In his heart, Simon Yakida knew he was digging his own grave.

A few days earlier, clashes between government troops and rebel forces near Bamurye, Yakida’s village in South Sudan, had left three soldiers dead. Now the local military commander stood before him, gesturing at one of the bodies. He told Yakida, “Killing you is payback for this soldier.”

Bamurye, a farming community whose residents live in mud-and-thatch huts called tukuls, lies in the southern part of the country. To feed his two wives and nine children, Yakida, a thirty-two-year-old with close-cropped hair and a wiry frame, grew cassava,…