In the crate there were chunks of bone that appeared to have been blown to bits, scorched scraps of flesh, a jawbone with 11 teeth and, most important, pieces of clothing, including part of a shirt with elaborate embroidery. The wear on the teeth indicated a man age 30 or younger, which Mr. Nawab was. But if family members were going to be able to get and bury the remains of Mr. Nawab, a driver from Ibrahim Kheil village, they would have to describe the embroidery and the type of fabric.

It came down to the victim’s mother, who remembered the embroidery because she had done it herself, allowing the family to describe a perfect match with the clothing scraps. Dr. Najibullah said he was satisfied, made the identification and returned Mr. Nawab’s remains to his family. (Like many Afghans, Mr. Nawab used and Dr. Najibullah uses only one name.)

The Nerkh disappearances led to a severe strain in relations between the Afghan government and the United States military, with President Hamid Karzai at one point ordering all Special Operations forces out of Wardak Province.

Afghan investigators have accused a man named Zakaria Kandahari, whom they identify as an Afghan-American man working with the American commando team, of detaining, torturing and murdering many of the missing men. They also accuse the American team of at the very least being aware of his actions, if not complicit in them.

The American military said it had repeatedly investigated the disappearances in Nerkh and had found no wrongdoing by any American military personnel. It also insists that Mr. Kandahari is not an American citizen, and that even though he had been employed by the military as an interpreter, he was no longer working for Americans at the time a videotape showed him engaging in at least one case of torture.