The arrest and trial of alleged al-Qaida spokesman Suleiman Abu Ghaith may resolve a long-standing debate inside the U.S. intelligence community on what Iranian officials did with members of the terrorist group who snuck into the country shortly after 9-11, hoping they would be treated, if not warmly, then as "the enemy of my enemy," as one U.S official put it.

Abu Ghaith, who was arraigned on Friday in federal court in New York on charges he plotted to kill Americans, described the conditions under which al-Qaida officials' were confined in Iran in a 22-page statement signed after his arrest last week in Jordan.

The statement, which was referenced in his court appearance, is expected to shed light on the accuracy of intelligence gathered by the U.S. in months after 9-11 indicating that the so-called al-Qaida “management council” detained in Iran was still conducting business, even discussing procurement of nuclear weapons.

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The debate among U.S. intelligence officers and agencies centers on how Iran treated the al-Qaida leaders and bin Laden relatives following their capture in Iran in early 2002, and how much it they were allowed to communicate with other members of the terrorist group. The faction in Iran, which with family and bodyguards numbered in the hundreds, bribed their way into the country but was rounded up not long afterward. As one U.S. official told NBC News Thursday, what happened next occurred inside the "blackest of the black boxes" of Iran's intelligence apparatus.

Some analysts believe that members of the group were more or less placed under house arrest. Iranian officials denied that, saying they were "in jail."

Another question is whether the group had significant operational communications with other al-Qaida leaders. One high-ranking former U.S. official told NBC News this week that he was unaware of any contact regarding al-Qaida operations.

But George Tenet, director of the CIA following the 9-11 attacks, painted a different picture in his memoirs, "At the Center of the Storm," written with William Harlow.

In the book, Tenet described incidents in which he learned that the group was not only communicating with Saudi-based al-Qaida leaders on operational matters, but also trying to obtain nuclear weapons. 

"From the end of 2002 to the spring of 2003, we received a stream of reliable reporting that the senior al-Qaida leadership in Saudi Arabia was negotiating for the purchase of three Russian nuclear devices,” Tenet wrote. “Saudi al-Qaida chief Abu Bakr relayed the offer directly to the al-Qaida leadership in Iran, where Sayf al-Adl and (Mohammed) Abdel al-Aziz al-Masri (described as al-Qaida’s “nuclear chief” by Khalid Sheikh Mohammed) were reportedly being held under a loose form of house arrest by the Iranian regime.

Tenet wrote that the al-Qaida leaders had learned lessons from previous attempts to procure nuclear devices in the nuclear black market in the early 1990s.

“Saif al-Adel told Abu Bakr that no price was too high to pay if they could get their hands on such weapons,” he wrote. “However, he cautioned Abu Bakr that al-Qaida had been stung by scams in the past and that Pakistani specialists should be brought to Saudi Arabia to inspect the merchandise prior to purchase.

"As soon as I got wind of al-Qaida negotiations to purchase nuclear components in Saudi Arabia, I contacted the Saudi ambassador to the United States, Prince Bandar, and gave him all the details we had," Tenet said.

The CIA also communicated its intelligence to the Iranians, being uncertain of what the Islamic Republic knew of the communications, according to the former CIA director’s account.

"One senior al-Qaida operative told us that Mohammed Abdel al-Aziz al-Masri, who had been detained in Iran, managed al-Qaida’s nuclear program and had conducted experiments with explosives to test the effects of producing a nuclear yield. We passed this information to the Iranians in the hope that they would recognize our common interest in preventing any attack against U.S. interests."

Another U.S. security official told NBC News that Tenet's message did get attention in Tehran and that, in 2003, the group in Iran’s communications with other al-Qaida leaders were down.

Beyond the historical debate, U.S. officials want to know what happened to the other leaders in the management council. Apart from Khalid Sheikh Mohammed, who is awaiting trial before a U.S. military court, the whereabouts of the others are unknown. There have been  intermittent reports over the years that Saif al-Adel, the Egyptian-born military director of al-Qaida, was permitted to leave Iran, but they have not been confirmed.  

