Sketch of Khalid Shaikh Mohammad and members of his defense team by Janet Hamlin.

Sketch of Khalid Shaikh Mohammad and members of his defense team by Janet Hamlin.

Guantanamo Naval Base, Cuba – The prosecution in the Sept. 11 case has entered into plea negotiations with legal teams for the five defendants accused of planning the attacks that would take the death penalty off the table in exchange for guilty pleas to war crimes, three sources with knowledge of the talks said this week.

Such agreements could end the strained, long-running attempt to hold accountable those charged with the worst-ever attacks on U.S. soil – a dogged effort that has now spanned four presidential administrations.

However, the stunning turn of events could equally be seen as merely the start of a complex, multiagency process that is far from guaranteed a successful outcome. The Pentagon official who oversees the military commissions, the convening authority, approves all plea agreements and sentences. The current convening authority, Jeffrey Wood, gave prosecutors the green light to start plea discussions with the defense teams, according to one participant in the talks. That source said that prosecutors asked the defense teams their preferred terms for plea deals, and then began discussing terms that would be brought to Wood’s office.

Just last week, it appeared the military commission against Khalid Shaikh Mohammad and his four alleged co-conspirators remained in eternal pretrial limbo with perhaps a year or more remaining before a trial that itself could last at least a year. Plea deals would foreclose a trial on the guilt or innocence of the accused – and the accompanying wars over the admissibility of evidence the defense teams claim is tainted by torture – paving the way towards a more concise sentencing trial at which a panel of military officers will serve as jurors.

The possible break in the case comes as it faces a 10-year anniversary of the defendants’ arraignment on May 5, 2012. Over the past several years, the case has borne a sustained torrent of acrimony over defense teams’ access to evidence and witnesses related to the past abuse of their clients at CIA black sites before they arrived on Guantanamo Bay in September 2006. The global Covid-19 pandemic also delayed the proceedings for about 18 months. The current judge, Air Force Col. Matthew McCall, is the fourth to preside over hearings in the case. This ongoing three-week session, just his third, did not begin with any open court sessions due to a request by one of the veteran lead lawyers to withdraw from the case.

While that twist seemed yet another in a maddening list of unpredictable delays, the prosecution used the opening to initiate negotiations that could finally push the historic case to its conclusion.

One of the prior convening authorities, Harvey Rishikof, failed in his effort to secure plea agreements after reaching out to defense teams in the middle of 2017. However, that was during the Trump administration, which opposed the closure of the Guantanamo Bay detention facility. Defense teams claimed that Rishikoff’s firing in 2018 resulted from his pursuing plea talks and that the case against their clients should be dismissed for “unlawful influence.” As part of that ligation, lawyers learned that Trump’s attorney general, Jeff Sessions, made his opposition to plea deals in the Sept.11 case known to Secretary of Defense James Mattis.

The second judge on the case, Marine Col. Keith Parrella, denied the unlawful influence claims in a January 2019 ruling that cited competing evidence from prosecutors that the termination resulted from unrelated management issues. The episode nevertheless highlighted some of the challenges – both practical and political – associated with a convening authority’s role in executing a plea deal for such a highly charged case connected to multiple stakeholder agencies.

The Biden administration has said it intends to close the facility and has resumed the process of releasing detainees who have not been charged in the military commissions. Thirty-eight detainees remain at the facility, including 10 facing charges in the commissions. The new chief defense counsel, Army Brig. Gen. Jackie L. Thompson Jr., who is currently on his first trip to Guantanamo Bay, declined to comment on inquiries related to plea discussions.

The acting chief prosecutor, Army Col. George Kraehe, also did not respond to written questions about whether the Biden administration had issued a policy encouraging the exploration of plea agreements in the 9/11 case or the three other commissions in pretrial litigation. Those include the case against Abd al Rahim al Nashiri, who faces a possible death sentence for his alleged role in the USS Cole bombing; Abd al Hadi al Iraqi, an alleged senior al Qaeda operative facing a life sentence; and the case of Encep Nurjaman, Mohammed Nazir bin Lep and Mohammed Farik bin Amin, who also face life sentences for accused roles in terrorist bombings in Indonesia in 2002 and 2003.

