In this file photo of a sketch by courtroom artist Janet Hamlin, alleged Sept. 11 co-conspirators sit with their legal teams inside the courtroom during a hearing at Guantanamo Bay in July 2009. (Reuters)

The behavior during their arraignment Saturday of the five defendants charged with orchestrating the Sept. 11, 2001, terrorist attacks was a form of “peaceful resistance to an unjust system,” according to one of their attorneys who spoke at a news conference Sunday.

“The accused refuse to acknowledge the legitimacy of the military commissions,” said James Connell, an attorney for Ali Abdul Aziz Ali. The “arraignment demonstrates that this will be a long, hard-fought but peaceful struggle against secrecy, torture and the misguided institution of the military commission.”

Khalid Sheik Mohammed and four co-defendants refused to speak during the 10-hour hearing Saturday, which included a reading of the capital charges against them, including murder in violation of the law of war, hijacking and terrorism.

The defendants variously prayed demonstratively in court, stripped off a shirt to show the marks of alleged ill treatment, read magazines, shouted at the judge and whispered constantly with each other.

“They are complaining, and our families can’t complain,” said Eddie Bracken, a New Yorker who lost his sister in the attacks on the World Trade Center and came to Guantanamo Bay for the arraignment. “But it’s our justice and they have rights. . . . It’s hurtful because they have no remorse. I don’t think they have any souls.”

Brig. Gen. Mark Martins, the chief military prosecutor, said that disruptive behavior is not new to courts but that judges tend to be “careful about employing the ultimate sanction of expulsion, choosing instead to build a patient and methodical record and moving the case forward while preparing the ground for eventual expulsion.”

The prosecution and the defense continued to spar over the issue of torture and how much the subject would be aired at Guantanamo Bay. All five defendants were held in secret overseas prisons by the CIA before they were transferred to Guantanamo in September 2006, and Mohammed was waterboarded 183 times in the first month after his capture in March 2003.

“The government wants to kill Mr. Mohammed. They want to extinguish the last eyewitness to his torture so he can never speak again,” said David Nevin, the civilian attorney for Mohammed, arguing that rules for classified information prevent him from even talking to Mohammed about his treatment. “The system is a rigged game.”

Martins said that illegal and embarrassing acts would not be covered up and that only clearly defined “sources and methods” would be protected, as they are in federal court. He said that Nevin and other attorneys can talk to their clients about their interrogations but that they cannot turn over certain, defined pieces of information to the detainees.

He also said a legacy of torture does not undermine the case.

“The remedy for torture or cruel treatment, the things that will make you ashamed that were done, that are deplorable and disappointing, the remedy is not to just dismiss all charges. It’s harder than that,” Martins said. “Everything — everything — is polluted and tainted? That means everyone goes free, everyone is free of accountability because someone else who may have been acting independently or out of control did something wrong. That’s not justice. It’s harder than that.”

One of the defense attorneys, Cheryl Bormann, appeared at the arraignment in a full-length black abaya that showed only her face. Bormann, who is from Chicago, refused to comment on reports that she had received death threats in the wake of the arraignment and said she wore the abaya in deference to the cultural and religious sensitivities of her client, Walid bin Attash.

Bormann also asked in court that a female member of the prosecution team dress more modestly, saying her clothing was a distraction for the defendants and might cause them to “commit a sin” by looking at her. Three women on the prosecution side wore knee-length skirts.

Martins said the request was not worthy of a response.

“The women on the prosecution team are dressed in an appropriate and professional manner,” he said Sunday at a news conference.

The defense also questioned the ability of the judge, Army Col. James Pohl, to oversee a capital case with multiple defendants.

“Judge Pohl admittedly does not have the knowledge nor the expertise to handle this kind of litigation,” Bormann said, “and as we go forward in this case that’s going to become apparent.”

The defense questioned why Pohl, the chief judge at Guantanamo, had appointed himself to the two major cases underway there — the Sept. 11 case and the prosecution of Abd al-Rahim al-Nashiri, a Saudi of Yemeni descent who was arraigned here in November on charges of murder and terrorism, as well as other violations of war, in connection with the 2000 al-Qaeda attack on the USS Cole in Yemen that killed 17 U.S. sailors. The defense noted that there are eight other judges available and that Pohl already has the two most high-profile cases at the military detention center.

“Do we think he is a glory hound? I cannot answer that,” Navy Cmdr. Walter Ruiz said in response to a question. He said it would be better to have separate judges ruling on similar issues in different cases rather than Pohl deciding in both cases.

The proceedings will now enter a long period of trial litigation, with the first motions scheduled to be argued at Guantanamo next month. The trial itself is at least a year away. The judge said he would set a tentative trial date at the next hearing and seemed inclined to pencil in May 2013 for the selection of a jury of military officers and opening arguments.