WASHINGTON — Across four presidencies, the question of how to obtain a measure of justice in court for the attacks of Sept. 11, 2001, has vexed American officials. A military tribunal case against five Guantánamo Bay detainees accused of conspiring with the hijackers has spun its wheels for more than a decade with no trial in sight.
Now it is the Biden administration’s turn. Prosecutors have proposed ending what could be more frustrating years of litigation, suggesting a deal in which the defendants would plead guilty in exchange for being spared the possibility of the death penalty. But prospects for resolving the case remain murky, underlining political and legal obstacles that have hardened in the generation since the attacks.
The White House is distancing itself from the negotiations, declining to weigh in and leaving it to the Pentagon to decide how best to proceed. Officials there, however, are said to be uncertain they have the right to decide on a course of action with such major implications.
The issue remains politically fraught. Some relatives of the nearly 3,000 victims of the Sept. 11 attacks want a trial with the prospect, however distant, of executing Khalid Shaikh Mohammed, who is accused of being the mastermind of the attacks, and his four co-defendants. Others oppose the death penalty on principle, have no faith that the tribunals will obtain justice or have become resigned to the idea that, because the defendants were tortured by the Bush-era C.I.A., capital punishment is unlikely.
Influential Republicans in Congress have opposed lifting legal restrictions on transferring detainees to a prison on domestic soil — a ban that makes it impossible to put the five defendants on trial before the more functional civilian court system.
For over a decade, the case has been bogged down by seemingly ceaseless disputes.
Under President Barack Obama in 2009, Attorney General Eric H. Holder Jr. intended to bring the five prisoners to Manhattan for trial in federal court. But the plan collapsed amid a wave of fear after an unsuccessful terrorist attack that Christmas. Congress barred the transfer of the detainees onto domestic soil, and the Obama administration reluctantly brought the case before a military commission instead.
A decade later, under President Donald J. Trump, Attorney General William P. Barr decided that the Guantánamo military commissions system “had become a hopeless mess,” as he wrote in his memoir, and concluded that it should be abandoned. The observation was especially notable because in September 2001, as a private citizen, he had suggested the use of tribunals to President George W. Bush’s White House.
Under Mr. Barr, the Justice Department had begun a fresh look at the evidence and determined it could win a conviction in federal court. Officials intended to keep pursuing the matter as a capital case, but they did not analyze the likelihood of sustaining any death sentences upon appeal in light of the torture, according to a person familiar with those deliberations.
Mr. Barr asked senior Republican lawmakers to drop the transfer ban to allow a trial in federal court after all, arguing that it should be separate from the idea of closing the Guantánamo prison. (Mr. Trump had vowed to keep the prison open, and lifted Mr. Obama’s closure order.) But congressional Republicans, who had invested heavily in undermining Mr. Holder’s plan a decade earlier, did not want to reverse course. The idea went nowhere.
Now, under President Biden, senior national security lawyers are wrestling with whether to endorse a plea deal. Prosecutors presented the question to the administration nearly a year ago, but the White House has so far steadfastly refused to weigh in, according to officials familiar with internal deliberations.
Instead, the question is currently being managed by the Pentagon’s general counsel, Caroline D. Krass. During the Obama administration, she had been the general counsel for the C.I.A.
What to Know: The Sept. 11 Case at Guantánamo Bay
The crime. Khalid Shaikh Mohammed, the accused mastermind of the Sept. 11 attacks, and four other defendants are facing charges in a U.S. military tribunal at Guantánamo Bay of aiding the hijackings that killed nearly 3,000 people. The charges carry the death penalty.
Late last year, Ms. Krass convened a secure videoconference meeting with senior lawyers from several other agencies. All signaled provisional support for trying to reach a plea agreement, according to people briefed on the sensitive internal deliberations and who spoke on the condition of anonymity.
The circle of officials Ms. Krass has consulted is said to include Rebecca Ingber, a senior State Department lawyer and expert in international and national security law, and Matthew G. Olsen, the head of the Justice Department’s national security division.
