The C.I.A. interrogated Ammar al-Baluchi 1,119 times over more than three years before he was ever charged in connection to the Sept. 11 attacks. At first, he was beaten, deprived of sleep, kept shackled and naked in a secret prison in Afghanistan.

Even after the brutality stopped, the questioning continued while he was kept in isolation and incommunicado during that time. Then, in 2006, he was transferred to Guantánamo Bay, and the F.B.I. took over the interrogations.

During those sessions, in 2007, Mr. Baluchi was fully clothed, with an ankle shackled to the floor. That is when he explained to agents building a criminal case against him how he sent money and provided other support to some of the hijackers who attacked the United States on Sept. 11, 2001.

Now a military judge will decide whether that 2007 confession can be used against Mr. Baluchi at his death-penalty trial.

The central question is: Was his confession to the F.B.I. voluntary, or was it the result of a campaign of state-sponsored torture that spanned his time in C.I.A. custody?

The Sept. 11 case is once again at a crossroads at Guantánamo Bay. Three defendants, including Mr. Baluchi’s uncle, Khalid Shaikh Mohammed, are awaiting resolution of a dispute over whether they can plead guilty in exchange for life sentences. A fourth defendant has been ruled not mentally fit to face trial.