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This March 10, 2009, file image of a courtroom drawing from U.S. District Court shows alleged al-Qaida sleeper agent Ali al-Marri as he made an initial appearance with his attorney Andy Savage in Charleston, S.C. to face terror charges for the first time after being held for more than five years as an enemy combatant. Nephew Saleh Garallah Kahlah al-Marri said Sunday, Jan. 18, 2015, that Ali al-Marri, a Qatari man declared an enemy combatant by the U.S. and imprisoned for years over terrorist links, returned home to the Gulf nation Saturday night. Image Credit: AP

The Obama administration has repatriated a Qatari man jailed for ties to Al Qaida, US officials said on Tuesday, putting an end to the 13-year legal saga of one of only three terrorism suspects held as enemy combatants on US soil.

Ali Saleh Mohammad Kahlah Al Marri, 49, was released from a maximum-security prison in Florence, Colorado, on Friday, officials at US Immigration and Customs Enforcement (ICE) said. Hours later, he boarded a commercial flight at Denver International Airport, escorted by ICE officers, and began his journey back to the Qatari capital, Doha.

Al Marri’s release and deportation, carried out without fanfare, is a milestone for the Obama administration as it seeks to unwind the web of military detentions and legal cases that resulted from the September 11, 2001, attacks on the US.

It comes as President Barack Obama redoubles his efforts to close the military prison at Guantanamo Bay, Cuba, where since 2001, hundreds of detainees have been held without trial. Although those prisoners at Guantanamo are considered enemy combatants, only a handful of prisoners on US soil were given that status.

Al Marri, a dual citizen of Qatar and Saudi Arabia, had arrived in the US on a student visa not long before the Federal Bureau of Investigation (FBI) arrested him at his home in Peoria, Illinois, in December 2001. US officials believed Al Marri had ties to senior Al Qaida operatives, including Khalid Shaikh Mohammad, the self-declared mastermind of the September 11 attacks, and had researched chemical weapons.

His case abruptly changed course in June 2003, when the George W. Bush administration declared him an enemy combatant and took him into military custody. For more than five years, Al Marri was held at a naval brig in Charleston, South Carolina. For much of that time, his lawyers said, Al Marri was subjected to harsh treatment, sometimes being deprived of sunlight and adequate clothing or bedding.

“At that point, it was transformed from an ordinary prosecution to a case with monumental civil liberties implications,” said Jonathan Hafetz, a law professor who has represented Al Marri. “The Bush administration was saying that the president had the authority to declare any person in the US an enemy combatant and strip that person of the most basic rights of due process based on allegations of terrorism.”

Al Marri’s case took another turn in 2009 when Obama, who vowed to end the military detention system at Guantanamo Bay, ordered a review of his detention. Al Marri was transferred back to the civilian justice system and, in 2009, he pleaded guilty to one charge of criminal conspiracy.

Later that year, a federal judge gave Al Marri 100 months in prison. He served most of his full term, the Federal Bureau of Prisons said.

Andrew Savage, another of Al Marri’s lawyers, said the US government had never connected Al Marri to any specific terrorist attack.

Savage said that Al Marri, who is not in government custody in Qatar, has been reunited with his family. He said Al Marri was “pretty overwhelmed” to be free after his years in solitary confinement.