Guantanamo Bay detainee Adnan Farhan Abdul Latif, in an undated photo provided by his attorney.

The Guantanamo detainee found dead in his prison cell last weekend had been cleared for  release three years ago by an Obama administration task force that concluded that his detention was no longer necessary, NBC News has learned. 

The disclosure that the detainee, Adnan Farhan Abdul Latif, a 32-year-old Yemeni citizen, had been approved for repatriation could raise new questions about the handling of his case and those of scores of others held in Gitmo who also have been cleared for release. Instead, the detainees remain stuck in legal limbo in the U.S. prison for suspected terrorists with no prospect for getting out any time soon.  

A special Obama administration task force review found in 2009 that Latif, who had been held at Gitmo since early 2002 and had waged a long legal battle for his freedom, could be released, a conclusion that could only be reached by a unanimous vote of all U.S. intelligence agencies. 

That finding was buttressed a year later when U.S. Judge Henry Kennedy ruled that the U.S. government's initial evidence that Latif had links to al-Qaida and the Taliban was "unconvincing."  Despite both findings, the Obama administration appealed the ruling --  because it did not want to return him to Yemen, a country it viewed as too unstable. 

That stance provoked criticism from human rights groups. At the time of Latif's death, Amnesty International was about to launch an international campaign calling for his freedom, according to David Remes, who headed a legal team that represented Latif. 

"Adnan spent more than ten years in Guantanamo-- nearly a third of his life -- but like most Guantanamo detainees, he was never charged with a crime or accused of violating any law," Remes said in a statement released Tuesday. 

He  "endured great suffering at Guantanamo -- physical and spiritual -- and lived in constant torment" but "could see no end to his confinement,"  it said.  "However he died, Adman's death is a reminder of the injustice of Guantanamo and the urgency of closing the prison." 

Remes told NBC News Tuesday that Latif had been “in despair” over his plight and had told him he would take any opportunity he could to commit suicide. He also said that Latif had been heavily sedated by guards there.

In a statement on its website Tuesday, Amnesty International USA called Latif’s death, “a tragic reminder of the numbing cruelty of the USA’s indefinite detention regime at its Guantánamo Bay detention facility, and the urgent need to resolve the detentions.” 

Latif's death is the ninth at Gitmo since the U.S. prison for terrorists opened in January 2002 and the third since last year. The case is now the subject of an investigation by the Naval Criminal Investigative Service. Military officials say that Latif, who had no serious medical problems, was found unconscious and unresponsive in his cell at Camp 5 on Saturday afternoon. After efforts to revive him failed, he was rushed to a hospital at the base and pronounced dead. An autopsy was conducted on Sunday, but the results have not yet been released.

Military officials say that Latif had been a disciplinary problem: He had been on a hunger strike that he ended in June and recently had hurled a "cocktail" of food and bodily fluids at guards, causing him to be placed in a special disciplinary cell in Camp 5, where he was isolated from other detainees.

But Remes said that Latif had ample grievances. Pentagon officials had first recommended he be released from Gitmo as early as 2004, but he was caught up in seemingly endless legal battles over the status of detainees. He was brought to the prison in early 2002 after being turned over to Pakistani police to the U.S. military following the invasion of Afghanistan. Latif had said he suffered from brain injuries as a result of an auto accident in Yemen and had gone to Pakistan for free medical help.

U.S. military officials originally claimed that he had been encouraged to leave Yemen by an al-Qaida facilitator named “Abu Khalud” and had received military training at a camp in Afghanistan. But Judge Kennedy noted in his ruling that there was no corroborated evidence that Latif ever met Khalud and that Defense Department officials had previously concluded that Latif  “is not known to have participated in combatant/terrorist training.”

In letters from Gitmo, Latif repeatedly asserted his innocence.  “This prison is a piece of hell that kills everything, the spirit, the body, and kicks away all the symptoms of health from them,” he wrote in one letter that was widely cited by human rights advocates.

