GUANTANAMO BAY NAVAL BASE, Cuba — The al Qaeda operative accused of masterminding the 2000 bombing of the USS Cole appeared relaxed as he was escorted into a courtroom with his defense team for a motions hearing Tuesday.

Abd al-Rahim Hussayn Muhammad al-Nashiri, 47, smiled and chatted with his lawyers before the hearing began. He looked toward the back of the courtroom, expressionless, where a dozen family members of the victims sat behind a glass window.

Al-Nashiri, a Saudi of Yemeni descent, is charged with nine counts related to orchestrating the Cole bombing, which killed 17 U.S. sailors, and an attempted attack on the USS The Sullivans in January 2000.

He faces the death penalty, the first capital punishment case to go before the military commission since it was reformed in 2009.

His defense team, led by civilian attorney Richard Kammen, began to argue the first of the nearly 100 pretrial motions being discussed before the military commission with Army Col. James Pohl presiding. Col. Pohl denied a defense motion that he recuse himself from the case.

Col. Pohl also ruled that the defense may take a photograph of al-Nashiri for trial preparation, but rejected a defense request to show al-Nashiri a video message from his parents.

The defense had argued that Col. Pohl should recuse himself because he had presided over the majority of the criminal cases from Abu Ghraib, the detention center in Iraq where U.S. soldiers abused detainees. Mr. Kammen said Col. Pohl had protected the senior military and civilian government leaders in charge of the detainees and should recuse himself to avoid any perception of partiality toward the government.

The defense also argued for recusal based on a monetary conflict of interest, noting that Col. Pohl, as a military judge who is paid by the Defense Department, would be subject to a 25 percent reduction in pay if he were to recuse himself from the al-Nashiri case.

Lastly, the defense argued that since Col. Pohl appointed himself as chief judge over all high-value detainees — including the cases of the 9/11 plotters — his rulings in the al-Nashiri case will taint his judgment in those cases.

“If there is only one judge on all these cases, it is a process only seen through one prism,” Mr. Kammen said. “You are the judge of first impression.”

Prosecutors argued that the defense’s accusations were based on innuendo, hypothetical situations and conjecture.

“Perception … is not the legal standard,” said Navy Cmdr. Andrea Lockhart, a member of the prosecution team led by Brig. Gen. Mark Martins, chief prosecutor for military commissions.

The defense team and human rights groups have argued that the military commissions’ convening authority is aligned with the prosecution and that the commissions lack experience in trying death penalty cases.

“All of this is a facade organized to do two things — to convict these people and kill them, and to do it in secret,” Mr. Kammen said Tuesday.

Alex Abdo of the American Civil Liberties Union was at the hearing, and said that much of what was discussed were “perfunctory matters” that arise in prosecuting a capital case under a new system that wouldn’t necessarily arise in a federal civilian court where there is plenty of historical precedent to guide decisions.

“We have to fill in the gaps, and we are paying the price for that,” said Mr. Abdo, a staff attorney. “We can’t create history with a stroke of a pen.”

Meanwhile, Gloria Clodfelter, mother of a victim of the Cole attack, 21-year-old Petty Officer 3rd Class Kenneth Clodfelter, wiped away tears during the hearing, and held hands with her husband, John.

The Clodfelters traveled from the U.S. to the courthouse in Guantanamo Bay with other family members and a dozen other observers.

Al-Nashiri’s trial could begin as early as November.

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