A senior Pentagon official Wednesday referred the first death penalty case under President Obama for trial by military commission at Guantanamo Bay, Cuba.

Abd al-Rahim al-Nashiri was charged in April by military prosecutors with murder, terrorism and other violations of the laws of war for his role in the October 2000 al-Qaeda attack on the USS Cole in Yemen.

Under military rules, the Pentagon official, known as the Convening Authority, independently examines the charges filed by military prosecutors and decides whether the defendant will be tried on all, some of none of the charges. In Nashiri’s case, the Convening Authority, Ret. Admiral Bruce MacDonald, forwarded the capital charges sworn by prosecutors.

Nashiri, a Saudi citizen of Yemeni descent, is one of 15 high-value detainees held at Guantanamo, and prosecutors allege that he was “in charge of the planning and preparation” of the Cole attack. Two suicide bombers in a small boat pulled alongside the Navy destroyer in the port of Aden and the ensuing blast, which ripped a 30-by-30-foot hole in the ship, killed 17 American sailors.

In submissions to the Convening Authority, attorneys for Nashiri argued that no case should be brought against their client because he was tortured while in CIA custody. Nashiri was captured in the United Arab Emirates in 2002 and held in secret CIA prisons overseas before he was transferred to Guantanamo Bay in September 2006.

Military prosecutors also swore capital charges in June against Khalid Sheik Mohammed, the self-proclaimed mastermind, and four co-defendants but the Convening Authority has not yet acted on those charges. The Obama administration had hoped to charge Mohammed in federal court in New York but abandoned that plan after fierce congressional and local opposition. Nashiri, on the other hand, was always designated for trial by a military tribunal.

Nashiri was one of three detainees who was waterboarded by the CIA, and he was also subject to mock executions when CIA operatives separately held a power drill and a gun to his head, according to a report by the CIA inspector general. The waterboarding was sanctioned by Justice Department lawyers, but the use of the drill and the gun fell outside interrogation techniques approved during the Bush administration and since abandoned by Obama.

The European Parliament, in a resolution, as well as human rights groups, have said that Nashiri should not be subject to the death penalty because of the legacy of his treatment by the CIA. His lawyers also argue that the agency’s destruction of videotapes of Nashiri’s waterboarding deprives the defense of potentially exculpatory evidence.

Nashiri, who has never been seen publicly since his capture, said at a closed 2007 military hearing that he confessed to involvement in the Cole bombing only because he was tortured.

Under the reformed system of military commission, the government cannot use any statements obtained under torture. And prosecutors are unlikely to rely on any statements Nashiri made while in CIA custody.

But one of Nashiri’s attorneys, Navy Lt. Cmdr. Stephen Reyes, has warned that he intends to call CIA officials involved in his client’s interrogation to the stand.

Since the military detention center opened in 2002, six cases have been completed, resulting in four plea bargains, a short sentence and a guilty verdict that led to a life sentence. Two of those six detainees have been released, and three more are scheduled to be sent home over the next few years as a result of the pleas.