After more than nine years in U.S. custody, four of them at secret CIA prisons, the alleged mastermind of the USS Cole bombing in Yemen in 2000 finally appeared in public Wednesday when he was arraigned in the first death-penalty military commission under President Obama.

Abd al-Rahim al-Nashiri, a Saudi of Yemeni descent, was one of three detainees who were waterboarded by the CIA. He entered the courtroom at Guantanamo Bay with a shoulder-rolling swagger, leaned back in his chair and gave his attorneys a thumbs-up.

A short time later, he glanced back at the public gallery, where victims’ relatives, members of the media and human rights activists sat behind three panes of glass. He then raised his right arm and gave an insouciant wave.

Nashiri — clean-shaven, stocky and wearing white prison garb — was arraigned on charges of murder and terrorism as well as other violations of war in connection with the al-Qaeda attack, which killed 17 U.S. sailors.

Nashiri, who said he wanted to work with both his civilian and military attorneys, reserved the right to enter a plea. He followed proceedings through an interpreter, saying he doesn’t speak English, although he did use a few English phrases. Asked by the judge what language he does speak, Nashiri replied with a large smile, “Arabiya.”

“He seemed cocky to me,” said John Clodfelter of Mechanicsville, Va., whose 21-year-old son, Kenneth, was killed in the attack. Clodfelter was among the family members who were flown to Cuba for the proceeding. The military also streamed video of the arraignment for relatives in Norfolk. “I think he deserves to get the death penalty, if not worse,” Clodfelter said.

In addition to being waterboarded, Nashiri was subjected to mock executions when CIA operatives held a power drill and a gun to his head. Justice Department lawyers sanctioned the waterboarding, but the use of the drill and the gun fell outside interrogation techniques approved during the George W. Bush administration.

As is allowed under military law, Nashiri’s attorneys on Wednesday questioned Judge James Pohl, an Army colonel, to decide whether they want to challenge him on grounds of impartiality. The defense, in the end, did not challenge Pohl, but the questioning about the death penalty and torture indicated that Nashiri’s treatment while in CIA custody will be central to the defense’s effort to prevent the defendant from being sentenced to death.

Defense attorney Richard Kammen, a civilian lawyer and death penalty specialist from Indiana, asked: “Do you believe that by torturing Mr. Nashiri, the United States has forfeited the right” to execute him?

Pohl declined to answer most of the questions, saying that his personal opinions were not relevant and that he will apply the law. “I’m a simple guy,” the judge said. “I follow what the rules say.”

Khalid Sheik Mohammed, the self-proclaimed mastermind of the Sept. 11, 2001, attacks, and four co-defendants were arraigned on capital charges at Guantanamo Bay during the Bush administration. Those charges were withdrawn by the Obama administration in anticipation of a federal trial but were sworn again this year by military prosecutors when the planned proceedings in New York collapsed in the face of congressional and local opposition. A second Guantanamo Bay arraignment in the Sept. 11 case is expected soon.

“For the Americans who lost friends and relatives in the attack on the USS Cole, nothing can bring those loved ones back,” said Gen. Mark Martins, the chief military prosecutor. “But know that the United States is committed to accountability under law for those who have plotted to attack our nation and our interests abroad.”

The case — in a system that Pohl described as “unique” because it remains untested — is expected to be protracted. On Monday, two days before the arraignment, the military released 202 pages of new procedures for commissions. And Kammen said in an interview that the court could still be hearing pretrial motions a year from now.

Human rights groups continued to criticize the proceedings, arguing that the commissions amount to second-class justice when compared with federal criminal court or military courts martial.

“The system is inherently flawed,” said Melina Milazzo of Human Right First. She attended the arraignment, arguing that because there is no substantial body of law underlying commissions, the system is prone to arbitrary rulings and will be subject to endless challenges. “In military commissions, every issue is one of first impression.”

The proceeding could also be contentious, with the government and the defense trading charges about bad faith. Defense attorneys complained that the government has stalled on turning over evidence that would allow them to prepare for trial and began reading privileged attorney-client mail, breaking with past practice, just as proceedings were about to begin.

The military alleges that Nashiri was a close associate of Osama bin Laden and was “in charge of the planning and preparation” of the attack, in which a small boat carrying two suicide bombers pulled alongside the USS Cole in the port of Aden and detonated, ripping a 30-by-30-foot hole in the Navy destroyer.

Asked whether Nashiri had ever expressed remorse for the deaths of 17 sailors, Kammen said that everything Nashiri says outside the courtroom is presumptively classified no matter how mundane or tangential to the case. But, Kammen added, “this is not a person in our view without heart or feeling.”

Pohl, who appeared to be somewhat exasperated with the commander of the Joint Task Force at Guantanamo Bay, granted a defense motion ordering the guard force not to read mail that is clearly marked attorney-client correspondence.

The judge set a trial date a year from now, with the understanding that the date could be pushed back further.