Noting President Barack Obama's one-time pledge to close Gitmo, Remes said: "The only detainees who have been released from Gitmo in the last two years have been in caskets."

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Reuters, file

Jalaluddin Haqqani (R), the Taliban's minister for tribal affairs, points to a map of Afghanistan while his son Naziruddin looks on in Islamabad in October, 2001. The Haqqani insurgent group is named after its patriarch and founder Jalaluddin Haqqani, who was a legendary anti-Soviet mujahideen commander in the 1980s. Back then he was admired by the Americans.

Senior members of the Haqqani network said that the United States' designation of the militant group as terrorists could endanger the life of an American soldier thought to be in their custody and jeopardize peace talks.

"The Obama administration and U.S. military commanders know that their soldier Bowe Bergdahl is in our possession," a Haqqani commander told NBC News in a telephone interview from an undisclosed location on Friday.  "He is in our custody, but his government failed to make any sincere effort for his release, and now this new development could add to his woes."

AFP - Getty Images

This image grab from an undated video reportedly posted on the internet by Afghan militants on Dec. 25, 2009, allegedly shows U.S. soldier Bowe Robert Bergdahl, who was captured in Afghanistan around six months previously.

The Haqqanis, a Pashtun tribe with strongholds in southeastern Afghanistan and across the border in Pakistan, have been blamed for an attack on the U.S. Embassy in Kabul and other high-profile assaults in Afghanistan.  The group is also believed to be holding U.S. Sgt. Bowe Bergdahl, who was captured in 2009 in Afghanistan’s Paktika province, bordering Pakistan’s South Waziristan.

Members of the network say Bergdahl was handed over to the Taliban when a delegation of senior Taliban leaders began peace talks with the U.S. in Qatar in exchange for the top five Taliban commanders from Guantanamo Bay. After those talks failed, the Taliban sources told NBC News that Bergdahl was returned to the Haqqani network.

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On Friday, U.S. officials announced that the Obama administration would formally designate the Haqqani network as a foreign terrorist organization. The move was part of a complicated political decision as the U.S. withdraws from Afghanistan and pushes for a reconciliation pact to end more than a decade of warfare.  

But the move would only undermine the United States' efforts in the region, one of the Haqqani commanders told NBC News.

NYT: White House backs listing Haqqani militant group as terrorists, officials say

"How (will) their talks with the Taliban bring peace to Afghanistan when they declared us terrorists?" the commander, who asked to remain anonymous, said. "It would further increase their hardship and they should wait for more losses in the coming days." 

Secretary of State Hillary Clinton signed a report to Congress saying the network met criteria for a terrorist designation on Friday, State Department officials told reporters.  

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The Obama administration has been trying to coax Afghanistan's fighting groups into peace talks, offering the prospect of a Qatar-based political office for insurgents and even the transfer of several prisoners being held at the U.S. naval base at Guantanamo Bay, Cuba. Negotiations have been dormant for months, and the Haqqanis have been among the least interested in talking.

Designation by the State Department as a foreign terrorist organization would bring sanctions such as criminal penalties for anyone providing material support to the group and seizure of any assets in the United States.

The Haqqani commanders also told NBC News that they were part of the mainstream Afghan Taliban headed by Mulla Mohammad Omar and declaring them as a terrorist group would make it worse for the United States and its allies in in Afghanistan.

"We are fighters of Islam Emirate of Afghanistan led by our supreme leader Mulla Mohammad Omar," a senior commander said. "Our aim is to expel all the occupying forces from Afghanistan and install a purely Islamic government there."

The Pentagon welcomed the designation of the group as a terrorist group.

"The Haqqani Network represents a significant threat to U.S. national security and we will continue our aggressive military action against this threat," said George Little, Acting Assistant Secretary of Defense for Public Affairs, in a statement. "These new group designations will build on our efforts to degrade the Network's capacity to carry out attacks, including affecting fundraising abilities, targeting them with our military and intelligence resources, and pressing Pakistan to take action."

