Sept. 11 Prosecutors Are in Plea Talks That Could Avert a Death-Penalty Trial

GUANTÁNAMO BAY, Cuba — Prosecutors have opened talks with lawyers for Khalid Shaikh Mohammed, the accused mastermind of the Sept. 11, 2001, attacks, and his four co-defendants to negotiate a potential plea agreement that would drop the possibility of execution, according to people with knowledge of the discussions.

Guilty pleas in exchange for life sentences could bring to an end the long-running case at the war court, which was set up by the George W. Bush administration and has been mired in pretrial proceedings focusing on the C.I.A.’s torture of the defendants. Nearly a decade after the men were arraigned, the military judge has set no trial start date.

No deal is expected soon. But guilty pleas resulting in life sentences could force the Biden administration to modify its ambition of ending detention operations at Guantánamo Bay and instead rebrand it as a military prison for a few men.

In an earlier, failed attempt at such talks during the Trump administration, the accused plotters demanded that they serve their sentences at Guantánamo, where they are able to pray and eat in groups. They specifically did not want to be sent to the supermax prison in Florence, Colo., where federal inmates are held in solitary confinement up to 23 hours a day.

The five men are accused of directing and training or providing travel arrangements and money to the 19 hijackers who crashed four commercial aircraft into the World Trade Center, the Pentagon and a field in Pennsylvania, killing nearly 3,000 people.

A plea deal would undoubtedly disappoint, if not enrage, death-penalty advocates among the victims’ family members. But other family members, including those troubled by the role of U.S. torture in the case and the delays, might see it as a fitting conclusion.

The path to a trial for the accused plotters of the worst terrorist attack in the United States has been impeded by legal and logistic challenges as well as a nearly two-year closure of the court during the coronavirus pandemic.

The discussions began last week amid the latest setback. The judge, defense and prosecution teams had traveled to Guantánamo Bay for three weeks of hearings meant to address disputes over evidence, particularly showing the role of the F.B.I. in the C.I.A. prison network where Mr. Mohammed and his co-defendants were tortured after they were captured in Pakistan in 2002 and 2003.

But before they could start, Cheryl Bormann, the lead lawyer for one of the defendants, Walid bin Attash, asked to step down from the case. She cited an unspecified in-house investigation of her “performance and conduct” by the chief defense counsel, Brig. Gen. Jackie L. Thompson Jr. of the Army.

No details were given. But the issue forced a delay in hearings that could stretch for months and provided an opening, according to a participant in the talks between the prosecution and the defense.

A lead case prosecutor, Clayton G. Trivett Jr., wrote on Wednesday to the defense teams proposing that they discuss “whether pretrial agreements are possible for all five cases.”

“While I cannot guarantee that we will come to terms over these next two weeks,” Mr. Trivett said in an email, “putting a concerted effort focused solely on possible agreements while we are all onboard Guantánamo, where your clients and teams are present, may be our best chance of at least determining if deals can be reached.”

Within days, the five defendants and their lawyers met in the courtroom to compile an initial list of requirements for the guilty plea, starting with removing the death penalty from the case. Lawyers for the five men submitted a joint list on Monday, participants said.

Although the prosecutors have begun the negotiations, a senior Pentagon official known as the convening authority must approve any deal. That role is currently held by Col. Jeffrey D. Wood of the Arkansas National Guard, who is also a lawyer in Little Rock, Ark., and was appointed to the civilian job by the Trump administration. Participants said the talks were expected to continue through the month to try to reaching some understandings to present to Colonel Wood.

The interim chief prosecutor, Col. George C. Kraehe of the Army, declined to comment, as did the chief defense counsel, General Thompson.

Both men are new to their jobs. Colonel Kraehe was mobilized to the job from the Justice Department in October. General Thompson, who runs the defense office but represents no single defendant, took over on Jan. 1.

A month later, General Thompson wrote President Biden to introduce himself, according to a person familiar with the matter. The general described the challenges that the military commissions system had experienced in getting cases to trial and proposed a new effort to improve relations between prosecutors and the defense, which were strained and not conducive to plea negotiations.

In early March, a lawyer at the National Security Council wrote back to General Thompson that the administration would not be taking a position on any of the cases, according to a senior administration official. The letter specifically did not take a position on plea deals — not endorsing the idea but not discouraging it, either.

Instead, the official described the letter as saying that Mr. Biden remained dedicated to responsibly reducing the detainee population at Guantánamo, which currently has 38 prisoners from the roughly 780 who were brought there from 2002 to 2008. Ten are charged but have yet to be tried.

The White House’s letter said that reducing the population could include resolving the pending military commissions cases through pretrial agreements, if appropriate, according to the official. But the letter also stressed that the White House would not prescribe what to do with any particular case or otherwise interfere with the process.

Caroline Krass, the general counsel of the Defense Department, was copied on the reply, the National Security Council lawyer said.

It is not clear what happened next. But on March 4, Colonel Kraehe met by video conference with the lead lawyers in all current prosecutions and told them his case prosecutors had the authority to begin negotiations.

Advocates for closure have suggested that some of the men who face charges could serve their sentences in the custody of another country. Convictions through plea deals might also persuade Congress — which forbids the transfer of detainees to the United States — to lift the restriction for the purpose of incarcerating inmates who have been convicted in secure, more efficient settings.

During the Trump administration, the convening authority, Harvey Rishikof, was exploring the idea of plea agreements. Attorney General Jeff Sessions found out about the talks, testimony in court showed, and called Defense Secretary James N. Mattis, demanding that there be no deal. Mr. Mattis then fired Mr. Rishikof, citing unrelated reasons.

A core issue is how many of the defendants beside Mr. Mohammed would serve life sentences without possibility of parole, and whether some of the accused accomplices with lesser roles in the attacks would serve shorter sentences. Lawyers for two defendants — a Saudi prisoner, Mustafa al-Hawsawi, and a Pakistani national, Ammar al-Baluchi, who is Mr. Mohammed’s nephew — have described them as ignorant of the Sept. 11 plot when they helped some of the hijackers with money transfers and travel arrangements from the United Arab Emirates.

Psychologists conducting interrogations for the C.I.A. waterboarded Mr. Mohammed 183 times; defense lawyers have pursued an overarching theory that because of its actions, the U.S. government lost the moral and legal authority to execute the defendants. Agents also kept the five defendants nude, beat them, strung them up by their arms in chains and subjected them to rectal abuse and sleep deprivation during the three and four years they were held in the so-called C.I.A. black sites before their transfer to Guantánamo in 2006.

As part of any plea agreement, the defendants would have to work with prosecutors, through their lawyers, on individual lengthy narratives known as a stipulation of fact — essentially a prosecution-approved admission of their crimes.

Once signed, the men could be brought to court for questioning by the trial judge, Col. Matthew N. McCall of the Air Force, on whether they cooperated willingly with the process. Under war court law, military juries — not judges — sentence defendants who plead guilty, generally from a range set in the plea agreement. The Pentagon would need to assemble a jury of U.S. officers to hear the statements and other presentations by both sides and then issue sentences, even if they are separately capped in secret pretrial agreements. That portion could span months.

People familiar with the talks said a military jury’s recent reaction to descriptions of C.I.A. torture of another prisoner in a lesser-known case might have contributed to the willingness of prosecutors to negotiate.

In October, the jury condemned as “a stain on the moral fiber of America” the agency’s cruel treatment of Majid Khan, a confessed courier for Al Qaeda, and urged the overseer of military commissions to grant clemency.