The Pentagon on Wednesday cleared the way for a death penalty trial against five Guantánamo Bay captives charged with engineering the Sept. 11 attacks.

Retired Vice Adm. Bruce MacDonald, in charge of military commissions, signed off on the capital trial against alleged mastermind Khalid Sheik Mohammed, 46, and four accused co-conspirators.

The men face charges of terrorism, hijacking aircraft, conspiracy and murder in violation of the law of war, among other charges, in the system set up by President George W. Bush within months of the attack, and then reformed by President Barack Obama in 2009.

If convicted, they could be sentenced to death using a method to be decided by Secretary of Defense Leon Panetta, or his successor.

The charges accuse the five men of organizing the attacks, including funding and training the 19 men who hijacked the four commercial airliners on Sept. 11, 2001, and then crashed them into the World Trade Center, Pentagon and a field in Shanksville, Pa., killing 2,976 people.

The lead trial attorneys are retired Army Col. Robert Swann and federal prosecutor Edward Ryan — the same two men who were designated to prosecute the case by the Bush administration.

Obama halted the previous trial and Attorney General Eric Holder was initially determined to prosecute them in Manhattan, not far from the site of the World Trade Center. But he reversed course a year ago after politicians protested, alternately, that a federal prosecution would put an even large al Qaida bull’s-eye on New York City, would snarl traffic for security concerns or would risk acquittal if a civilian judge or jury concluded that the evidence against them was the fruit of torture.

Pentagon prosecutors have been preparing their case since then.

At the White House, spokesman Jay Carney said the decision to go forward with the trial at Guantanamo did not diminish Obama's desire to close the detention center.

“There have obviously been obstacles in achieving that. But he remains committed to doing that,” said Carney. “In the meantime, we have to ensure that Khalid Sheik Mohammad and others who are accused of these heinous crimes are brought to justice. And a procedure is now underway to ensure that that happens.”

The decision drew a rebuke from the American Civil Liberties Union, which has funded some of the 9/11 defense lawyers.

The Obama Administration “is making a terrible mistake by prosecuting the most important terrorism trials of our time in a second-tier system of justice,” said Anthony Romero, the ACLU executive director. He said the war court was “set up to achieve easy convictions and hide the reality of torture, not to provide a fair trial.”

“Whatever verdict comes out of the Guantánamo military commissions will be tainted by an unfair process and the politics that wrongly pulled these cases from federal courts, which have safely and successfully handled hundreds of terrorism trials.”

All five men were interrogated by the CIA in secret overseas prisons — Mohammed was waterboarded 183 times, according to declassified CIA documents — before their 2006 transfer to Guantánamo for trial. Once in Cuba, he bragged to a panel of U.S. military officers that he was responsible for the Sept. 11 attacks “from A to Z.”