The United States accuses Pakistan's intelligence agency of supporting the Haqqani network and using it as a proxy in Afghanistan to gain leverage against the growing influence of its archrival, India.

Pakistan denies the allegations.

Photos: Pakistan -- A nation in turmoil

A senior Pakistani foreign ministry official, who asked to remain nameless because of the sensitivity of the issue, both denied claims that Pakistan was working with the network and dismissed the designation. 

"If we are sponsoring the Haqqanis, which we are not because they cause more problems for Pakistan than anyone else, then only will this new labeling equate to something," he told NBC News. "No responsible person has proven that we are directing them in any way. Obviously there are contacts, but the U.S. has contacts for the purposes of negotiations, etc. too with these guys."

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BAMAKO, Mali -- An al-Qaida-linked Islamist militant group in control of northern Mali stoned to death a couple accused of engaging in extramarital affairs, the group's spokesman said.

The couple were publicly executed in the remote town of Aguelhok, near the vast West African nation's northern border with Algeria, on Sunday, a spokesman for the Ansar Dine group told Reuters.

"These two people were married and had extra-conjugal relations. Our men on the ground in Aguelhok applied shariah (Islamic law)," said Sanda Ould Bounama, reached by telephone on Monday.

"They both died right away and even asked for this application. We don't have to answer to anyone over the application of shariah," he said.

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A local government official told the AFP news agency that he was on the scene. "The Islamists took the unmarried couple to the center of Aguelhok. The couple was placed in two holes and the Islamists stoned them to death," he said.

"The woman fainted after the first few blows," he said. The man shouted out once and then was silent, he added.

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Most people living in northern Mali have long practiced Islam, but frustrations with the strict form of shariah being imposed by Islamists have sparked several protests in recent months.

Ansar Dine and well-armed allies, including al-Qaida splinter group MUJWA, have hijacked a separatist uprising by local Tuareg rebels and now control two-thirds of Mali's desert north, territory that includes the regions of Gao, Kidal and Timbuktu.

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Western and African governments are struggling to muster a response to the crisis as politicians in the capital Bamako continue to squabble over how the country should be governed after a March coup removed the country's president.

NBCNews.com staff contributed to this report from Reuters.

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Secretary of State Hillary Rodham Clinton told reporters Tuesday that terrorists keep trying to come up with “more and more perverse and terrible ways to kill innocent people” after a plot by al-Qaida's affiliate in Yemen to bomb a U.S.-bound airliner was foiled by the CIA.

U.S. officials said Monday that the plot involved a bomb that improved on the one that had been sewn into the underpants of Umar Farouk Abdulmutallab, who failed in a plot to blow up a Detroit-bound airliner on Christmas Day 2009.

The latest bomb had a more refined detonation mechanism and was "totally non-metallic," which officials told NBC News would have made it more difficult to detect by traditional screening processes.

“With respect to the plot that was discussed in Washington, as the White House said, the device did not appear to pose a threat to the public air service, but the plot itself indicates that these terrorists keep trying,” Clinton, who is in New Delhi, India, said.

“They keep trying to devise more and more perverse and terrible ways to kill innocent people, and it's a reminder as to why we have to remain vigilant at home and abroad … protecting our nation and protecting friendly nations and peoples like India and others,” she added.

Clinton also called for India’s neighbor Pakistan “to do more” to tackle terrorists. “It needs to make sure that its territory is not used as a launching pad for terrorist attacks anywhere, including inside of Pakistan, because the great unfortunate fact is that terrorists in Pakistan have killed more than 30,000 Pakistanis,” she said.

CIA foiled al-Qaida plot to destroy US-bound airliner

The new underwear bomb had some “refinements on reliability” that made it more likely to explode, a U.S. counterterrorism official told NBC News. In addition to being a threat to commercial planes, this type of bomb could be used in crowded places, on other transportation systems or for assassinations, the official said.