 

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Lawyers for terror suspects held at the U.S. detention facility at Guantanamo, Cuba, said Tuesday that detainees are engaged in widespread protests of conditions at the prison, including a hunger strike that may imperil their lives.

Calling the situation “alarming,” the lawyers said in a statement that some of their clients are “coughing up blood” and “losing consciousness.”  A letter making similar assertions was sent earlier this week to Navy Rear Adm. John W. Smith, the commander of the Joint Task Force at Guantanamo and signed by a dozen lawyers who represent most of the detainees at Guantanamo.  

A spokesman for U.S. military at Guantanamo   disputed the lawyers’ claims of a widespread hunger strike, saying they and their clients were merely trying to get attention and keep Guantanamo “in the news. ” 

The spokesman, Navy Capt. Robert Durand, said that a half-dozen detainees are currently on a hunger strike -- five of whom are being force fed through tubes -- and that no lives were in danger. Durand added that the figure was consistent with the average number of hunger strikers at Guantanamo over the past several years. He also acknowledged that “some detainees” have been disciplined and moved out of Camp 6 -- the most permissive of the camps at Guantanamo, with communal living arrangements -- but he declined to say how many or give the reasons for the action. 

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The conflicting claims underscored the difficulty of obtaining information about conditions at the facility, which President Barack Obama vowed to shut down on his first day in office after his 2008 election but which still remains open as a result of congressional opposition to its closure. There are 166 detainees remaining at the camp, but military rules forbid them from communicating in any way with members of the news media and visits to the camp by outsiders are tightly regulated. Even their communications with their lawyers must be cleared by military censors.

One of those lawyers, David Remes, told NBC News in a telephone interview from Guantanamo Monday night that he saw one of his clients -- Hussain Almerfedi, a Yemeni -- earlier that day and that he had lost “substantial weight” and was “very sick.” Under Guantanamo rules, Remes said he could not share anything that his client told him until the censor cleared the communication. But he said that he offered Almerfedi some trail mix during their meeting and he declined to take it -- a sign,  Remes said,  that his client was participating in the hunger strike.

“The men are at their wit’s end,” he said. “This is their eleventh year of being there and they have no prospect for release.” He also said that since taking over last year as commander,  Adm. Smith had “turned the clock back” to 2002 and 2003, imposing harsher restrictions on the detainees and more-rigorous searches in which personal items were being seized. The searches are being carried out by guards -- some of whom are returning soldiers from Afghanistan and Iraq -- who he asserted appear to be extracting vengeance for what they encountered overseas, he said.   

One flashpoint appears to have been a Feb. 6 search at Camp 6 in which, according to the lawyers, camp authorities seized blankets, sheets, towels, sleeping mats, razors and other items from the detainees,  including family photos and religious CDs from the detainees. In their letter to Smith, the lawyers alleged that Arabic interpreters at the camp inspected Qurans “in ways that constitute desecration.” 

Durand, the Guantanamo spokesman, disputed that any harsher restrictions had been imposed by the new commander and said the search last month was in keeping with past practice. He said that search, and earlier ones, have turned up  “a Wal-Mart worth of stuff,” including improvised weapons, illegal electronics and other illicit contraband. But he said that handling of the Qurans was tightly regulated  and that no guards are even permitted to touch the Islamic Holy Books during the searches.

Durand also acknowledged that some of the dispute between camp authorities and the detainees’ lawyers may be about defining terms. Guantanamo officials define a hunger strike as refusing to eat nine meals in a row. But, he said, some of the detainees may be hoarding food in their cells even when they claim to be on a hunger strike.  

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GADSDEN, Ala. -- Ivan Stobert was in many ways the ideal immigrant.

In 2006, he traveled from Moldova to the United States on a visa. While here, he fell in love and in 2008 married a U.S. citizen. He became a permanent legal resident, bought a house in the Atlanta area and started a cleaning business.

“Finally I made my dream,” Stobert told NBC News. “I buy my house, I have my business. I thought, ‘Wow, I love America!’”

