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

Ali Saleh Mohammad Kahlah al-Marri, 49, was released from a maximum security prison in Florence, Colo., on Friday, officials at U.S. 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.

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 Sept. 11, 2001, attacks on the United States.

It comes as President 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 U.S. soil were given that status.

José Padilla, a New York-born man arrested for allegedly plotting a “dirty bomb” attack, and Yaser Esam Hamdi, born in Louisiana and arrested with pro-Taliban forces in Afghanistan, were also held as enemy combatants on U.S. soil. Padilla was later convicted in federal court, while Hamdi was sent to Saudi Arabia in 2004.

Marri, a dual citizen of Qatar and Saudi Arabia, had arrived in the United States on a student visa not long before the FBI arrested him at his home in Peoria, Ill., in December 2001. U.S. officials believed Marri had ties to senior al-Qaeda operatives, including Khalid Sheik Mohammed, the self-declared mastermind of the Sept. 11 attacks, and had done research into 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, Marri was held at a naval brig in Charleston, S.C. For much of that time, his lawyers said, 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 Marri. “The Bush administration was saying that the president had the authority to declare any person in the U.S. an enemy combatant and strip that person of the most basic rights of due process based on allegations of terrorism.”

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. 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 Marri 100 months in prison. He served most of his full term, the Federal Bureau of Prisons said.

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

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

Julie Tate contributed to this report.