The Justice Department has quietly recanted nearly every major claim the Bush administration had made about "high-value" detainee Abu Zubaydah, a Guantanamo prisoner who at one time was said to have planned the 9/11 attacks and was the No. 2 and 3 person in al-Qaeda.

Additionally, Justice has backed away from claims intelligence officials working in the Clinton administration had also leveled against Zubaydah, specifically, that he was directly involved in the planning of the 1998 embassy bombings in East Africa.

Zubaydah's name is redacted throughout the 109-page court document, but he is identified on the first page of the filing by his real name, Zayn Al Abidin Muhammad Husayn. He was the first detainee captured after 9/11 who was subjected to nearly a dozen brutal torture techniques, which included waterboarding, and was the catalyst, the public has been told, behind the Bush administration's "enhanced interrogation" program. Former Vice President Dick Cheney has publicly admitted that personally approved of Zubaydah's waterboarding.

His torture was videotaped and the tapes later destroyed. The destruction of 90 videotapes of his interrogations is the focus of a high-level criminal investigation being conducted by John Durham, a federal prosecutor appointed special counsel in 2008 by then-Attorney General Michael Mukasey.

In recent months, former Bush speechwriter Marc Thiessen has been on a public relations campaign promoting his book, "Courting Disaster," in which he defended the torture of Zubaydah, claiming, among other things, that he reviewed classified intelligence that revealed Zubaydah's torture produced actionable intelligence that thwarted imminent plots against the United States.

But court documents unclassified last week debunk Thiessen's assertions as well as those made by, among others, George W. Bush, who said Zubaydah was one of al-Qaeda's "top operatives plotting and planning death and destruction on the United States."

For the first time, the government now officially admits that Zubaydah did not have "any direct role in or advance knowledge of the terrorist attacks of September 11, 2001," and was neither a "member" of al-Qaeda nor "formally" identified with the terrorist organization.

The government has a new set of eharges it is leveling against Zubaydah and claims he is being detained by the United States based on his "actions" as an "affiliate" of al-Qaeda that may have included the planning of a counterattack against US forces after the US invaded Afghanistan in November 2001 and a "thwarted" attack at the time of his arrest.

"The Government's accounts frequently have been at variance with the actual facts, and the government has generally been loath to provide the facts until forced to do so," said Zubaydah's attorney, Brent Mickum, in an interview. "When the Government was forced to present the facts in the form of discovery in Zubaydah's case, it realized that the game was over and there was no way it could support the Bush administration's baseless allegations. So it changed the charges."

The government wants the judge presiding over the habeas case to deny defense requests for evidence that would "undermine" government claims that Zubaydah worked in Bin Laden's "military and security plan to confront an American counterattack" in Khost, Afghanistan, after 9/11.

"The Government does not rely on any contention that [Zubaydah] did this work as an 'al-Qaida' deputy or because he was subject to al-Qaida command," according to the court document.

But the exact charges the government appears to be making here is unknown because the information is classified.

"Evidence suggesting that [Zubaydah] lacked knowledge of plans by other persons or groups would not undermine the Government's allegations about [Zubaydah's] own thwarted plans, or any other allegations" against him, according to the Justice Department's filing.

The government acknowledges that it’s case against Zubaydah is based entirely on the first six volumes of his diaries that he wrote beginning in 1992 [Please see this report for details about Zubaydah's diaries.] In the court filing, the government says that it filed a “factual return” on April 3, 2009, which included “six volumes of diaries written by REDACTED" and "an undated “propaganda video [Zubaydah] recorded before his capture in which [he] appears on camera expressing solidarity with Usama Bin Laden and al-Qaida.” The government further says that it does not rely on “any statements [Zubaydah] made after his capture” in Pakistan in March 2002.

But later in the filing, however, the government concedes that Zubaydah was not aligned with or directly associated with Bin Laden or al-Qaeda.

The government "does not contend that [Zubaydah] was a 'member' of al-Qaida in the sense of having sworn bavat (allegiance) or having otherwise satisfied any formal criteria that either [Zubaydah] or al-Qaida may have considered necessary for inclusion in al-Qaeda. Nor is the government detaining [Zubaydah] based on any allegation that [Zubaydah] views himself as part of al-Qaida as a matter of subjective personal conscience, ideology or worldview.

