The October 2000 attack on the USS Cole ripped a 30-by-30-foot hole in the Navy destroyer and killed 17 American sailors. (File photo/REUTERS)

U.S. military prosecutors on Wednesday charged one of the most prominent detainees at Guantanamo Bay, Cuba, in a death penalty case that could prove to be a major test of the nation’s revised system of military commissions.

Abd al-Rahim al-Nashiri, one of 15 high-value detainees at the U.S. military prison, was charged with murder, terrorism and other violations of the laws of war in connection with an October 2000 attack on the USS Cole in Yemen.

The military alleges that Nashiri 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 and detonated, ripping a 30-by-30-foot hole in the Navy destroyer and killing 17 American sailors.

The case is the first capital military tribunal to be announced under President Obama, whose administration recently lifted a ban on new trials at Guantanamo Bay. Although the administration said this month that it would try Khalid Sheik Mohammed and four co-defendants in a military commission, prosecutors have not sworn charges or confirmed that they will seek the death penalty.

Nashiri, 46, a Saudi citizen of Yemeni descent, has been in U.S. custody since 2002 and at Guantanamo Bay since 2006. After his capture in the United Arab Emirates, he was held overseas at secret CIA prisons, where he was waterboarded and subject to mock executions in which agency operatives separately held a power drill and a gun to his head, according to a report by the CIA inspector general and other government documents.

Abd al Rahim al Nashiri ( FO/ALQAEDA /NONE)

Nashiri said at a 2007 military hearing that he confessed to involvement in the Cole bombing only because he was tortured.

The case raises difficult legal questions — about the legacy of harsh interrogation methods, about the use of military tribunals to prosecute acts that occurred before Sept. 11, 2001, and about the destruction of evidence by CIA officers — that could complicate prosecution.

“Now we get serious,” said Eugene Fidell, president of the National Institute of Military Justice and a lecturer at Yale Law School. “It’s a mare’s nest of legal issues.”

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. 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.

But Nashiri, who is said to have been a senior associate of al-Qaeda leader Osama bin Laden, has a far bigger profile than any of the detainees convicted so far.

Under the military justice system, a senior Pentagon official known as the convening authority decides whether to refer the charges to trial by a military commission. The authority could reject any or all of the charges.

Nashiri has a military attorney, but under the revised system of military commissions, he is also entitled to a “learned counsel,” either a military or a civilian lawyer with experience in capital cases. That person must be appointed before charges are referred.

“I am absolutely thrilled that this long-overdue prosecution is moving forward and that the crew and families will finally see justice,” said Kirk Lippold, the former commander of the Cole.

In 2000, the United States did not treat the attack on the Cole as an act of war, sending FBI and Naval Criminal Investigative Service personnel to Yemen to investigate. Congressional authorization for the use of military force against al-Qaeda did not come until immediately after the Sept. 11 attacks, and some legal experts say that raises questions about whether a military court has the jurisdiction to try the Nashiri case.

The 2009 Military Commissions Act says offenses committed before Sept. 11, 2001, can be tried. But David Glazier, a professor at Loyola Law School in Los Angeles, writes in a forthcoming article for a law journal that “Supreme Court precedent clearly limits commission jurisdiction to the period of actual hostilities.”

Military prosecutors are unlikely to rely on any statements Nashiri made while in CIA custody.

Ali Soufan, a former FBI agent, wrote in an op-ed in the New York Times last year that “there is enough evidence to convict Mr. Nashiri based on confessions we gained legally” from his two indicted co-conspirators. Moreover, in military commissions, FBI agents will probably be able to relay to the court what witnesses in Yemen told them — hearsay testimony that would typically be barred in federal court.

Nonetheless, the case is complicated by the CIA’s destruction of videotapes of Nashiri’s waterboarding. The defense is likely to argue that the destruction of potentially exculpatory evidence should lead the military judge to dismiss the charges.

Even if the matter of Nashiri’s treatment at the hands of the CIA never surfaces during the trial, it will almost certainly come up in any sentencing phase as a factor mitigating against a death sentence.

“Anyone who approved or participated in the torture of my client should be prepared to take the witness stand,” Navy Lt. Cmdr. Stephen Reyes said.