To reach a deal, defense attorneys in the 9/11 case and the government will have to agree on sentencing ranges for defendants accused of varying degrees of culpability for the attacks that killed nearly 3,000 people. Mohammad is alleged to have received assistance from Ramzi bin al Shibh, believed to be an important assistant in the planning as well as the organizer of the cell of hijackers in Hamburg, Germany; Walid bin Attash, who is accused of helping to train hijackers and conducting early “casing” missions to test flight security; and Ammar al Baluchi and Mustafa al Hawsawi, who allegedly sent money and other forms of assistance to the hijackers. Al Baluchi is Mohammad’s nephew.

Critics of the detention operations and the commissions have long said that plea agreements are consistent with the goal of closing the detention facility, given the protracted nature of the proceedings – not to mention anticipated appellate reviews that would likely take several years. The location of any post-conviction confinement presents a potential quandary, however, one whose policy implications are out of the hands of Wood and the prosecutors. It has been widely understood for years that at least some defendants would prefer to serve significant parts of their sentences at Guantanamo Bay to avoid the disruption and uncertainty of new confinement arrangements. Over the years, lawyers for the defendants have reported an increasing number of health ailments resulting from their past torture, isolation and humiliation inflicted by the U.S. government.

The inclusion of this provision in proposed plea deals could find opposition from Biden administration officials who want the detention facility completely closed; other officials may be satisfied with limiting the facility only to individuals who have been convicted of war crimes.

Presently, federal law bars the transfer of detainees to the United States. The State Department has led negotiations with countries willing to take Guantanamo Bay detainees – a process that has proven challenging even for detainees deemed to be safe for release by an interagency review process run by the Periodic Review Board. The current political climate has signaled the need for any plea deals to bind their terms past the Biden administration.

Beyond these thorny details, the government and defense lawyers first will have to hash out stipulations of war crimes to which the defendants are willing to admit. Prosecutors would then present a case of aggravating factors to a jury of military officers to outline the horrors of Sept. 11, 2001 and the continuing tragedy that includes the devastating impact on multiple generations of surviving family members.

Defense lawyers would also insist that, at the sentencing trial, details of their clients’ past torture by the CIA and conditions of confinement at Guantanamo Bay are presented – a process that will likely involve considerable legal wrangling and involvement from the intelligence community.

A recent case suggests this evidence could have an impact on a jury. Last fall, a panel of military officers recommended clemency for Majid Khan, a former courier for al Qaeda, after he gave a lengthy and graphic statement at his sentencing trial about his past torture by the CIA and subsequent hardships while on Guantanamo. As part of a 2012 plea deal, Khan admitted sending money to the Southeast Asian terror group Jemaah Islamiyah for the August 2003 bombing that killed eight people and wounded several dozen others at the J.W. Marriott in Jakarta, Indonesia. Wood, in his capacity as convening authority, gave Khan a 10-year sentence last week that made him immediately eligible for release. The government has not yet announced a country willing to take Khan.

On Tuesday afternoon, following news articles on plea negotiations by Lawdragon and the New York Times, lawyers for al Baluchi confirmed the reports.

“Negotiated agreements are part of all criminal cases, and negotiations have taken place throughout the case,” James Connell, the lead lawyer, said in a written statement.

Connell added that “the vast majority of capital cases in the United States are resolved by plea.”

At the start of this session in the 9/11 case, Cheryl Bormann, the lead lawyer for bin Attash, asked to withdraw from the case as a result of an internal investigation by the Military Commissions Defense Organization into her “performance and conduct.” She later departed the U.S. Naval Base, but other long-time lawyers and staff on her team have remained here. The government’s managing trial counsel, Clay Trivett, emailed the five defense teams last Wednesday suggesting that the parties use the next two weeks to explore deals, according to an individual participating in these talks. The next day, Judge McCall wrote in a brief order that he was delaying the hearings until at least March 21 based on “a joint request” by the prosecution and defense.

One of the complications of Bormann’s withdrawal – if approved by McCall – is that defendants facing the death penalty require representation by a learned counsel experienced in capital defenses. However, lawyers have previously said that plea talks involving a maximum sentence of life or less may not need input or approval from a learned counsel. The chief defense counsel is nevertheless likely to find a replacement for Bormann who meets the learned qualifications.

The source who is participating in these plea negotiations expected them to continue throughout this week and next.

About the author: John Ryan ( is a co-founder and the Editor-in-Chief of Lawdragon Inc., where he oversees all web and magazine content and provides regular coverage of the military commissions at Guantanamo Bay. When he’s not at GTMO, John is based in Brooklyn. He has covered complex legal issues for 20 years and has won multiple awards for his journalism, including a New York Press Club Award in Journalism for his coverage of the Sept. 11 case. View our staff page