But the love affair ended in December 2010, when the slight 25-year-old found himself locked up indefinitely in the Etowah County Detention Center in northeast Alabama, charged with an aggravated felony and facing deportation.

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More than 250 detention facilities around the country are used to hold the tens of thousands immigrants detained each year by U.S. Immigration and Customs Enforcement, known as ICE, as they await court dates or deportation. Even those accused of relatively minor infractions, such as overstaying a visa, can be held for months – or even years – fighting their cases without the benefit of rights and resources guaranteed to those accused of criminal acts.

 

Immigrant advocates have for years called Etowah one of the worst facilities in ICE’s sprawling detention system.

In late July, conditions in the isolated facility, which also serves as the county jail, prompted some immigration detainees to refuse food in an act of protest to demand better treatment. A hundred detainees signed a letter to ICE and operators of the jail.

“Some Detainees life’s (sic) are at stake and to disregard this fact is inhumane and not in compliance with ICE (standards),” they wrote.

“They were sending us rotten food, food that’s spoiled,” detainee Javian Lawrence, a 27-year-old Jamaican national, told NBC News in a phone interview from the jail. 

Those detained in Etowah are locked up for myriad reasons -- including overstayed visas or entering the country illegally. But others, like Stobert, say they were caught in the immigration law enforcement web by mistake.

Checking the wrong box
Stobert says his troubles began in April 2009 when he accidentally checked the “U.S. Citizen” box on a motorcycle license application. He said that even though he presented his green card and Moldovan passport along with the application, indicating he was in the country legally, two law enforcement officers arrived at his home more than a year and a half later and arrested him for providing false statements on a government application. He was booked into jail in Atlanta, held for more than a month, then transferred to Etowah.

For what he says was an innocent mistake, Stobert spent nearly a year behind bars. And while he was locked up, he says, he lost his house to foreclosure, his wife left him and his budding cleaning business collapsed.

“I lost everything while I been there,” he said. “I lost my house. I lost my wife. I lost all my cars, whatever I had. I lost everything.”Though his case was dismissed, a hearing on his immigration status is still pending and he remains unsure of whether he’ll be deported or–even worse, from his perspective–locked up again. “I’m not sure,” he said, “if America will keep me or not.”

Locked up in limbo
After scandals including sexual abuse by guards, deaths in custody and the detention of children, ICE announced in August 2009 plans to consolidate its network of detention centers, many of them county jails, and improve oversight.

Three years later, however, the agency still houses nearly 34,000 immigration detainees on any given day in some facilities that critics say are intended to be short-term way stations in the criminal justice system, not used for long-term civil detention. 

Many of the more than 300 men at the Etowah County Detention Center – who spend much of their time in cramped cells, denied access to the outdoors – face open-ended stays in the jail. They include asylum seekers; immigrants fighting deportation or petitioning for special status that would enable them to remain in the U.S.; immigrants from countries unwilling to take them back; and people without the proper paperwork to be repatriated.

ICE’s decision to hold long-term detainees in the Alabama jail is rooted in cost-savings: At just $40 a day per detainee, Etowah has one of the lowest rates of any ICE detention facility in the country.

But it also has its challenges. At the end of 2010, ICE attempted to terminate its use of the facility, citing a number of factors, including expensive transportation costs to and from court, and lack of access to ICE staff and attorneys. Its remoteness also makes it difficult for lawyers and the detainees’ family members to visit.

But money from ICE has become an essential source of revenue to the county, bringing in about $5 million a year that funds a host of programs and services in the community. Losing that revenue would be a “devastating blow” to the budget, Etowah Sheriff Todd Entrekin told the Gadsden Times in 2011.

After a political fight to keep the detainees there, the facility came under the control of ICE’s New Orleans field office. About 100 female detainees once housed at Etowah were moved out. New Orleans now uses the 350 beds Etowah reserves for ICE to house male detainees, almost all of whom ICE expects to linger in the system.

Both ICE and Etowah County officials declined repeated requests by NBC News to speak on camera. But advocates for the detainees object to using a jail like Etowah to detain immigrants for the long term.

