Janet Hamlin / AFP - Getty Images

This courtroom sketch shows alleged 9/11 mastermind Khalid Sheikh Mohammed as he holds up a piece of paper during a court recess at his hearing on Monday at the U.S. Navy base in Guantanamo Bay, Cuba.

Updated at 5:20 p.m. ET: The self-professed mastermind of the Sept. 11, 2001, attacks on the United States, which resulted in the deaths of 2,976 people, appeared before a military judge at Guantanamo Bay Naval Base in Cuba on Monday after months of delays due to scheduling conflicts, religious observances, an Internet outage and a tropical storm.

Khalid Sheikh Mohammed shocked some observers by appearing with a long, full beard that had been dyed bright reddish-orange. He appeared before Judge Army Col. James Pohl for the start of a week of pretrial hearings, along with co-defendants Ali Abdul Aziz Ali, a Pakistani; Mustafa Al Hawsawi, a Saudi; and Walid Bin Attash and Ramzi Binalshibh, two men from Yemen.

Unlike their last appearance in court in May, which was disrupted several times by the defendants, the five men sat quietly at the defense table, under the watchful eyes of military guards and several family members of the 9/11 victims, The Associated Press reported. All seemed to be cooperating with their attorneys. Mohammed read legal papers. Two others responded politely to the judge when they were asked questions, according to the AP.

All the defendants wore white robes and turbans, and spoke openly with one another throughout the course of the day.

The men, being prosecuted in a special military tribunal for war-time offenses, are charged with conspiring with al-Qaida, attacking civilians and civilian targets, murder in violation of the laws of war, destruction of property, hijacking and terrorism. All five could face the death penalty if convicted.

Associated Press

Khalid Sheikh Mohammed, the alleged Sept. 11 mastermind, is seen shortly after his capture in Pakistan in this photo taken on March 1, 2003.

The families of people killed in the Sept. 11 attacks were invited to military installations in New Jersey, Massachusetts, Maryland and New York City to watch the pretrial hearings on closed-circuit television, NBCNewYork.com reported.

Getting the terror suspects to this point has been a years-long process mired in political and legal arguments over the defendants' rights, the use of evidence that may have been derived through torture, and the proper venue for the proceedings. The actual trial is expected to be at least a year away.

The pretrial hearings this week will cover a series of motions filed by the various defense teams, dealing primarily with secrecy issues and the detainees' rights.

The most controversial issue, which was not taken up by the end of the first day, is a challenge to the government's gag order on any information gained during interrogation of the detainees. The ACLU and more than one dozen news organizations filed a motion to oppose to government's gag order. The government maintains the order is necessary to protect classified intelligence-gathering techniques.

Defendants may skip hearings
On Monday, prosecutors and lawyers spent hours arguing the most preliminary of issues, including whether the defendants have to be in court at all, with one attorney saying the hearings may dredge up bad memories of their harsh treatment in CIA detention.

Defense attorney Capt. Michael Schwartz argued that the detainees should not be forced to come to court because the process of forcibly removing them from their cells is traumatic and reminiscent of harsh interrogation techniques.

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Schwartz said that if the court was considering forced cell extraction it had to talk about torture.

"No we don't," the judge said quickly.

"I think we do," Schwartz said.

"I'm telling you I don't think that's relevant in this issue. That's the end of that, move on to something else," Pohl retorted.

But Schwartz persisted, saying he needs to address the issue of torture.

"No you don't," the judge said more forcefully this time, adding that the defense does not have the opportunity to make an argument that he sees as irrelevant.

After a prolonged and heated back-and-forth, the detainees were granted the right to waive their attendence at the hearings at least until jurors are assembled for the actual trial, but they must sign a waiver each day they choose not to attend.

Toward the end of the day, the judge asked each of the five detainees a series of questions to ensure they understand their new rights to waive attendance at their sessions.

Binalshibh answered each of his questions in imperfect English, veering into a perplexing discussion about escaping from Guantanamo and alleging unfair treatment from his guards.

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When asked whether he understands that the trial could ultimately continue even if he is not present, Binalshibh looked perplexed, saying, "that is a very wide word, can you be concrete?"

"I'm not implying that I think you are going to escape," the judge said, adding that if that were to happen, the trial could continue without him being there.

"Escaping from custody?" Binalshibh asked.

"I'm not saying you're going to," the judge said, asking again whether he understands that the trial could continue without him. Binalshibh seemed to smile as he said, "Yes I do."

