This secretiveness has prompted some lawmakers to call for greater scrutiny of the military’s clandestine units. “There is not enough oversight, certainly from Congress,” said Representative Seth Moulton, Democrat of Massachusetts and a member of the House Armed Services Committee, who is a former Marine officer and served four tours in Iraq.
It is not uncommon for the Pentagon or American spy agencies to rely on Americans such as Mr. Darden, 47, a Florida-born Muslim convert who speaks fluent Arabic, to ferry supplies and money around the world. As the head of Transoceanic’s operations in Yemen, Mr. Darden oversaw several dozen employees and offices in Sana, the capital, as well as in Aden and Hodeidah, two of the country’s most important ports.
But why Mr. Darden, a bespectacled, heavyset man before he was detained, risked venturing into to the maelstrom in Yemen was unclear.
By late 2014, chaos gripped the country. Houthi rebels allied with army units loyal to a former president, Ali Abdullah Saleh, had seized the capital and sent the government into exile. The Houthis have been fighting for control of the country against groups at least nominally loyal to the current president, Abdu Rabbu Mansour Hadi, who is backed by Saudi Arabia and its Persian Gulf allies.
As Yemen hurtled toward civil war, the United States shut down its embassy in February 2015 and evacuated its personnel in Sana because of safety concerns, hampering the American government’s efforts to conduct intelligence and counterterrorism operations in the country.
As Yemen became increasingly dangerous for foreigners, Mr. Darden, who split time between Yemen and Dubai, where his wife and young son lived, arranged the next month to fly to Sana. He had begun working for Transoceanic in November 2014, just a few months earlier.
Special Operations officials warned Mr. Darden not to go to Yemen, as did Sam Farran, a security expert working for Transoceanic and a former Marine who had worked at the United States Embassy in Yemen. His wife, Diana Loesch, said she did not understand why her husband had to rush back; Mr. Darden said his company needed him there.
But days after arriving, a panicked Mr. Darden called Mr. Farran, who had him taken to a safe house tucked away in one of the city’s warrens.
“He was scared,” Mr. Farran recalled in an interview. Unlike many in his field, Mr. Darden had no previous military or law enforcement experience.
Hours later, on March 27, Houthi fighters raided the villa and detained Mr. Darden and Mr. Farran on suspicion of being spies. They were among a handful of Americans swept up by the rebels as Yemen unraveled in 2015. One, John Hamen, an Army veteran from Virginia, was tortured and killed.
For months, Mr. Darden endured beatings and interrogations.
After word leaked on Facebook in September 2015 that Mr. Darden was being held captive in Yemen, a spokesman for Transoceanic issued a statement saying Mr. Darden “was in Yemen coordinating the warehousing and delivery of humanitarian aid as part of his job in international logistics.” No mention was made of his secret work with the military.
Later that month, after the men had been in captivity almost six months, prison guards knocked on Mr. Farran’s cell, asking for his shirt and shoe sizes. The brought him out of his cell and forced him to sit in a hallway, he said, where Mr. Darden joined him. They had been separated and saw each other only once during their imprisonment, Mr. Farran said.
“He looked pretty shabby,” Mr. Farran recalled. The men hugged and started crying.
The guards shaved the beards of the two men and brought them clothes. Mr. Farran recalled that guards started videotaping Mr. Darden, but he does not know what Mr. Darden said.
They left the prison and headed to the airport in Sana, where they boarded a Boeing 737 sent by the sultan of Oman, who served as a go-between to gain the Americans’ release. On the flight to Oman, Mr. Darden confided to his friend that he regretted what he had told the Houthis. Mr. Farran tried to comfort him by reminding Mr. Darden that he had been coerced. But, Mr. Farran said, Mr. Darden never told him about a relationship with the American military or why he had rushed back to Yemen.
Yemen has been one of the most active conflict zones for Special Operations forces in the post-Sept. 11 era. It is where the United States is battling hardened Qaeda fighters and where a member of the Navy’s SEAL Team Six died in January in the first commando raid approved by President Trump.
At the time Mr. Darden was captured, about 125 Special Operations advisers had been working closely with Yemeni military and counterterrorism forces. Those advisers and other clandestine operators relied on companies like Transoceanic for much of their logistical support.
The company says it delivers “vital cargo worldwide on time and intact for humanitarian relief, defense and peacekeeping missions, and reconstruction projects.” According to Transoceanic, the “world’s leading N.G.O.s, relief organizations, and governments rely on it.”
Mr. Darden also handled contracts with Unicef and the International Committee of the Red Cross, according to his LinkedIn profile and people familiar with his work in Yemen.
Anna K. Nelson, a spokeswoman for the I.C.R.C., said it was unaware of Mr. Darden’s relationship with the American military. Transoceanic had a six-month contract with the Red Cross that began in June 2014, according to Ms. Nelson.
“Transoceanic’s role was strictly related to the processing of standard paperwork,” she said. Transoceanic helped the Red Cross clear customs, serving as a middleman between the relief organization and Yemeni government ministries.
Najwa Mekki, a spokeswoman for Unicef, said the organization had contracted with Transoceanic through September 2016 “to provide warehousing services in Yemen,” but was not aware that the company was also helping supply the military.
“We would not enter into contracts that would create risks for Unicef operations or our personnel,” Ms. Mekki said in a statement.
Using the cover of humanitarian aid is fraught with serious risks, and the consequences can be deadly. In 2011, the news media revealed that the Central Intelligence Agency had hired a Pakistani doctor to run a vaccination campaign to obtain the DNA of Osama bin Laden. Afterward, health workers in Pakistan were attacked, and the C.I.A. said it would no longer use vaccine programs as cover.
Mr. Darden was born in Miami and grew up in Atlanta, later attending Georgia State University. Raised Catholic, Mr. Darden studied Arabic in Saudi Arabia in the late 1980s and early 1990s and eventually converted to Islam, his wife said.
He briefly worked at an Apple store in Charlotte, N.C., a decade ago, but starting with a job at Maersk, a transport and logistics company, in Kuwait, he developed deep ties to the world of military logistics and has traveled widely, including to Iraq and Afghanistan, Ms. Loesch said.
According to his LinkedIn profile, Mr. Darden worked for Wilhelmsen Ships Service from 2010 to 2012, when he oversaw the return of more than 40,000 American troops leaving Iraq through the ports of Aqaba, Jordan, and Umm Qasr, Iraq.
Mr. Darden had a quiet homecoming — no public welcome, no interviews. After reuniting with his wife and son in Oman, where the F.B.I. interviewed him — agents familiar with the case will not say what he told the agency — Mr. Darden spent time in Atlanta with his mother.
Ms. Loesch said her husband has talked little about what happened inside the Houthi prison. He never told her about his relationship with the military, she said, and withdrew after his abduction. “He was not really present,” she said a recent interview.
In April, after 15 years of marriage, Ms. Loesch said, she and her husband separated. He lives in Dubai with their son, now 11, works for a company called PAE as a logistics manager and travels extensively, she said.
“Scott is a man of many secrets,” she said.