In 2009, Mr. Olsen led an interagency task force that re-examined the roughly 240 detainees still at the prison and recommended who should be transferred, prosecuted or held in indefinite wartime detention without trial.
Mr. Obama had established the task force as a first step toward closing the prison. The idea was to transfer to other countries as many detainees as possible, put on trial those who could be prosecuted, and house both convicts and those deemed untriable but too dangerous to release in a different prison inside in the United States. Congress blocked that plan, but Mr. Obama significantly reduced the detainee population. Today, only 35 prisoners remain.
The current discussions over a plea agreement do not address where the men would serve their sentences, which could be up to life in prison. For now, because of the transfer ban, they would stay at Guantánamo.
Instead, the talks have focused in part on how they would serve any sentence. The defendants want pledges that they will not be held in supermax conditions or solitary confinement — they are allowed to eat and pray together now — and will have periodic access to lawyers, according to people familiar with the proposed deal.
Some also want a civilian-run mental health program aimed at treating what they say are the continuing effects of torture from their Bush-era C.I.A. interrogations: traumatic brain injuries, sleeplessness and other disorders.
Prosecutors call these factors “policy principles,” and in court filings have said they have been “under active consideration by various levels of the government” since March.
Ms. Krass, Mr. Olsen and Ms. Ingber declined to comment, as did a spokesperson for the National Security Council. A senior Pentagon spokesman, Chris Meagher, said by email that “U.S. government officials are continuing to discuss the proposed policy principles in connection with extremely complex cases involving numerous interagency equities.”
In March, as The New York Times has reported, a lawyer at the National Security Council wrote a letter to officials in the military commissions system saying that the White House would take no position on any case. The letter copied Ms. Krass.
The letter said that Mr. Biden remained dedicated to reducing the detainee population at the prison and that the goal could include resolving pending cases through pretrial agreements — a framing that seemed to refer to comparatively minor cases, in which a detainee could serve out a sentence and then be released. But it stressed that the White House would not prescribe what to do in any case or otherwise interfere.
Mr. Mohammed and the other four prisoners were captured in Pakistan in 2002 and 2003 and tortured by the C.I.A., which prioritized gathering intelligence on Al Qaeda and future attacks over obtaining lawful evidence. They were transferred to the military prison at Guantánamo in 2006.
Logistical challenges, fights over the rules and resistance by the C.I.A. to declassify information about the defendants’ first years of detention have loomed over the proceedings. Years of revelations about their torture in detention and the potential for the F.B.I.’s evidence against them to be contaminated by their prior treatment have led even proponents of the death penalty to privately question whether such a sentence could be sustained on appeal.
For now, the current military judge in the case, Col. Matthew N. McCall, has canceled all public hearings since March, when prosecutors who had been on the case for more than a dozen years proposed the plea talks.
But none of the parties seem to want to return to court for yet more pretrial hearings as they wait for the Biden administration to decide.
If hearings toward a trial do resume, it will ultimately be up to Colonel McCall, or a future judge, to continue examining crucial pretrial issues, including which evidence is too tainted by torture for use, and whether a remedy would be to remove the possibility of capital punishment. The process could grind on for an undetermined period of time even before a jury is seated for what could be a yearlong trial, followed by more years of inevitable appeals.
Senator Lindsey Graham, a South Carolina Republican who has long favored military commissions and having a wartime prison where terrorism suspects could be held and interrogated without trial, said this month that he had supported Mr. Barr’s idea of bringing the case to federal court, as long as Mr. Trump was in office. But he did not support the idea now, he said, because he did not trust Mr. Biden to keep Guantánamo open once its most notorious detainees were gone.
“I told Barr that I get the desire to accelerate this trial and bring about justice for the 9/11 families,” he said. “That is a worthy goal. But I don’t want to do anything to undermine the ability to hold someone, if we capture someone who has valuable intelligence.”