Guantamo guards make things 'difficult'
He raised concerns about the fact that guards would be sent to bring him to the hearings, though, saying, "dealing with the guard is very difficult. They didn't report everything so correctly. Problems with guards can misreporting all things."

"Some guard when you have problem with them they can make it very difficult for us," he said.

When the judge recommended reporting any problems to his attorney, Binalshibh said, "Where can I call him? There is no time to contact him. Very difficult communication for us."

Mohammed answered his questions through his interpreter. He looked down and answered simply "yes" to every question, until at the end when asked whether he understands he doesn't have to attend the sessions.

"Yes, but I don't think there is any justice in this court," he said through his interpreter.

The court was in session for about five total hours, with several breaks throughout the day. It then adjourned until 9 a.m. ET. Tuesday.

Pohl was also expected to hear requests from news organizations on limiting closed courtrooms for secret sessions and be asked to decide whether the U.S. Constitution governs tribunals held at the U.S. base in Cuba.

The testy exchanges occurred during a hearing that was otherwise calm and orderly, in stark contrast to the chaotic 13-hour arraignment hearing in May, when defendants made defiant outbursts and refused to answer the judge's questions or listen through earphones to an Arabic-English translation of the proceedings. In those proceedings, one of the men was briefly restrained and two of them stood up to pray at one point.

Subsequent hearings had been pushed back for various reasons.

A hearing in July was postponed to allow the defendants to observe the holy month of Ramadan. Hearings in August were delayed when an Internet outage left the lawyers unable to access their electronic legal documents. That hearing was later canceled altogether as Tropical Storm Isaac approached. The storm caused no damage to the base.

A hearing scheduled for late September was also delayed because the work space for the defense lawyers was shut down due to a rat infestation and mold, which lawyers claimed were making them sick, Reuters reported.

Pohl ruled on Oct. 5 there would be no further postponements to the hearings.

An earlier attempt to try the five men at Guantanamo ended when the Obama administration tried to move the trials to New York City, where two of the hijacked planes slammed into the World Trade Center.

That was abandoned under pressure from Congress and from New Yorkers, and the charges were re-filed in Guantanamo.

Reuters and The Associated Press contributed to this report. 

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Janet Hamlin / Pool via AP

Pentagon-paid civilian defense lawyer Cheryl Bormann, defense attorney of accused Sept. 11 co-conspirator Walid bin Attash, argues a point during the military hearing at the Guantanamo Bay U.S. Naval Base in Cuba, Saturday, May 5, 2012.

The civilian defense attorney of one of the men accused of plotting the Sept. 11 attacks wore a black hijab and long black robe at the arraignment of the five Guantanamo prisoners Saturday, and she wants other women to dress more modestly.

Attorney Cheryl Bormann, 52, who is from Chicago and is not Muslim, said she wore the modest garment that revealed only her face to show respect for the religious sensitivities of her client, Yemeni terror suspect Walid bin Attash.

Bormann asked the court to order the other women present at the hearing to dress more modestly so as not to distract the defendants, who would be "committing a sin under their faith" by looking at them.

According to The Washington Post, chief military prosecutor Brig. Gen. Mark Martins deemed the request not worthy of a response.

"The women on the prosecution team are dressed in an appropriate and professional manner," Martins said Sunday at a press conference.

Bin Attash’s military attorney, Air Force Capt. Michael Schwartz, told msnbc.com he didn't think Martins had the opportunity to see what sparked Bormann's request due to the setup of the courtroom. Schwartz said one of the female attorneys present in the courtroom was wearing a skirt whose bottom hemline appeared closer to her waist than to her knees when she was seated.

“Knowing our clients' conservative religious beliefs we were concerned about their ability to really participate in the defense of their case without losing focus for fear of committing a sin under their religion,” Schwartz said.

He said Bormann wears the hijab or abaya whenever she's around their client "out of respect for [bin Attash's] religious beliefs."

"Our client has never seen Ms. Bormann’s hair, he’s never seen her arms, he’s never seen her legs,” Schwartz added.

The military attorney did not comment on whether Bormann had received threats following the arraignment.

After chaotic start, long fight predicted in Guantanamo 9/11 case

The five defendants face 2,976 counts of murder and terrorism in the 2001 attacks that sent hijacked jetliners into New York's World Trade Center and the Pentagon. The charges carry the death penalty.

On Saturday, the self-described mastermind of the attacks Khalid Sheikh Mohammed and his co-defendants refused to respond to the judge or use the court's translation system and demanded a lengthy reading of the charges. One of them got up and started praying.

