Why Khalid Sheikh Mohammed’s 9/11 Trial Has Taken So Long

More than two decades after the September 11, 2001 attacks, Khalid Sheikh Mohammed and three co-defendants are still awaiting trial. A US military judge has now set June 5, 2028 as the start of the trial on the merits, rejecting the prosecution's proposed January 2027 date because unresolved pre-trial litigation requires more time.

The delay is extraordinary. Mohammed was captured in 2003, the charges were referred to the military commission in 2012, and the case has since been consumed by disputes over evidence, classified information, discovery and the consequences of his years in CIA custody.

So why has a case arising from one of the most consequential terrorist attacks in US history taken so long to reach trial?

Who Is Khalid Sheikh Mohammed?

The 9/11 Commission called Khalid Sheikh Mohammed the “principal architect” of the attacks and identified him as the chief manager of al-Qaeda's “planes operation”. It said he developed the idea of training pilots to hijack aircraft and crash them into buildings in the United States before presenting the proposal to Osama bin Laden.

What Happened After His Capture?

Mohammed was captured in Pakistan on March 1, 2003, according to the FBI, and subsequently held in US custody, including the CIA's secret detention programme.

The Senate Intelligence Committee documented the CIA's use of coercive interrogation techniques, including waterboarding, during the programme. Its report records that Mohammed was waterboarded 183 times.

His treatment in CIA custody would later become central to disputes over whether statements attributed to him and other defendants were obtained voluntarily and could be admitted as evidence.

What Is Mohammed Charged With?

The military commission charges Mohammed with offences including conspiracy, murder in violation of the law of war, attacking civilians, attacking civilian objects, destruction of property, aircraft hijacking, terrorism and intentionally causing serious bodily injury.

The charges were referred to the military commission in 2012, after the federal prosecution had been abandoned.

Why Wasn't He Tried In A Federal Court?

The case was not originally headed to Guantanamo.

In November 2009, Attorney General Eric Holder announced that Mohammed and four co-defendants would be prosecuted in federal court in New York.

That plan was later abandoned after Congress imposed restrictions on transferring Guantanamo detainees to the United States for trial.

In April 2011, the Justice Department announced that the five defendants would instead be referred to military commissions and that the federal prosecution would be dismissed.

The military-commission system therefore added another layer of procedural complexity to an already difficult case.

Why Did The CIA Interrogations Become A Legal Problem?

The issue is not simply whether Mohammed was subjected to coercive treatment. It is whether that history affected the admissibility and reliability of statements prosecutors want to use.

The military commission has spent years litigating statements made during and after CIA detention. One continuing dispute concerns FBI Letterhead Memoranda, or LHMs, which summarise statements defendants allegedly made to FBI personnel after the CIA detention period.

The defence has sought to suppress those statements, while the government has defended their use. The commission has had to examine the circumstances surrounding the interviews and their relationship to the defendants' earlier detention.

The result was a legal problem that went beyond the original allegations: before prosecutors could present their case over the events of 2001, the commission had to determine how evidence gathered after years of secret detention and coercive interrogation could be used at trial.

Why Has The Trial Taken So Long?

The delay has no single cause.

The first was the change in legal forum, from a planned federal prosecution to military commissions. The second was the CIA detention programme, which generated years of litigation over statements and the circumstances in which they were obtained. A third involved the classified nature of some of the government's evidence, requiring separate procedures governing disclosure and use.

Then came years of discovery, suppression and procedural litigation.

The commission's June 2026 Trial Conduct Order illustrates the extent of that process. Rather than simply setting the prosecution's proposed trial timetable, the commission established a framework intended to drive the outstanding discovery, evidentiary and compliance disputes towards resolution.

The later scheduling order rejected the prosecution's proposed January 11, 2027 start because it was incompatible with the existing timetable. The commission said more time was needed to address outstanding pre-trial matters, including the FBI LHM suppression litigation.

The key point is that the trial has been delayed not because the charges remain undefined, but because the legal fight over how prosecutors can prove those charges remains unfinished.

What Happened To The 2024 Plea Deal?

The case briefly appeared to have another route to a conclusion.

On July 31, 2024, the military commission's convening authority signed pre-trial agreements with Mohammed, Walid bin Attash and Mustafa al-Hawsawi. Under those agreements, the defendants would plead guilty in return for the government not seeking the death penalty.

Two days later, Defence Secretary Lloyd Austin intervened. He withdrew the convening authority's power to enter such agreements and withdrew from the three agreements himself.

The agreements did not bring the case to a conclusion after Austin withdrew from the three agreements, leaving the prosecution to continue before the military commission.

What Happens In 2028?

The latest order sets June 5, 2028 as the start of the trial on the merits and provides an overarching timetable for the proceedings while preserving existing orders governing discovery, evidentiary and compliance matters.

A trial date, however, is not a guarantee of a verdict. Further motions and legal developments could affect the schedule as the parties continue preparing for trial.

The attacks took place in 2001. Mohammed was captured in 2003. The charges were referred to the military commission in 2012. A plea deal briefly offered an alternative in 2024, before being withdrawn. Now, in 2026, the commission has set its latest timetable for reaching the merits.

More than two decades after September 11, the central question is not simply whether Khalid Sheikh Mohammed and his co-defendants will face trial. It is what evidence can legally be used when that trial finally begins.