WASHINGTON – Aboard the USS Boxer, somewhere in the Indian Ocean, Ahmed Abdulkadir Warsame was sitting across from a team of interrogators, talking and talking. In secure meeting rooms in Washington, senior officials in the Obama administration were wringing their hands over what to do with him.

Some in the administration desperately wanted to prosecute Warsame — a key facilitator between al-Qaida franchises — in federal court. To do that, though, they needed a “clean team” of FBI agents to come in and read the Somali his rights, perhaps jeopardizing his willingness to keep talking. The quandary was particularly acute because Warsame had intelligence on Anwar al-Awlaki, a U.S. citizen and a senior leader in al-Qaida in the Arabian Peninsula (AQAP).

“There was a fair amount of debate because some of the intel guys didn’t want to stop the interrogation,” said a former administration official who spoke on the condition of anonymity to discuss internal government deliberations. “Others were getting antsy because they thought the longer you hold the guy and don’t Mirandize him, the worse off you are” if prosecutors try him in federal court.

In late June 2011, after two months of interrogation, the president’s national security advisers made the call. A team of FBI agents gave Warsame a Miranda warning, advising him of his right to remain silent and his right to counsel. “Then there was a kind of hold-your-breath moment,” the former official said.

Warsame waived his rights and continued to talk.

In that instant, the Obama administration may have preserved its ability to use the federal courts to prosecute high-value terrorists captured overseas.

Warsame was detained in April 2011, the same month that Attorney General Eric Holder abandoned a criminal civilian trial in New York for Khalid Sheik Mohammed, the self-proclaimed mastermind of the Sept. 11, 2001, attacks. Holder sent the case back to a military commission at Guantanamo Bay. On Capitol Hill, Republicans and Democrats were insisting that all terrorists captured overseas be sent to the military detention center in Cuba.

But inside the administration, senior lawyers calculated that Warsame could be interrogated for actionable intelligence while preparations were under way to bring him to federal court in New York for prosecution. For an administration that is determined not to add to the detainee population at Guantanamo, the handling of the Somali’s case has become something of a template for other terrorism suspects captured overseas.

Detainees are first held under the laws of war and questioned by an interagency team of interrogators, including military, intelligence and law enforcement personnel, without being advised of their rights. At some point, the interrogation is halted and — in the parlance of prosecutors — a “clean break” is established before a fresh team of only FBI agents informs the prisoner of his right to counsel. Shortly afterward, the suspect is put on a plane and flown to a federal district, most often New York, for trial.

According to the Justice Department, federal prosecutors since the Sept. 11 attacks have secured 67 convictions of terrorists captured overseas; a significant number have also been cooperative, providing information to authorities. In the same period, there have been only seven convictions in the military commissions at Guantanamo Bay. Two of those have been overturned on appeal.

Moreover, in military commissions, unlike federal courts, there is serious doubt about the viability of two of the charges most commonly used against terrorists — material support and conspiracy — as law-of-war charges in cases in which suspects cannot be tied to a specific act of violence.

Last month, federal prosecutors unsealed court documents that show that Warsame, who pleaded guilty to nine terrorism charges in December 2011, has continued to cooperate with authorities in the U.S., almost certainly with the expectation that his cooperation will lead the government to petition the judge to sentence him to less than life in prison. It could be a while before any sentencing takes place; prosecutors may use him as a witness in other prosecutions.

Priya Chaudhry, an attorney for Warsame, said she could not comment on his cooperation. She said she was “working very hard to keep his family safe,” adding that the U.S. government was helping.

In the wake of Warsame’s detention, other high-profile cases have followed, including that of Osama bin Laden’s son-in-law Sulaiman Abu Ghaith, who was arrested in Jordan in February and proceeded to speak at length with U.S. investigators. European allies have also extradited suspects to the U.S. on the express condition that they be tried in federal court. These include Abu Hamza al-Masri, the radical preacher, who was extradited from Britain in 2012, and al-Qaida veteran Ibrahim Suleiman Adnan Adam Harun, who has been held secretly in New York for months and has been cooperating with U.S. investigators since before he was extradited from Italy in October.

“Rather than make a big argument for it, the administration has just brought these cases into the (civilian legal) system,” said Karen Greenberg, director of the Center on National Security at Fordham Law School. “And they have done them with an emphasis on getting information and getting it by legal means.”