Defense lawyer James Connell called the tactics "peaceful resistance to an unjust system."

The arraignment, Connell said, "demonstrates that this will be a long, hard-fought but peaceful struggle against secrecy, torture and the misguided institution of the military commissions."

The defendants' actions outraged relatives of the victims.

"They're engaging in jihad in a courtroom," said Debra Burlingame, whose brother, Charles, was the pilot of the plane that flew into the Pentagon. She watched the proceeding from Brooklyn on one of the closed-circuit video feeds around the United States.

NBC News' Michael Isikoff contributed to this report.

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Janet Hamlin / AP

In this sketch reviewed by the U.S. Department of Defense, Khalid Sheikh Mohammed reads a document in court on Saturday.

Updated at 10:20 p.m. ET: GUANTANAMO BAY NAVAL BASE, Cuba -- Accused Sept. 11 mastermind Khalid Sheikh Mohammed and his co-defendants defied a military judge Saturday by refusing to answer his questions, and one of them got up and started praying as the long-awaited arraignment of the terror suspects got off to a rocky start in a military courtroom in Guantanamo.

Mohammed -- dressed in a white turban and robe -- sat silently, taking off his headphones when Judge James Pohl first addressed him. "One cannot refuse to participate and frustrate the proceedings," a clearly irritated Pohl snapped.

"The reason he's not putting the earphones in his ears is because of the torture that was done to him," his lawyer, David Nevin, told the judge. 

Ramzi Binalshibh, another alleged 9/11 plotter, at one point disrupted the court by standing up and shouting -- first in Arabic and then in English --  that "the era of Gadhafi is over but it continues at this camp. Maybe you aren't going to see me anymore ... there are threats we have seen at this camp. Maybe they will kill us and say we have committed suicide."

When Pohl ordered him to sit down, saying such issues could be raised later, Binalshibh shot back: "The time to discuss these things is now, not tomorrow."

While families of the 9/11 victims watched in the courtroom, and on closed-circuit television at seven sites in the United States, the  dispute - and other protests by the defendants and their lawyers --  appeared to initially tie up the proceedings  in knots. 

The chaotic hearing ended with the reading of the 87 pages of charges, which took more than two hours. The judge then declared the court in recess until June 12. 

Binalshibh earlier brought the court to a halt when he stood up and then dropped to his knees in prayer.

Another defendant, Walid bin Attash, sat in court in restraints -- apparently because of a dispute with guards -- and his lawyer said he couldn't participate because his client was "in pain." The restraints were later removed.

With his long flowing beard, Mohammed was a striking presence in the courtroom. But his refusal to utter a word -- despite repeated entreaties by the judge -- stood in stark contrast to previous court appearances where he has chanted Koranic verses, denounced  the United States, and taken credit for the terror attacks.

AP

At left, a 2003 photo obtained by the Associated Press shows Khalid Sheikh Mohammed, the alleged Sept. 11 attacks mastermind, shortly after his capture. At right, a photo downloaded from www.muslm.net purports to show Mohammed in 2009.

When the defendants declined to wear their headsets so they could listen to translations of the judge's questions, Pohl ordered a translator to repeat them out loud in Arabic. And he plowed ahead, asking each of the defendants detailed questions about their knowledge of the lawyers who had been appointed to represent them and whether they accepted them. None of the defendants responded and refused to even look at the judge.

During a break, the defendants could be seen leaning back in their seats, laughing, smiling and chatting among themselves -- apparently pleased with their ability to frustrate the judge.

The lawyers did their part, raising repeated objections. Cheryl Borman, a lawyer for Attash and dressed in a muslim hajib, objected to the attire of women members of the prosecution team, several of whom were dressed in military skirts with their legs showing.

"There are issues of cultural sensitivity here," she said. "I am suggesting the prosecution team make decisions of appropriate dress of their female colleagues so that our clients are not forced to look (at them) for fear of commiting a sin under their faith."

Nevin, Mohammed's lawyer, asked Pohl to force prosecutors to identify the men sitting in the back of the courtroom. "Given what Mr. Mohammed has been through with unknown, shadowy people it will affect his ability to proceed," Nevin said. The men were later ID'd as paralegals and FBI agents.

The tactics appeared designed to highlight objections their lawyers have raised to the fairness of the proceedings before a military commission.

In recent days, defense lawyers have filed motions objecting to rules that allow military guards to inspect the mail they send their clients, a lack of translators, and orders that make anything their clients as "presumptively classified."

