How the legacy of torture has vexed the quest for 9/11 justice

Now, 25 years later, the costs and trade-offs made then are still reverberating in the agonising wait for a trial in a faraway military court where the legacy of torture hangs over the September 11 case.

Military judges have now thrown out all of the key confessions in the death penalty cases at Guantanamo Bay, Cuba, because the defendants were tortured by the CIA.

The fifth and final ruling came early last month. Within weeks, the Supreme Court declined to review a plea deal between prosecutors and Mohammed and two others accused of conspiracy in the case. The prisoners would have received life sentences in exchange for publicly admitting to their specific roles in the plot.

Could this be a turning point for the September 11 families who have waited so long for a day of reckoning? The judge recently set a June 5, 2028, trial date.

“I do think it’s an important moment,” said Jessica Trant, whose father, Dan, a bond trader, was killed at the World Trade Centre. “A trial would at least give us the chance to hear the evidence, confront what happened and maybe take back a little of the power we’ve lost along the way.”

That said, Trant added, “I also know that just because we’re moving towards a trial doesn’t mean we’ll actually get one.”

John Ryan, a former taskforce commander at ground zero and chief of the Port Authority Police, said two years was too long to wait. He worries that lawyers who have been serving on the case as capital defenders could age out, or another issue could emerge.

“Let’s move the trial date up so that no unforeseen issues can surface,” he said. “This would also support the elder family members who want to see justice in their lifetimes.”

But the other death penalty case at Guantanamo is going first: jury selection began last month in the trial of a Saudi man who is accused of having a key role in the suicide bombing of a US Navy warship in a harbour in Yemen on October 12, 2000. Seventeen US sailors were killed in the Qaida attack, and dozens more were wounded.

Hearings in that case recently focused on whether the defendant, Abd al-Rahim al-Nashiri, is too damaged by his torture while he was in CIA custody from 2002 to 2006 to go to trial.

Here is a look at five fateful decisions that led to this day.

Mohammed was captured in Pakistan in March 2003 and taken to a secret CIA prison in Poland, called a black site. He was, among other things, waterboarded in a desperate search for the whereabouts of Osama bin Laden and information about other potential sleeper cells and plots.

Call it the original sin. The United States could have transferred him to Guantanamo, where the military was holding about 650 detainees from more than 40 countries at the time. Or he could have been sent to the United States.

“From the very beginning he said, ‘Take me to New York, give me a lawyer, and I’ll be happy to talk to you,’” Rita Radostitz, one of his lawyers, said in court in September 2021. “But instead of doing that, instead of taking him up on that offer, the government made a choice to take a different path.”

But the CIA cannot operate on US soil.

The United States took him on a three-and-a-half-year odyssey through US-controlled prisons from Eastern Europe to Afghanistan, where he was held incommunicado and, according to his lawyer, questioned hundreds of times, sometimes three times a day.

By 2006, the existence of the once-secret prison system had been revealed, and Bush had the defendants transferred to Guantanamo for trial.

But there was a problem. What the prisoners had told US interrogators hundreds of times in the black sites was undeniably coerced and would be inadmissible at any US court.

Putting them on trial, Bush Administration lawyers decided, would require new evidence. So federal agents called “clean teams” were summoned to Guantánamo to obtain fresh confessions.

This time, in January 2007, the prisoners were told their participation was voluntary.

The prisoners were taken in blindfolds and shackles to a former CIA black site at Guantanamo for questioning. The Bush administration also chose to omit a few key components: the prisoners still had not been allowed to consult lawyers, and they were not told that their hundreds of previous statements could not be used against them.

These decisions would prove catastrophic two decades later.

Hearings in the case of Mohammed and four other men also accused of conspiracy had barely begun when Barack Obama was elected in 2008. The new President suspended the proceedings at Guantanamo.

Attorney-General Eric Holder announced, after a period of analysis, that the Obama Administration had chosen to put the September 11 defendants on trial in federal civilian court in New York.

The Obama Administration did not immediately transfer the defendants to New York or any other trial venue, even as civilian prosecutors concluded they could not use the so-called clean-team confessions.

The federal prosecutors thought they would be inadmissible because the agents who questioned the men at Guantánamo had not read them a Miranda warning.

The decision to try the men in New York had led to a political outcry, and Congress forbade the use of federal funds to transfer them to the United States for trial.

The case was returned to Guantanamo, and military prosecutors chose a different path. They would seek to use the clean-team confessions – which have now been rejected by three military judges and a military court of appeals because of the prisoners’ years of torture and isolation.

Still bitter in 2024, Holder blamed “the politicians and hacks who second-guessed my decision to bring cases in the effective federal courts”. He said, “Had it not been for their political machinations, Khalid Sheikh Mohammed would just be a bad memory now”.

In 2018, the first military judge in the case, Colonel James L. Pohl of the Army, suppressed the clean-team confessions of the then-five defendants in the September 11 case. (Since then, one was found to be mentally unfit to face trial.) The judge ruled that a framework set up by prosecutors to protect CIA secrets was unfair. The information provided to the defence lawyers, the judge ruled, denied them the “particularity and nuance necessary to present a rich and vivid account of the 3-to-4-year period in CIA custody”.

Prosecutors appealed, declaring the 2007 statements crucial capital trial evidence. Years of litigation examined the CIA programme of violence and isolation, culminating last month with the military judge throwing out the statements of the fourth and final September 11 defendant.

In the summer of 2024, Defence Secretary Lloyd J. Austin III withdrew from plea agreements that prosecutors had said were “the best path to finality and justice in this case”.

Prosecutors had not so secretly negotiated for years with Mohammed and two other defendants. In exchange for life sentences, the defendants would openly admit to their specific roles in the hijacking plot that killed 2976 people and give up nearly every avenue of post-conviction appeal.

Prosecutors would present their case to a military jury. The prisoners agreed to answer written questions from relatives of the dead through a process known as restorative justice.

But Austin said he was unaware of the deal and chose to revoke it.

That decision led to two more years of litigation. Lower courts ruled that Austin acted too late to withdraw from the contract; then, a civilian court ruled that he had the power to do it. On October 19, the Supreme Court decided not to second-guess Austin’s authority to make that decision.

For now, the trial of Mohammed and the others is on track to start June 5, 2028.

Tom Resta has gone to Guantanamo four times to watch the proceedings and has no faith that the trial date will hold.

“We were supposed to have a trial starting in 2021,” said Resta, whose brother John and sister-in-law Sylvia were killed at the World Trade Centre. She was seven months pregnant.

This article originally appeared in the New York Times.

Written by: Carol Rosenberg

Photographs by: Dave Sanders, Erin Schaff and Doug Mills

©2026 THE NEW YORK TIMES

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