More than 30 Yemeni troops killed in militant attack

The official noted that the bomb “was never near a plane” and “never posed a risk.” The plot was disrupted well before it threatened Americans or U.S. allies, the official added.

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The U.S. received the device last month. The FBI is conducting technical and forensic analyses on it.

The official would not specify which international security service provided the intelligence that led to the unraveling of the plot, as there is concern about retaliatory attacks against U.S. targets inside Yemen.

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The FBI said in a statement that the successful operation was the "result of close cooperation with our security and intelligence partners overseas."

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Gonzalo Fuentes /Reuters

Said Hicheur (center), father of Franco-Algerian nuclear physician Adlene Hicheur, and Halim (right), Adlene's brother, outside the Paris courthouse Friday.

PARIS -- A French court sentenced an Algerian-born nuclear physicist to five years in prison Friday for his role in plotting terrorism with al-Qaida's north African wing. 

Adlene Hicheur, a former researcher at Switzerland's CERN laboratory, was convicted of "criminal association with a view to plotting terrorist attacks." 

Hicheur, who has been behind bars since he was arrested in October 2009, could have received up to 10 years in prison. 

The 35-year-old scientist and his defenders say he was a victim of allegedly overzealous French anti-terrorism laws and that he explored ideas on jihadist websites but never took any concrete step toward terrorism. 

Speaking after the judgment, Hicheur's lawyer called the verdict "scandalous." 

Lawyer Patrick Baudouin said Hicheur hasn't decided whether to appeal the verdict. If he does not, with time off for good behavior, his client "should be out rather quickly," he added. 

Didn't want to be a suicide bomber
The case centered on about 35 emails between Hicheur and an alleged contact within al-Qaida in the Islamic Maghreb named Mustapha Debchi, who tried to convince him to carry out a suicide bombing.

Hicheur declined, but in one response suggested striking at the barracks of a battalion of elite Alpine troops in the eastern town of Cran-Gevrier. 

Hicheur claimed he was on morphine for a herniated disk and going through a personal "zone of turbulence" when he wrote a 2009 email that advocated an attack on the barracks. 

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Prosecutor Guillaume Portenseigne rejected Hicheur's claims of a lack of lucidity and characterized the defendant as "a man who had everything going for him ... but just got led astray in a radical jihadist Islam." 

Al-Qaida operative found guilty of bomb plot

At the two-day trial in March, the prosecutor called Hicheur "a budding terrorist" who only needed a "determining meeting" to slip into concrete action. 

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Hicheur's lawyer argued that "everything has been done to demonize" his client, "to make him into ... France's most dangerous terrorist, potentially susceptible to participate in a bombing." 

Hicheur's defenders said recent terror attacks in France did not help his case. 

In an apparently unrelated case in March, a young man also of Algerian descent killed three Jewish schoolchildren, a rabbi and three paratroopers in the cities of Toulouse and Montauban and claimed ties to al-Qaida. Mohamed Merah, 23, died later in a shootout with police.

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Faisal Mahmoud / Reuters

Hafiz Saeed, the head of Jamaat-ud-Dawa and founder of Lashkar-e-Taiba, attends the funeral of Muslim cleric Moulana Showkat Shah in Islamabad April 11, 2011. Saeed is now wanted by the U.S. for $10 million.

ISLAMABAD, Pakistan -- The United States has offered a $10 million bounty for the founder of the Pakistani militant group blamed for the 2008 attacks in the Indian city of Mumbai that killed 166 people, a move that could complicate U.S.-Pakistan relations at a tense time.

Hafiz Saeed founded Lashkar-e-Taiba in the 1980s, allegedly with Pakistani support to pressure archenemy India over the disputed territory of Kashmir. Pakistan banned the group in 2002 under pressure from the U.S. but has done little to crack down on its activities.