The Obama administration had previously sought to try the suspects in federal court in New York City -- a move that stirred up a storm of political opposition. Since then, the case has been moved back to military court here at Guantanamo and some of the family members that gathered here this week said they are anxious to see the suspects brought to justice.

"I'm from Brooklyn and you know what, you face your, you face your fight," said Eddie Bracken, whose sister Lucy was killed in the World Trade Towers.

He said he wanted to see Mohammed and his co-defendants in the courtroom. "I want to see him eye to eye. That's the man that killed my sister -- him and the other cohorts or whatever you want to call them."

Background on the long, winding road to arraignment
Pentagon releases video of US troops interrogating bin Laden's driver
Honor student pleads guilty in 'Jihad Jane' terror plot
NYT: Role of torture revisited in bin Laden narrative
Bin Laden in hiding: Hatching horrific plots despite crippling attacks on al-Qaida 

It was the first public appearance by the five men in more than three years.

Mohammed, a Pakistani citizen who grew up in Kuwait and attended college in Greensboro, N.C., was joined by four co-defendants:

• Binalshibh, a Yemeni -- allegedly chosen to be a hijacker but couldn't get a U.S. visa and ended up providing assistance such as finding flight schools;
• Attash, also from Yemen, allegedly ran an al-Qaida training camp in Afghanistan and researched flight simulators and timetables;
• Mustafa Ahmad al-Hawsawi, a Saudi accused of helping the hijackers with money, Western clothing, traveler's checks and credit cards;
• Ali Abd al-Aziz Ali, a Pakistani national and nephew of KSM, allegedly provided money to the hijackers. 

Like Mohammed, Binalshibh also earlier told the court he was proud of the attacks in New York, Washington and Shanksville, Pa. 

Defendants before military commissions typically do not enter a plea during arraignment. Lawyers for the men said they were prohibited by secrecy rules from disclosing the intentions of their clients. 

But Jim Harrington, Binalshibh's civilian lawyer, didn't expect any of the defendants to plead guilty, The Associated Press reported.

And attorney James Connell, who represents al-Aziz Ali, told reporters at the base that the arraignment is "only the beginning of a trial that will take years to complete, followed by years of appellate review."

"I can't imagine any scenario where this thing gets wrapped up in six months," he added.

Also in court Saturday were six 9/11 family members who won a lottery to attend the proceedings. Others were watching on closed-circuit video at military bases in New York City and the eastern U.S. 

Cliff and Christina Russell traveled from New York to honor the memory of Cliff's younger brother, Stephen, a firefighter killed responding to the attacks, AP reported.

Cliff Russell said he hopes the tribunal will end with the death penalty for Mohammed and his co-defendants. "I'm not looking forward to ending someone else's life and taking satisfaction in it," he said. "but it's the most disgusting, hateful, awful thing I ever could think of if you think about what was perpetrated." 

The Associated Press contributed to this report.

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WASHINGTON - In northern Bucharest, in a busy residential neighborhood minutes from the heart of the capital city, is a secret the Romanian government has long tried to protect.

For years, the CIA used a government building — codenamed "Bright Light" — as a makeshift prison for its most valuable detainees. There it held al-Qaida operatives Khalid Sheikh Mohammed, the mastermind of 9/11, and others in a basement prison before they were ultimately transferred to Guantanamo Bay, Cuba, in 2006, according to former U.S. intelligence officials familiar with the location and inner workings of the prison.

The existence of a CIA prison in Romania has been widely reported, but its location has never been made public. The Associated Press and German public television ARD located the former prison and learned details of the facility where harsh interrogation tactics were used. ARD's program on the CIA prison is set to air Thursday.

The Romanian prison was part of a network of so-called black sites that the CIA operated and controlled overseas in Thailand, Lithuania and Poland. All the prisons were closed by May 2006, and the CIA's detention and interrogation program ended in 2009.  

 Unlike the CIA's facility in Lithuania's countryside or the one hidden in a Polish military installation, the CIA's prison in Romania was not in a remote location. It was hidden in plain sight, a couple blocks off a major boulevard on a street lined with trees and homes, along busy train tracks.

• Excerpt: 'Black Banners: The Inside Story of 9/11 and the War Against al-Qaida'

The building is used as the National Registry Office for Classified Information, which is also known as ORNISS. Classified information from NATO and the European Union is stored there. Former intelligence officials both described the location of the prison and identified pictures of the building.