"It’s absolutely inhumane,” said H. Glenn Fogle, an Atlanta-based immigration attorney who represented Stobert and others detained in the jail. “If you hold somebody long term they’re supposed to go to a proper jail, a long-term jail facility where they can go outside. In these short term facilities you can’t. You’re basically in a jail cell 80 to 90 percent of the time.”

Detainees currently are held at Etowah an average of 49 days, records show. Yet some, like Stobert, remain far longer.

Challenging deportation
Immigrants face major barriers to challenging their detention and deportation, in part because they operate in a civil, rather than criminal, system. To sneak across the border is a crime, but to overstay a visa – one of the most common ways that people lose legal status – is a legal infraction akin to a moving violation.

But due to the civil nature of the crime, immigrants caught in the deportation process have fewer legal protections than someone accused of murder. They lack the right to representation, a speedy trial, double jeopardy protections or standard habeas corpus.

A report by the Vera Institute of Justice found that between 2006 and 2007, more than 80 percent of detained immigrants fought their cases without a lawyer. Stobert was one of the lucky few who could afford one.

Even so, in April 2011, an Atlanta immigration judge ordered Stobert’s deportation, claiming he had intentionally checked the U.S. citizen box. Stobert, already locked up for over five months, decided to fight and his lawyer appealed. He applied to be released on bond, which would include supervision that costs much less than detention. The motion was denied.  Fogle, Stobert’s attorney, said he believes ICE keeps people in Etowah so that detainees will give up hope.

“People have legitimate cases to stay here in the United States, but if they give up and their spirit is broken in these detention centers they’re just going to sign” their deportation papers, he said. “And that’s not right.”

‘Undeportable’
Many of the detainees in Etowah have complicated cases, stemming from criminal charges or diplomatic intricacies. Even some willing to be voluntarily deported cannot be. Countries like China, Cuba or certain Caribbean Islands regularly rebuff U.S. efforts to return their citizens.

Immigration detainees have constitutional protections against indefinite detention. In 2001 the U.S. Supreme Court ruled ICE has approximately six months to deport or release immigrants after their case is decided.

ICE can, however, hold people longer if it can show that certain special circumstances apply – such as the detainee posing a terrorism risk – or if it can show an immigrant will be deported in the near future. But ICE records show the agency regularly opposes even the release of detainees who it has struggled to deport, and prevails.

Barbados national Hanson Marshall, 35, for example, has been detained by ICE for 23 months. He spent time in detention centers in five states before arriving at Etowah last June.

Marshall, who wears the green shirt that at Etowah signals he’s considered a medium-risk detainee, came to the United States legally when he was 16 and settled in Brooklyn with his family. His visa expired, but he stayed.

Marshall had tangled with the law. In 2003, he pleaded guilty to a misdemeanor charge for possessing a firearm. In 2010, he was picked up in New York City on a warrant for a misdemeanor. He spend a week in jail. The day he was to be released, he was instead transferred into ICE custody.

ICE has switched tactics in recent years, concentrating on deporting more immigrants facing criminal charges, like Marshall. But in his case, the deportation has become a Catch-22: Until Barbados issues the necessary travel documents, the United States can’t send him home.

“I would be more than pleased to go back to Barbados but I can’t make it happen,” said Marshall. “It’s not up to me. It’s up to the consulate. But if you stay in immigration for a period of time, and they can’t acquire travel documents, then I shouldn’t have to sit up in jail for the rest of my life.”

Inside Etowah
ICE, which operates the largest detention system in the U.S., relies heavily on jails like Etowah to detain immigrants. Critics have argued for years that jails are not appropriate for ICE detainees, because they live as prisoners -- wearing uniforms, confined in small cells and forced to mingle with general inmate populations.

ICE, too, has emphasized that detention is not meant to be punishment.

“We’re not a penal institution,” John Morton, director of ICE, in a 2010 speech at the Migration Policy Institute, a Washington, D.C.,-based think tank. “We detain people for purposes of removal. We detain people because if we release them they would pose a danger to people or run away. We’re not incarcerating anyone.”

