GUANTANAMO BAY NAVAL BASE, Cuba -- Held in a secret prison in Guantanamo that is under such tight security even its exact location on the base is classified, Khalid Sheikh Mohammed and his co-defendants until Saturday had not been seen in public since a pretrial hearing the day after President Barack Obama's Jan. 21, 2009, inauguration.
Their arraignment Saturday also came more than three years after the Obama administration's failed effort to try the suspects in a federal civilian court and close the prison at the U.S. base in Cuba.
Attorney General Eric Holder announced in 2009 that Mohammed and his co-defendants would be tried blocks from the site of the destroyed trade center in downtown Manhattan, but the plan was shelved after New York officials cited huge costs to secure the neighborhood and family opposition to trying the suspects in the U.S.
The men never entered formal pleas in previous hearings, but Mohammed had told the court that he would confess to planning the attacks "from A to Z" and hoped to be a "martyr."
He dismissed the military justice system, saying, "After torturing, they transferred us to inquisition land in Guantanamo."
The arraignment is expected to be followed by a hearing on defense motions that challenge the charges and extreme secrecy rules imposed to prevent the release of information about U.S. counterterrorism methods and strategy.
New rules adopted by Congress and Obama forbid the use of testimony obtained through cruel treatment or torture. The defendants were held at secret CIA prisons overseas where they were subjected to what the government called "enhanced interrogation techniques." Mohammed was waterboarded 183 times, officials have said.
The American Civil Liberties Union filed a motion Friday asking the judge to prohibit the government's use of a 40-second delay and a white noise machine to prevent any spectators from hearing classified information, including details about the harsh treatment in the secret CIA detention sites overseas.
"If the defendants are unable to express themselves directly to the American public then how are we to know whether justice is being served," said ACLU director Anthony Romero.
Kenneth Roth, executive director of Human Rights Watch and a former federal prosecutor, say coerced testimony from witnesses is still admissible, even if it isn't from defendants, and the case would be better off in civilian court instead of being heard by a judge and jury panel picked by the Pentagon.
"There still are major problems in terms of whether the trial will be fair and, more important, will they be perceived as fair," Roth said.
The government has pledged to make the proceedings more transparent by broadcasting the hearing to families at U.S. military bases. News cameras, however, are still not permitted inside the courtroom, where the media and other observers are kept behind double-paned, soundproof glass.
Lawyers for the defendants had opposed the government's plan to show the hearings just to the families.
"We believe that the world needs to see what's happening," said Cheryl Bormann, a civilian attorney appointed to represent Walid bin Attash.
Prisoners now have access, at government expense, to civilian defense attorneys who specialize in complex death penalty cases. But human rights groups and defense lawyers still condemn the proceedings as flawed and fundamentally unfair.
Lawyers appointed to represent the men say they face hurdles they would never encounter in a civilian court, including strict limits on what they can say about their clients, whose every utterance is treated as presumptively classified.
"All I can do is try and protect my client's rights to every extent I can and try and hold the government to their burden to provide a fair and transparent justice system and to actually mean it," Bormann said.
Mohammed and his co-defendants were first arraigned on the U.S. base in Cuba in June 2008. The case quickly bogged down in pretrial motions and was put on hold as Obama sought to move the case to the federal court in New York.
But members of Congress balked and blocked the administration from transferring prisoners from the base to the mainland. That prevented the closure of the prison, where the U.S. still holds 169 prisoners.
"There is a consensus now ... that military commissions have a narrow but critical role in our counterterrorism and justice system," said Brig. Gen. Mark Martins, a Harvard Law School classmate of Obama's who was appointed chief prosecutor last year.
Mohammed confessed to military authorities that he planned or carried out about 30 plots around the world. He admitted personally killing Wall Street Journal reporter Daniel Pearl and said he conceived the plot to blow up a trans-Atlantic flight by would-be shoe-bomber Richard Reid in 2001. Mohammed was captured in 2003 in Pakistan.
Roth, who will be part of a human rights contingent observing Saturday's arraignment at Guantanamo, said the prosecution can work around the ban on coerced testimony, perhaps even unwittingly, by introducing classified summaries of intelligence to support their case.
Even with the changes, the defense lawyers say the commissions are anything but fair. They complain that their mail is improperly reviewed by the military, interfering with attorney-client privilege, that they aren't given enough resources to investigate cases the government spent years building, that too many hearings are still held in secret and that they are barred from disclosing anything their clients tell them.
"You can take a $5 mule and put a $10,000 saddle on it and call it reformed," said Navy Cmdr. Walter Ruiz, a military lawyer for Mustafa Ahmad al-Hawsawi. "You still have a $5 mule; it just has a fancy saddle."