In an interview at the building in November, senior ORNISS official Adrian Camarasan said the basement is one of the most secure rooms in all of Romania. But he said Americans never ran a prison there.

"No, no. Impossible, impossible," he said in an ARD interview for its "Panorama" news broadcast, as a security official monitored the interview.

The CIA prison opened for business in the fall of 2003, after the CIA decided to empty the black site in Poland, according to former U.S. officials, who spoke on condition of anonymity because they were not authorized to discuss the detention program with reporters.

Shuttling detainees into the facility without being seen was relatively easy. After flying into Bucharest, the detainees were brought to the site in vans. CIA operatives then drove down a side road and entered the compound through a rear gate that led to the actual prison.

The detainees could then be unloaded and whisked into the ground floor of the prison and into the basement.

Imported Halal meat
The basement consisted of six prefabricated cells, each with a clock and arrow pointing to Mecca, the officials said. The cells were on springs, keeping them slightly off balance and causing disorientation among some detainees.

The CIA declined to comment on the prison.

During the first month of their detention, the detainees endured sleep deprivation and were doused with water, slapped or forced to stand in painful positions, several former officials said. Waterboarding, the notorious interrogation technique that simulates drowning, was not performed in Romania, they said.

• Video: Report: CIA spied on bin Laden for months

After the initial interrogations, the detainees were treated with care, the officials said. The prisoners received regular dental and medical checkups. The CIA shipped in Halal food to the site from Frankfurt, Germany, the agency's European center for operations. Halal meat is prepared under religious rules similar to kosher food.

Former U.S. officials said that because the building was a government installation, it provided excellent cover. The prison didn't need heavy security because area residents knew it was owned by the government. People wouldn't be inclined to snoop in post-communist Romania, with its extensive security apparatus known for spying on the country's own citizens.

Human rights activists have urged the Eastern European countries to investigate the roles their governments played in hosting the prisons in which interrogation techniques such as waterboarding were used. Officials from these countries continue to deny these prisons ever existed.

"We know of the criticism, but we have no knowledge of this subject," Romanian President Traian Basescu said in a September interview with AP.

The CIA has tried to close the book on the detention program, which President Barack Obama ended shortly after taking office.

"That controversy has largely subsided," the CIA's top lawyer, Stephen Preston, said at a conference this month.

'Years of official denials'
But details of the prison network continue to trickle out through investigations by international bodies, reporters and human rights groups. "There have been years of official denials," said Dick Marty, a Swiss lawmaker who led an investigation into the CIA secret prisons for the Council of Europe. "We are at last beginning to learn what really happened in Bucharest."

During the Council of Europe's investigation, Romania's foreign affairs minister assured investigators in a written report that, "No public official or other person acting in an official capacity has been involved in the unacknowledged deprivation of any individual, or transport of any individual while so deprived of their liberty." That report also described several other government investigations into reports of a secret CIA prison in Romania and said: "No such activities took place on Romanian territory."

Reporters and human rights investigators have previously used flight records to tie Romania to the secret prison program. Flight records for a Boeing 737 known to be used by the CIA showed a flight from Poland to Bucharest in September 2003. Among the prisoners on board, according to former CIA officials, were Mohammed and Walid bin Attash, who has been implicated in the bombing of the USS Cole.

• Video: Report: CIA lacks accountability

Later, other detainees — Ramzi Binalshibh, Abd al-Nashiri and Abu Faraj al-Libi — were also moved to Romania. A deceptive al-Libi, who was taken to the prison in June 2005, provided information that would later help the CIA identify Osama bin Laden's trusted courier, a man who unwittingly led them the CIA to bin Laden himself.

 Court documents recently discovered in a lawsuit have also added to the body of evidence pointing to a CIA prison in Romania. The files show CIA contractor Richmor Aviation Inc., a New York-based charter company, operated flights to and from Romania along with other locations including Morocco and the U.S. military prison at Guantanamo Bay.

For the CIA officers working at the secret prison, the assignment wasn't glamorous. The officers served 90-day tours, slept on the compound and ate their meals there, too. Officers were prevented from the leaving the base after their presence in the neighborhood stoked suspicion. One former officer complained that the CIA spent most of its time baby-sitting detainees like Binalshibh and Mohammed whose intelligence value diminished as the years passed.

The Romanian and Lithuanian sites were eventually closed in the first half of 2006 before CIA Director Porter Goss left the job. Some of the detainees were taken to Kabul, where the CIA could legally hold them before they were sent to Guantanamo. Others were sent back to their native countries.

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