because of its inconsistencies.

The alterations are extensive. Sentences were rewritten. Footnotes that described disputes and discrepancies in the government's case were deleted. Even the date and circumstances of Uthman's arrest were changed. In the first version, the judge said Uthman was detained on Dec. 15, 2001, in Pakistan by Pakistani authorities. Rewritten, Kennedy said in the public opinion that Uthman admitted being captured "in late 2001 in the general vicinity of Tora Bora," the cave complex where bin Laden was thought to be hiding at that time.

The creation of the additional opinion stemmed from a mishap inside the Justice Department: Kennedy's first opinion was accidentally cleared for public release before government agencies had blacked out all the classified information it cited.

While the government privately took responsibility for the error, it initially refused to correct it. Two people familiar with the discussions said prosecutors in the Justice Department's Civil Division gave Kennedy a choice: his entire decision would remain classified or he could write a new version that did not reference classified evidence.

Justice Department sources offered a different account. They said the department later relented and gave Kennedy a properly redacted version of the opinion, in which classified material had been blacked out. The sources said this opinion was meant to be published. But for reasons that remain unclear, the edited opinion became the starting point for the creation of an entirely new version.

Matthew Miller, a spokesman with the Justice Department, said "the department's practice in all of these cases is to propose release of a properly redacted opinion."

The second opinion, drafted after a contentious exchange between Kennedy and the prosecutors, did not refer to the earlier version and gave no indication material had been removed.

Legal scholars and classification experts said the drafting of a second opinion was a deception. All previous opinions in Guantánamo habeas cases have noted when material has been blacked out or removed to protect security.

Stephen Gillers, who teaches legal ethics at New York University School of Law, said Kennedy may well have had a legitimate concern about "national security issues."

"But that concern then inspired him to participate in the creation of a parallel universe that fools everyone except a small circle of judges. We don't allow the justice system to create false impressions," Gillers said.

ProPublica obtained the original version of Kennedy's opinion when it appeared briefly in the court record and conducted a line-by-line comparison with what was published five weeks later. That comparison, highlighting information that was removed, can be found here.

Reporting for this story was complicated by the fact that much of the evidence is classified, and judges, lawyers and prosecutors are barred from discussing most aspects of the litigation. But an examination of the opinions and additional documents, as well as interviews with government and intelligence officials, former military prosecutors and key players in the habeas cases, makes it possible for the first time to publicly examine the evidence against a detainee designated for indefinite detention.

To justify Uthman's incarceration, the government relied on statements from five current or former detainees who were previously discredited by judges in other cases, questioned by internal Obama administration assessments or found unreliable by military psychiatrists because they were mendacious, mentally ill or subjected to torture.

Kennedy's first opinion reveals that some of the government's evidence came from a detainee who committed suicide at Guantánamo three years ago after months of hunger strikes. In the second opinion, the detainee's name is concealed, making it impossible for the public to know he is dead.

DOJ's Miller said witness testimony is thoroughly reviewed before it is presented. "In every habeas case where we ask the court to rely upon detainee statements, we do so because we believe courts can and should consider their accounts based on the totality of the evidence," Miller said.

The Justice Department has appealed Kennedy's ruling and officials there declined to say what they might do if the government does not prevail.

Uthman, according to senior government officials, is on the secret list of 48 Guantánamo detainees who the Obama administration designated for indefinite detention and, officials said, he is the first of those men to win his habeas petition.

Further complicating matters, Uthman hails from Yemen -- a country the White House has deemed too unstable to handle such a transfer. Should he send Uthman home, President Obama risks a fierce political backlash from Republican lawmakers eager to portray the president as weak on terrorism.

Disclosure of the Uthman case comes at a pivotal moment in the government's complicated efforts to prosecute detainees and close the prison at Guantanamo Bay, Cuba. On Oct. 6, a federal judge in New York barred the government from using its main witness against a terrorism defendant because the information that led investigators to the witness was obtained through torture.

Botched Classification

When Kennedy, who serves on the U.S. District Court for the District of Columbia, ruled in February that Uthman was being improperly detained, his 27-page opinion was turned over to a court security officer for classification review.

The judges themselves have very little insight into the process and no sway over what is redacted. Government security officials review filings in the habeas litigation and other cases involving classified evidence and remove sensitive information.

In the Uthman case, that clearance process took three weeks. Kennedy's decision was stamped "Redacted," by the court's security officer and returned to his chambers on March 16. The deletions were minimal. For the first 16 pages, the only word blacked out was "secret," stamped at the top and bottom of each page.

