Khalid Shaikh Mohammed, a Pakistani national, is accused of being both the mastermind of the attacks and a high-ranking al-Qaeda operative. He has been in US custody since 2003 and was transferred to Guantanamo Bay prison in 2006. He appeared in court with the four other accused, each defendant and team of lawyers at their own table, with interpretation available.
They all wore traditional Islamic or Middle Eastern garb, Mohammed with a striped headscarf wrapped around his hair, highlighting his reddish-orange-dyed beard. Some had Palestinian scarves on display. Decisions by the judge in the coming weeks and months are vital to the framework of the trial itself, which Cohen last month set for January 2021, after years of pretrial proceedings.
The hearings come just days before the US is set to hold memorial services for the nearly 3,000 people killed in the attacks carried out by al-Qaeda 18 years ago.
The process is to continue throughout the month, with hearings even scheduled for Wednesday, the anniversary of the attacks. US President Donald Trump is to take part in some of the services on Wednesday in Washington, while additional events are to be held in New York City, the scene of the largest devastation and most fatalities, after planes crashed into the World Trade Center.
The events of that fateful day were not directly mentioned in the morning session of the pretrial hearings. Instead the focus turned to legal wrangling over what evidence might be allowed, how torture would affect that evidence and the type of question the defence would be able to ask witnesses during trial.
The judge insisted repeatedly that he was determined to "ensure there is a fair trial." Mohammed, who confessed to being involved in the capture and murder of Wall Street Journal reporter Daniel Pearl, was subjected to extensive torture and water boarded 183 times, according to a Department of Justice memo. The procedure simulates drowning.
Lawyers for the defence are arguing that any confessions or other material be invalidated because of the torture. They are likely to file motions to have the entire trial set aside. James Connell, a lawyer for defendant Ammar al-Baloshi, went to great lengths to stress that his ability to present a proper defence of his client would be hamstrung if he could not openly question witnesses due to censorship of confidential material. Al-Baloshi is a relative of Mohammed.