"Rather, [the government's] detention of [Zubaydah] is based on conduct and actions that establish [Zubaydah] was 'part of' hostile forces and 'substantially supported' those forces," states the Justice Department's point-by-point response to 213 discovery requests Zubaydah's attorneys made in connection with his habeas corpus case, which sought evidence to support the government's position that Zubaydah was a top al-Qaeda official.

The Justice Department declined to comment on what appears to be contradictory claims in its court filing.

The Bush administration claimed in April 2002, days after Zubaydah was captured in Afghanistan and moved to a CIA-operated black site prison in Thailand that he was a top al-Qaeda official.

Former Secretary of Defense Donald Rumsfeld described Zubaydah on April 1, 2002, as a "close associate of [Osama Bin Laden], and if not the number two, very close to the number two person in the organization. I think that's well established."

Nor did the Bush administration deviate from that position after Zubaydah was transferred to Guantanamo in 2006 and declared an "enemy combatant" in 2007 following a Combatant Status Review Tribunal.

John Bellinger, former legal adviser to Secretary of State Condoleezza Rice, said during a June 2007 briefing on Guantanamo Bay that Zubaydah helped plan the 9/11 attacks and was "extremely dangerous."

The Justice Department's response to discovery request "No. 21" says that "the Government has not contended in this [habeas] proceeding that [Zubaydah] had any direct role in or advance knowledge of the terrorist attacks of September 11, 2001, so [to] the extent that this request seeks information 'tending to show ... that [Zubaydah] did not know of the planned attacks of 9/11', the request seeks evidence about contentions the Government has not made."

The government's new position is significant because one of the August 2002 torture memos prepared for the CIA and signed by former Justice Department Office of Legal Counsel attorneys Jay Bybee, now a Ninth Circuit Appeals Court judge, that described the torture techniques interrogators could use against Zubaydah, asserted that he "is one of the highest ranking members of the al-Qaeda terrorist organization," "has been involved in every major terrorist operation carried out by al-Qaeda," and was "one of the planners of the September 11 attacks" and that his torture was necessary in order to thwart pending attacks on US interests, which the CIA claimed Zubaydah knew about.

Exactly what Zubaydah's attorneys had requested from the government in their discovery filing is unknown as the document has not been cleared for release. The Justice Department asked the judge presiding over the case to deny virtually every discovery request sought by his attorneys, explaining, in some instances, that the government no longer relied upon the explosive allegations the Bush administration made about Zubaydah when he was captured and subsequently tortured.

At the time the response to the discovery requests was filed in the fall of 2009, the government argued that the court should “stay further evidentiary proceedings” because it could interfere with Durham’s criminal probe into the destruction of the torture tapes. Durham filed a motion under seal thereafter that said as much. A report published in the Washington Post last week said Durham’s probe is now winding down.

According to Mickum, the government's "entirely new position" about Zubaydah was revealed late last year in a 50-page Factual Return that included 2,500 pages of exhibits.

"I'm not surprised at all that the Government has dropped the old charges against our client and is alleging new charges against him," Mickum said in an interview.

"That is their tried and true modus operandi. That's exactly what they did with my client Bisher al Rawi. He was initially charged with associating with a known al-Qaeda figure in London. Unfortunately, Bisher was associating with him at the express request of Britain's MI5 [intelligence service]. After we established that he worked for MI5, the US simply changed the charges against him, alleging that he had terrorist training in Bosnia and Afghanistan.

"Once again, we were able to show those charges were utterly bogus when we proved that Bisher had never left England from 1998 until his fateful business trip to Africa, where he was arrested by the CIA, rendered to the 'Dark Prison' in Afghanistan and tortured, tortured at Bagram Air Force base and tortured in Guantanamo. What all these cases have in common is torture, and [Zubaydah's] case has that in spades. Given, the government's history, it is not likely they would simply let him go and apologize. No, when their case falls apart, they rejigger the evidence, and come up with new charges and we will defend the new charges with the same zeal we defended the earlier bogus charges."

Zubaydah's attorneys argued in his initial petition for habeas corpus filed in February 2008 that he was not a member of al Qaeda, that he had no knowledge of any terrorist operations, and that the military camp he was alleged to be affiliated with, Khaldan, was closed by the Taliban after it refused repeated demands that it fall under the formal control of Osama bin Laden and al-Qaida.

