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But thanks chiefly to the efforts of the Levinson family and of former Senator Bill Nelson of Florida, where Mr. Levinson and his wife lived, the truth about his relationship with the C.I.A. slowly emerged. Over time, Mr. Levinsons family made repeated efforts either directly or through intermediaries to learn about his fate. His wife, Christine, and son Dan traveled to Tehran and to Kish Island.

After an internal investigation, the C.I.A. disciplined 10 employees, including the three veteran analysts who were forced to leave the agency. The C.I.A. eventually paid Mr. Levinsons family a $2.5 million annuity and an additional $120,000, the cost of renewing Mr. Levinsons contract. Both sides wanted to avoid a lawsuit that would publicly reveal details of the arrangement.

Mr. Levinson was last seen alive in a 2010 hostage video pleading for help and in photographs wearing a Guantnamo-style orange jumpsuit. Neither the video nor the images disclosed the identities of his captors. The video had a Pashtun wedding song popular in Afghanistan playing in the background, but F.B.I. investigators concluded that it was so artfully staged that it was probably made by a state-sponsored intelligence group.

At one point during the Obama administration, Iranian officials secretly informed American officials that they had received intelligence that the remains of an American had been buried in Balochistan, a rugged, lawless region in western Pakistan that borders Afghanistan and Iran. Americans officials assumed that the remains were Mr. Levinsons.

But the Pakistani authorities found no remains at the site, and American officials concluded that the report, rather than a gesture of good will, was a gambit by Iran to further cloud its role in Mr. Levinsons fate.

During the Obama administration, officials overseeing efforts to find him had no clear evidence that Mr. Levinson was either alive or dead.

Last year, Iran acknowledged for the first time that it had an open court case involving Mr. Levinson. In a filing to the United Nations, Iran said the case was ongoing before its Revolutionary Court, without elaborating.

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Ex-F.B.I. Agent Who Vanished on C.I.A. Mission to Iran Is Most Likely Dead, U.S. Concludes - The New York Times