Kennedy's clerk added the document to the electronic court file late in the day. Twenty-five hours later, the security office sent out urgent notices to attorneys and the judge that the opinion had not been ready for release and needed additional deletions. The decision was promptly removed from the public docket.

In a closed hearing in his courtroom four days later, Kennedy lashed out at the government for releasing classified information. He and Justice Department attorneys then argued over what to do, according to three sources familiar with the discussion.

Kennedy insisted that the reasoning behind his first habeas ruling be made public. But the Justice Department resisted releasing it in redacted form, arguing that blacked out portions would call attention to the exact material the government wanted to conceal.

With Uthman slated for indefinite detention, the stakes were high.

During the next month, government lawyers scoured the Internet for the original decision; the legal database Westlaw was asked to remove it from archives; defense attorneys were instructed to destroy their electronic copies.

Even the court docket was altered. When the opinion was originally posted on March 16, the docket noted Kennedy's grant of the writ of habeas corpus to the petitioner. Today, the entry for March 16 simply reads: "Document Entered In Error Erroneously."

Kennedy ordered the Justice Department to explain how the information was released and to suggest solutions. In the written response, according to three people who saw it, the department took responsibility for the error. Kennedy rejected the government's initial attempt to keep the opinion classified, insisting on other options, according to three people with knowledge of the matter.

One Justice Department source said the department relented, gave Kennedy a properly redacted copy of his opinion, and expected him to publish it. But two others said no such intention was conveyed to Kennedy.

Classification experts could not recall another case in which a second decision was secretly created.

"Reconstituting and replacing a judicial opinion without public notice is active deception," said Steven Aftergood, a classification expert with the Federation of American Scientists in Washington. "There is a role for classification and there are things that need to be redacted, but there is never a justification for deception in the judicial process and that's what this is," Aftergood said, after reviewing both versions of Kennedy's ruling in the Uthman case.

Two senior officials in the Obama administration and two others with direct involvement in habeas cases were surprised to learn that Kennedy's final opinion was a different version than the original.

Changing the Record

Uthman was 21 years old and traveling with about 30 other men when he was taken into custody by Pakistani police in the town of Parachinar, near the Afghan border. It was Dec. 15, 2001, and U.S. troops were in the middle of a five-day battle against an al-Qaida stronghold known as Tora Bora, where bin Laden was believed to have taken shelter. Parachinar and Tora Bora are 12 miles apart but separated by a treacherous mountain range that takes two to three days to traverse.

The government maintains that Uthman was in Afghanistan to fight for bin Laden; Uthman has claimed he went there to teach the Quran to children. Some facts of his story are not in dispute, some critical ones are. They look different depending on which of Kennedy's two opinions you read.

Kennedy's original opinion noted that Uthman was seized in Parachinar; that he reached the town after an eight-day trek from the Afghan town of Khost, nowhere near Tora Bora; and that his journey to Pakistan began around Dec. 8, 2001. Those facts make it difficult to portray Uthman as a fighter in a battle that took place between Dec. 12 and Dec. 17 at Tora Bora. Two footnotes in the original opinion note that the government does not contest that Uthman was taken into custody in Parachinar.

Both were removed in the second opinion and Kennedy substituted wording to write instead that Uthman admitted he was seized "in late 2001 in the general vicinity of Tora Bora, Afghanistan."

The intent of this editing may have been to conceal the role of the Pakistanis in capturing al-Qaida fighters although those details were long ago declassified. But the effect was to link Uthman more closely to the retreat of bin Laden and his inner circle through Tora Bora.

It is unclear precisely what restrictions or classification requests guided Kennedy's alterations. Neither the judge nor the Justice Department would say.

Gillers said such editing has an effect on public opinion, even when it doesn't change the outcome of the case.

"The ability to influence Kennedy's opinion gives the government a public relations advantage," Gillers said. "These battles are fought outside the court system as well as within it."

Another advantage has been the government's ability to largely conceal the identities of its witnesses.

In ordinary federal proceedings, from mob cases to white-collar crime, prosecutors would be loath to attempt such strategies because repeated use of a discredited witness would provide a significant opening to defense attorneys. In the habeas cases, it is difficult for defense lawyers and judges to learn of the roles played by flawed witnesses in previous cases.

The issue arose in a separate habeas case in May 2009, when Judge Gladys Kessler of the U.S. District Court for the District of Columbia noted that a government witness had been diagnosed by Guantánamo medical staff as suffering from "psychosis." In a footnote, she said she was troubled that the diagnosis had come to her attention "through the diligent work" of the defense attorney "and not as a result of the government's obligation to provide" it.