Republicans on Capitol Hill continue to object to such criminal prosecutions. The administration “risks missing important opportunities to gather intelligence to prevent future attacks and save lives,” Republican Sens. John McCain, Lindsey Graham and Kelly Ayotte said in a joint statement after Ghaith’s court appearance. “A foreign member of al-Qaida should never be treated like a common criminal and should never hear the words ‘you have a right to remain silent.’ ”

Among some CIA officials, the emphasis on prosecutions has seemed to amount to an overcorrection at times. “There’s a concern that things are tilting the wrong way,” said a former senior U.S. intelligence official who would discuss intelligence issues only on the condition of anonymity. “Instead of questioning people and trying to get data from them, there is a push to put them in the legal process.”

Current and former administration officials say criminal prosecution does not preclude intelligence gathering. David Kris, the former head of the Justice Department’s national security division, said suspects talk for all kinds of reasons, but “one of the things the government can do in the criminal justice system, by offering somewhat shorter sentences in exchange for valuable cooperation, is to balance and re-balance over time the sometimes competing national security values of disrupting and incapacitating a particular target and gathering intelligence from that target that may help disrupt and incapacitate others.”

Warsame, who is now 26, had been a high-priority target for capture in the months before April 19, 2011, when the U.S. military picked him and another man up in the Gulf of Aden from a fishing skiff leaving Yemen. The intelligence community identified Warsame as a key liaison between al-Shabab, the al-Qaida affiliate in Somalia, and AQAP.

Officials in Washington first debated whether Warsame should be moved to Somalia for interrogation, but that was deemed too dangerous. They also discussed whether keeping him on a ship at sea would violate the Geneva Conventions. “The decision was to hold him on a ship but inform the Red Cross because if there was a Geneva Convention concern they would express it,” said the former administration official. Warsame was transported to the USS Boxer, an amphibious assault ship with a brig that was in the region.

The International Committee of the Red Cross visited the ship shortly after the capture, and the man who was detained with Warsame was let go. “He was a very small fry,” the former administration official said. “Everyone was comfortable with that.”

Justice Department officials decided to withhold from the interagency team the evidence they had previously assembled against him. Even if a judge threw out evidence secured by the interrogators aboard the vessel, the pre-existing evidence could still be used.

When Warsame was captured, he had a laptop and other electronic media that included letters between the leadership of al-Shabab and AQAP; dozens of pages of handwritten notes on how to build bombs; and correspondence that detailed why he was sent to Yemen, according to court documents.

Warsame began to talk almost immediately. Officials said the Somali, who attended college in Britain, was a sophisticated operator who was fluent in English. He understood how the U.S. legal system worked and “realized that his best chance at a reasonable outcome for himself was to cooperate,” said the former administration official.

After some initial skepticism about the intelligence Warsame was providing, counterterrorism agents grew increasingly confident about its accuracy and its potential use in planning future U.S. operations. According to court documents, investigators corroborated his information with four people who “interacted extensively with Warsame in East Africa.”

Three of those four witnesses are cooperating defendants in Minnesota who had been members of al-Shabab, and the fourth is in custody overseas and charged with capital crimes. They confirmed Warsame’s seniority and the fact that he once “commanded hundreds of al-Shabab fighters,” according to court documents.

He also provided information about al-Awlaki, who had become a major target for a capture or kill operation after he was tied to an attempt to bring down a commercial aircraft over Detroit. “He was a guy who was in fairly regular contact with (al-)Awlaki and talked about his contacts with (al-)Awlaki and (al-)Awlaki’s patterns of life,” said the former administration official.

In Washington, there “were numerous interagency meetings to receive updates on the status of the intelligence collection from the interrogations and to discuss his detention status and his ultimate disposition,” according to a background briefing by a senior administration official in July 2011.

“The big question was when to Mirandize him,” said the former administration official.

To establish a “clean break,” the administration decided in late June 2011 to give Warsame a four-day rest from questioning and invite the Red Cross back to see him. The former administration official said it was important he understand that he “has entered a different phase and that he has a new set of choices to make.”

Warsame, when confronted with a new team of FBI interrogators, chose to continue cooperating. After seven more days of questioning at sea, he was taken ashore at an undisclosed location and put on a plane to New York.

Several weeks later, on Sept. 30, 2011, al-Awlaki was killed in Yemen in a U.S. drone strike.