On a tour of the Etowah County Detention Center in May by NBC News, ICE detainees in Unit 10 crowded to the door of the glassed-in recreation area to speak with reporters. Men from countries like Sierra Leone, Morocco, Poland and Guatemala shouted to be heard while other detainees worked out in the room behind, lifting weights and doing pull-ups on metal bars.

The rec room in each unit provides the detainees with their only exposure to natural light or open air, both of which come through a narrow grating high on one wall. Otherwise, detainees go outdoors only when bused to court proceedings, for emergency medical care or when taken to the airport to be deported.

The facility that houses the detainees is by most appearances a jail. Two levels of cells line the large rectangular units. Detainees eat at tables in the middle of the pod, and bunk in small cells behind heavy doors. Mattresses are thin, the showers are bare and public.

Like the rest of the jail’s inmates, the immigrants are not allowed contact visits with family or friends, except under special circumstances. Visitation takes place via a video screen. Detainees interviewed said the no-contact policy discouraged their spouses, children and friends from driving hours to see them.

Detainees also said the commissary, where they can purchase extra food or toiletries, is prohibitively expensive. Phone calls, often the single link to families sometimes thousands of miles away, can cost up to $1 per minute.

Immigration lawyers, and courts, are also difficult to access from Etowah. Many detainees described inadequate medical care, although the detention center operates a clinic with a full-time nurse and weekly visits from a doctor.

ICE’s own reports have noted deficiencies. A 2008 inspection report noted two suicides by county inmates within a six month period. ICE records from that year also indicate that a female detainee tried to hang herself in her cell. The food supply was the subject of a grand jury investigation in 2010.  Jurors concluded it was sufficient.

Since coming under control of the New Orleans Field Office, ICE detention monitors have worked “worked hand-in-hand with facility staff to address these issues and work to implement corrective where necessary,” ICE spokeswoman Gillian Christensen wrote in January 2012 in response to a query about conditions.

Passed inspections
Human rights monitors from the Women’s Refugee Commission also indicate Etowah has made steps to improve the facility, but a recent report from the group indicated problems persist, including complaints about food. The human rights group said the county had been addressing some of the concerns raised in the report.

During the visit by NBC News in May, the menu listed meals with beans, tortillas, fruit, hot dogs, and hamburgers. But Stobert and other former and current detainees said such improvements were recent. 

Also new are some niceties in the units at Etowah that house the immigrants, who were recently allowed to participate in programs formerly available only to county inmates. The wall of one, for example, is adorned with a painted mural of the world. There also are fish tanks in each unit. Officials have also implemented programs for detainees and improved access to medical care, among other reforms.

According to an ICE spokesperson, inspectors found no violations during the facility’s most recent review. Etowah County is currently soliciting bids to build an outdoor recreation center on top of the jail in order to bring the facility up to ICE’s most recent standards, which would also increase pay for officers who oversee ICE detainees.

In May, a detainee in Unit 4, which holds those with the lowest risk classification, was training a dog as part of a new Puppies Without Borders program, intended as an “outlet to relieve the stress of being detained.” The man, a native of the Philippines who declined to give his name, said he was being held while he awaited a decision on his petition for a U-Visa, a special visa offered to immigrants who have been victims of a crime. Smiling as the puppy scurried across the catwalk, he said Etowah was far better than the ICE jail in Illinois that he was transferred from. 

“This is like heaven,” he said of Etowah. “The other was like hell.”

But by July, when detainees staged a brief hunger strike, many complained that the facility had reverted back to some of its old ways, serving food that was rotten and nutritionally inadequate. 

“The situation has not been resolved,” detainee Anthony Orlando Williams said in a phone interview from the facility, where he has spent nearly three years because he has no official country of origin to which the U.S. can deport him. “It’s just been tolerated.”

Following the protest, detainees in Unit 9 were on lockdown, held for nearly 22 hours a day in their cells, according to detainees and their advocates. Nonetheless, they say the strike may just be the first in a series of actions aimed at forcing ICE to move them out of Etowah. 

