According to the State Department, Mr. Kotey “likely engaged in the group’s executions and exceptionally cruel torture methods, including electronic shock and waterboarding. Kotey has also acted as an ISIL recruiter and is responsible for recruiting several U.K. nationals to join the terrorist organization.” ISIL is another name for the Islamic State.
Mr. Elsheikh traveled to Syria in 2012 and joined Al Qaeda in Syria before aligning himself with the Islamic State. “Elsheikh was said to have earned a reputation for waterboarding, mock executions and crucifixions while serving as an ISIS jailer,” the State Department said.
Mr. Kotey, 34, and Mr. Elsheikh, 29, were detained by the American-backed Syrian Democratic Forces, a Kurdish-led militia, which is fighting the last pockets of Islamic State insurgents in Syrian towns and villages along the Euphrates River south to the border with Iraq. American officials were informed in mid-January that the militia might have captured the men.
The S.D.F. suspected that the two men were foreign fighters and gave them access to American Special Operations forces, United States officials said. The Americans confirmed their identities using fingerprints and other biometric measurements.
Their capture and detention were described to The New York Times by several United States officials who spoke on the condition of anonymity because details of the case remain secret. Cmdr. Sarah Higgins of the Navy, a Pentagon spokeswoman for detention policy issues, declined to comment.
The series of gruesome beheadings that started with Mr. Foley in 2014 rocked the Obama administration, which had been accused by the victims’ families of failing to do enough to save their loved ones. The American military did raid the prison in Raqqa in July 2014, but the Islamic State had already moved its hostages.
Because of the families’ complaints, the Obama administration made major changes to the way the government handles the abduction of United States citizens. It created a Hostage Recovery Fusion Cell, which is led currently by the F.B.I., and a special presidential envoy for hostage affairs. The Trump administration has yet to fill the envoy role.
The families have long hoped to recover the bodies of their loved ones, but the Islamic State’s control of chunks of Syria rendered the task nearly impossible.
It was not clear whether the Justice Department would prosecute the two men or when the United States military would take custody of them. For the F.B.I. agents and other officials who have long worked on the case, bringing back the men to face federal prosecution would be a major victory.
But Attorney General Jeff Sessions has been an outspoken supporter of continuing to use the wartime prison at Guantánamo Bay, Cuba, and the military commissions held there. Thomas P. Bossert, the president’s chief counterterrorism adviser, has also pushed for the suspects to be sent to the military prison.
Britain, a close ally of the United States, could object to sending the men to the wartime prison, which has a toxic image abroad. It negotiated the repatriation of all nine of its citizens whom the Bush administration had brought there by 2005; the last resident of Britain held at the prison, Shaker Aamer, a Saudi citizen who lived for years in Britain with his family, was sent back there in 2015.
But the British government has stripped Mr. Kotey and Mr. Elsheikh of their citizenship, according to a United States official. Last year, The Times of London reported that the government had rescinded the British citizenship of about 150 dual citizens who were suspected of having joined the Islamic State, in order to keep them from re-entering the country.
In addition, because the men are suspected of being members of the Islamic State, not Al Qaeda, taking them to Guantánamo — where detainees have a right to bring habeas corpus challenges to their detention — would create a legal headache that national security officials want to avoid. It would give a judge an opportunity to rule on the dispute over whether the congressional authorization for use of military force against the perpetrators of the attacks of Sept. 11, 2001, legitimately covers the Islamic State.
Moreover, if the United States fails to prosecute the men in federal court, it could anger the victims’ families, causing yet another disappointment. The Guantánamo military commissions system has struggled to get contested cases to trial, even as prosecutors in civilian court have won numerous convictions in terrorism cases.
The United States government has in the past avoided taking on the difficulties of handling the long-term detention or prosecution of Islamic State detainees caught in the war zone.
In 2016, an Iraqi woman, known by the nom de guerre Umm Sayyaf, was captured in a raid on an Islamic State compound in eastern Syria. She was implicated in the imprisonment of an aid worker, Kayla Mueller, 26, of Prescott, Ariz., who was killed in 2015. (The circumstances surrounding Ms. Mueller’s death remain a mystery. The Islamic State said she was killed in a bombing raid.)
Some American law enforcement officials wanted to prosecute Ms. Sayyaf in Virginia, and federal prosecutors filed charges against her, but after a lengthy interrogation, she was turned over to Iraqi government custody instead.
Ms. Mueller had been originally imprisoned by the British militants, but was moved to another location, where she is believed to have been badly abused by the leader of the Islamic State before her death.
A senior United States official said Mr. Kotey and Mr. Elsheikh had provided valuable information to military interrogators about the remaining Islamic State leadership and support structure, which are under tremendous pressure from air and ground attacks.
There were some indications that the two men initially sought to hide their identities, but the Special Operations forces routinely run fingerprint checks and other biometric measurements to identify known terrorist leaders and catalog rank-and-file militants.
Other information has been collected from cellphones and other electronic equipment they were carrying, the United States official said. The men could also have information about other hostages, including the British journalist John Cantlie, who was abducted with Mr. Foley in 2012. Since he was taken hostage, Mr. Cantlie has appeared in several Islamic State propaganda videos.
American officials had sought to keep the capture of the two British suspects under wraps to allow analysts more time to pursue the intelligence leads developed from their detention and prepare raids against unsuspecting Islamic State targets.
American warplanes and Kurdish-led ground forces are hunting for the several hundred remaining Islamic State fighters hiding along the Euphrates River Valley near the border between Syria and Iraq.
The American-led military command in Baghdad said in a statement last week that four senior Islamic State commanders and officials, including two operatives dealing with logistics and immigration, were killed in the region in the past month.
The most prized Islamic State target, however, has proved the most elusive: Abu Bakr al-Baghdadi, the group’s leader. While rumors have surfaced repeatedly over the past three years of Mr. Baghdadi’s death or wounding in airstrikes, American counterterrorism officials believe he is alive and most likely hiding in the Sunni border areas straddling Iraq and Syria.
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