Attorneys with security clearances can access classified information the government plans to raise in court at a secure facility near the Pentagon. But the material is not easy to use.

The facility is staffed by court security officers and Justice Department officials who determine what information the lawyers can remove from the facility, including, in some cases, their own notes. No classified information can be shared over the telephone or Internet, a significant burden for lawyers who reside outside the Washington area.

"It's monumentally difficult to fight these battles when the government holds all the cards," said David Remes, one of the attorneys representing Uthman. Neither Remes nor Uthman's other Washington attorneys, including William Livingston at Covington & Burling, would discuss the details of the Uthman case.

Near Total Secrecy

Although President Obama inherited many aspects of U.S. detention policy from his predecessor, Guantánamo detainees have been fighting their detentions in the U.S. District Court for the District of Columbia almost entirely on his watch.

The U.S. Supreme Court ruled in June 2008, as Obama was campaigning for president, that detainees could challenge their detentions in federal court under the constitutional doctrine of habeas corpus, which protects individuals from unlawful imprisonment by the government.

Obama, still a senator then, issued a statement calling the ruling "an important step toward re-establishing our credibility as a nation committed to the rule of law, and rejecting a false choice between fighting terrorism and respecting habeas corpus. Our courts have employed habeas corpus with rigor and fairness for more than two centuries, and we must continue to do so as we defend the freedom that violent extremists seek to destroy." The first challenges were decided on Nov. 20, just three weeks after Obama's election.

Lawyers from the Justice Department's Civil Division handle the Guantánamo litigation in coordination with intelligence agencies and the Department of Defense, which acts as warden of Guantánamo. The litigation process was built around the government's assertion that the bulk of the evidence is classified, a claim that has enabled the government to operate under a cloak of near total secrecy, with judges and defense attorneys barred from publicly discussing most aspects of the litigation. Court filings that reveal details about the cases undergo classification review before they are made public.

Intelligence and military officials take the lead in determining what can be released. As this story was going to publication, the Justice Department released an unclassified version of its appeal brief in the Uthman case. A number of details that were excised from Kennedy's final opinion appear in the appeals brief.

Justice Department spokesman Miller said, "as a general matter, Justice Department litigators are not responsible for classification or declassification decisions in habeas cases."

Officials at other agencies said they had a fairly free hand in removing information supplied for the government's case. "Whenever a court security officer identifies a document slated for posting on the court's public docket as potentially containing classified information, the officer refers that document to appropriate agencies for classification review," Maj. Tanya Bradsher, a spokeswoman for the Pentagon, said.

One government official who spoke on the condition of anonymity acknowledged that the classification process has been plagued with inconsistencies and that no one is coordinating the effort. In most declassified habeas filings, the names of all detainee-witnesses are removed; in others, a name or two slips past the redaction process.

Some government-ordered deletions clearly appear designed to conceal names of confidential informants, associations with foreign intelligence services and the identities of certain federal agents. But the Uthman case shows that many of the deletions go further.

"This censorship has nothing to do with protecting 'national security' and everything to do with covering up government mistakes and malfeasance," said Jonathan Hafetz, a professor at Seton Hall University School of Law who has represented a number of detainees in habeas litigation. The practice, he said, allows the government to "mislead the American public on issues of profound importance to the country by skewing the perception of who really is at Guantánamo."

There have been some attempts, but with limited results, to make more of the habeas proceedings public. Nearly two years ago, as the litigation was getting under way, three media organizations -- The Associated Press, The New York Times and USA Today -- sought access to the court filings in which the government argued for holding the detainees.

The government fought the request but Judge Thomas Hogan, then the chief judge of the U.S. district court in Washington, ordered the government to release redacted, unclassified versions of its filings within 14 days.

David Schulz, a First Amendment attorney who is representing the media group, said the government is flouting Hogan's order.

"The frustrating thing about this litigation is that the judge in no uncertain terms upheld the public's constitutional right to inspect the records of the habeas proceeding and yet, nearly two years after the documents were supposed to be filed and publicly available, we are still waiting to get properly redacted filings," Schulz said.

The government is now seeking to amend Hogan's order to include six new broad categories of information that it can restrict without review by a judge unless the detainee objects. Schulz has opposed this idea. Both sides are waiting to hear from Hogan.

When the media group first fought for access, just weeks after the 2008 presidential election, the Bush administration was still in office. But Schulz said the election has had no impact on the department's position in this area.

Said Schulz: "The Obama Justice Department has fought as hard and resisted as strongly the right that the public has to see these court records."