“It’s hit a fever pitch,” said Abraham Paulos, executive director of Families for Freedom, an immigrant rights group that has been tracking conditions at Etowah. “We’ve never seen a demand of leaving Etowah. They don’t care if they’re still detained, they just don’t want to be detained in Etowah.”   

Read Part 2: When ICE sought to shutter immigration jail, politics intervened.

GUANTANAMO BAY, Cuba -- The U.S.-run Guantanamo Bay detention center in Cuba, targeted for closure by Barack Obama during his campaign for the presidency, is instead quietly undergoing millions of dollars of upgrades that could allow it to remain open for years as a prison for suspected terrorists, NBC News has learned.

Among the recent improvements to the facility commonly known as “Gitmo”: a heavily guarded soccer field for detainees known as “Super Rec,” which cost nearly $750,000 and opened this week; cable television in a  communal living quarters and “enriching your life” classes for detainees, which include instruction on learning to paint, writing a resume  -- even handling personal finances.

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“Well, that's one class, but it’s not a popular (one),”  Army Col. Donnie Thomas, commander of the military guards at camp, said with a laugh. “But it’s a class. It’s just to keep these guys busy.”

Other improvements are more practical, such as a new headquarters for the guards and a new hospital, which is still in the planning stages.

Navy Adm. David B. “Woody” Woods, commander of the Guantanamo facility, told NBC News that the improvements have “made it safer for the detainees, safer for the guard force,” and have not adversely impacted security at the facility.

“We treat them all as a threat only because if you don't then you're gonna get surprised, and that's not our business,” he said.

Many of the improvements have been made at the most modern facility in the detention center, known as Camp VI, a communal living compound that houses about 80 percent of the 169 detainees currently held at Gitmo. There, detainees who are deemed to be compliant with the rules and therefore eligible for more privileges are able to watch 21 Cable TV channels, DVD movies, read newspapers and borrow books from a library.

The detention center, located within the U.S. Guantanamo Bay Naval Base, was established in 2002 by President George W. Bush to hold detainees from the war in Afghanistan and later Iraq. The base in Cuba was selected as part of a Bush administration strategy to prevent judicial review of the legal status of the prisoners, who were initially denied lawyers.

Obama made its closure a centerpiece of his presidential campaign, arguing that U.S. courts were capable of handling the cases. After taking office, he signed an executive order on Jan. 22, 2009, directing that Gitmo be shut down within a year. The order also called for an immediate case-by case review of detainees at the facility with an eye toward either repatriating them or bringing them to trial in U.S. civilian courts.

But the president’s efforts to shutter the camp were blocked by Congress out of concerns that transferring the detainees to U.S. jails would pose a security risk and invite escape attempts or terrorist attacks on the facilities.

A little more than two years after Obama’s first executive order, on March 7, 2011, he signed another executive order making a number of policy changes regarding Gitmo, including a reversal of his order seeking to bring detainees to trial in civilian courts. Instead, he said, suspects would face military tribunals that would decide their guilt or innocence.

Khalid Shaikh Mohammed, the self-described mastermind of the 9-11 terrorist attacks on the U.S., and four other Guantanamo detainees were the first to go before a military tribunal last month, when they were formally charged with crimes that include murder and terrorism. They face the death penalty if convicted for their roles in the attacks that claimed 2,976 lives in New York, Washington and Shanksville, Pa.

But for the remainder of the detainees – including some who are eligible for release but have no country willing to take them – there is little prospect of leaving Gitmo anytime soon.

And that means U.S. taxpayers will continue to foot the bill for their presence in a U.S. prison that costs $140 million a year to operate – or some $800,000 per detainee.

Woods, the commander of the Guantanamo detention center, said he doesn’t anticipate the closure of the facility any time soon.

“As far as being able to close down the operation, I could do that … in a couple of months, the buildings and the people,” he said. “We have removed these belligerents from the battlefield and our job is to detain them, and we do that very well.”

Michael Isikoff is NBC's national investigative correspondent; Mike Brunker of msnbc.com contributed to this report.