Saeed operates openly in the country, giving public speeches and appearing on TV talk shows. The U.S. also offered up to $2 million for Lashkar-e-Taiba's deputy leader, Hafiz Abdul Rahman Makki.

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The bounties were posted on the U.S. State Department Rewards for justice website late Monday, the U.S. Embassy in Islamabad said Tuesday.

The reward for Saeed is one of the highest offered by the program and is equal to the amount for Taliban chief Mullah Omar. Only Ayman al-Zawahri, who succeeded Osama bin Laden as al-Qaida chief, fetches a higher, $25 million bounty.

Slideshow: Pakistan: A nation in turmoil

Khuram Parvez / Reuters

Images of daily life, political pursuits, religious rites and deadly violence.

Launch slideshow

U.S. Undersecretary of State Wendy Sherman announced the bounty for Lashkar-e-Taiba's leader and deputy on Monday during a visit to India, according to The Times of India newspaper. 

"[The bounty] sends a strong signal to Lashkar-e-Taiba as also its members and patrons that the international community remains united in combating terrorism," Indian ministry of external affairs spokesman Syed Akbaruddin said on Twitter.

Al-Jazeera's correspondent in Lahore reported that Saeed has denied any links to militancy.

Troubled Pakistan-US relationship
The move comes at a particularly tense time in the troubled relationship with the U.S. and Pakistan. Pakistan's parliament is currently debating a revised framework for relations with the U.S. in the wake of American airstrikes that killed 24 Pakistani soldiers in November at two posts along the Afghan border.

Pakistan retaliated by kicking the U.S. out of a base used by American drones and closing its border crossings to supplies meant for NATO troops in Afghanistan.

The U.S. hopes the parliamentary debate will result in Pakistan reopening the supply lines. The closure has been a headache for the U.S. because it has had to spend more money sending supplies through an alternate route that runs through Central Asia. It also needs the route to withdraw equipment as it seeks to pull most of its combat forces out of Afghanistan by the end of 2014.

But it's unclear whether the U.S. will be willing to meet Pakistan's demands, which include higher transit fees for the supplies and an unconditional apology for the airstrikes, which the U.S. has said were an accident. Pakistan has also demanded an end to American drone strikes in Pakistan, but it's unclear if that will be tied to the reopening of the supply line.

Msnbc.com staff and The Associated Press contributed to this report.

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London's Times newspaper reported on a suspected terrorist plot in Kenya Wednesday.

Updated at 11:17 a.m. ET: LONDON -- A woman believed to be the widow of one of the four suicide bombers that killed 52 London commuters in July, 2005, is being sought by Kenyan authorities in relation to a terrorist plot in that country, The Times newspaper reported on Wednesday.

Kenyan police were searching for a woman who evaded them when they tried to capture members of a group thought to be planning an attack on the city of Mombasa in December, 2011, the newspaper reported. (The Times operates behind a paywall.)

One of the identities the suspect was believed to be traveling under was Samantha Lewthwaite, the widow of Jermaine Lindsay, who blew up a subway train at King's Cross station on July 7, 2005, Kenyan police told The Times.

The suspect had claimed to be Natalie Faye Webb, a South African, but the passport with this name was determined to be fake, the newspaper reported.

Lindsey's backpack-borne bomb claimed 26 lives on 7/7, as the attack is known in the U.K.

A Kenyan police spokesman Eric Kiraithe told The Times: "We know quite a bit about her now. She has had three identities in the past and that [Samantha Lewthwaite] is one possible identity."

Kenyan police have been working with British police over the operation and have sent a large team to Nairobi to help with the investigation, the newspaper reported.

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Lewthwaite, 28, a convert to Islam who called her husband's actions on July 7, 2005, "abhorrent," is suspected of being part of a cell directed by terrorist group al-Shabab, according to The Times.

Lewthwaite's family say they have not had any contact with her in years, the newspaper reported.

Police are also searching for another British suspect, Habib Ghani of London, according to the Times.

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Msnbc.com staff contributed to this report.