"We have never deviated from that position, and now the government admits that we were correct all along," Mickum said.

Indeed, the Justice Department's response agrees with Zubaydah's attorneys that Khaldan was "organizationally and operationally independent" of al-Qaeda's camps and backed off of other claims made by Bush administration officials that Zubaydah knew the identities of specific individuals who trained at Khaldan and later went on to al-Qaeda-operated camps and allegedly took part in terrorist activities.

"The Government has not contended in this proceeding that petitioner selected or knew the identities of specific persons who were selected to leave Khaldan for training at al-Qaida camps," the filing states.

Nor does the government contend that Zubaydah was responsible for paying Khaldan's "expenses" or that he financed specific terrorist operations that may have had ties to Khaldan. Therefore, the Justice Department said, evidence Zubaydah's attorneys requested to support these earlier claims should be denied.

The government's new position also dramatically changes the substance of the final contents of the 9/11 Commission's report, as it relates to Zubaydah. The report said he was the leader of Khaldan.

When she revealed last year that Zubaydah had been waterboard 83 times in August 2002, blogger Marcy Wheeler noted that the 9/11 Commission had obtained "just ten pieces of information are sourced to Abu Zubaydah’s interrogation reports."

"...There are several other damning details that come from this analysis," Wheeler wrote. "One of the ten pieces of intelligence that appears in the 9/11 Report–regarding Abu Zubaydah’s role running terrorist training camps–came from July 10, 2002, before the CIA first received oral authorization to use torture. Thus, it either came from persuasive, rather than coercive, techniques. Or it came from treatment that had not been legally approved."

The 9/11 report also said Zubaydah was a "major figure" in the "Millennium plot," claiming he was one of the masterminds behind a plan to blow up a hotel in Jordan and the Los Angeles International Airport (LAX). The 9/11 report cited several intelligence memoranda from then-counterterrorism czar Richard Clarke that Zubaydah was planning "a series of major terrorist attacks" on Israeli and possibly US targets and was working closely with Bin Laden.

Clarke declined numerous requests for comment.

But the Justice Department no longer supports any of those claims, according to the court document.

When asked about what the 9/11 Commission was told, Mickum suggested that the panel was lied to by the CIA.

"After torturing our client, the CIA knew he was never a member of al-Qaeda and that he had no knowledge of any al-Qaeda terrorist activities," Mickum said. "And this fact was confirmed after other members of al-Qaeda like [self-professed 9/11 mastermind Khalid Sheikh Mohammed] and the [alleged mastermind of the USS Cole bombing] al Nashiri were tortured."

Zubaydah was also identified as Bin Laden's "lieutenant" in the infamous August 6, 2001, Presidential Daily Brief titled, "Bin Laden Determined to Strike in US, " which alleged that he "helped facilitate" the plot to detonate a bomb LAX. FBI officials obtained that information from Ahmed Ressam, who was actually convicted for the crime in April 2001.

In exchange for a lenient sentence he made up stories about Zubaydah's connections to Bin Laden and his role at Khaldan, which Ressam attended for five to six months in 1998). Ressam also said Zubdaydah told him in 1998 that, independent of Bin Laden, he was preparing his own attack against the United States. He later recanted those claims.

In an exclusive interview last year, Jack Cloonan, a former FBI special agent assigned to the agency’s elite Bin Laden unit, said the CIA and the Bush administration were flat wrong in designating Zubaydah as a top official in al-Qaeda.

"To cast him and describe him as the al-Qaeda emir or leader for the subcontinent or worse … I think was a mistake…. Based on his age and ethnicity, [he] would [n]ever

be brought into the inner circle of al-Qaeda," Cloonan said.

There was also the question of Zubaydah’s personality. “My partner had a chance to look at a lot of Abu Zubaydah’s diaries [which forms the basis of the government's case], poems and other things that he has written and he said that after reading this you just come away with the feeling that this is a guy who can’t be trusted or be given huge amounts of responsibility.”

At his Combatant Status Review Tribunal in March 2007, Zubaydah said that his torturers eventually apologized to him and told him they concluded he was not a top al-Qaeda lieutenant as the Bush administration and intelligence officials had claimed (h/t Marcy Wheeler).

“They told me sorry we discover that you are not number three [in al-Qaeda], not a partner, even not a fighter,” Zubaydah said during his tribunal hearing.

Editor's note: This story has been updated.