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, maize, and sorghum. The work had always been hard, but his life was peaceful. In recent months, however, the soldiers in the local barracks had grown increasingly abusive—­detaining and mistreating ­civilians and accusing them of supporting the antigovernment rebels. In February, the killings began: Three young men were murdered by soldiers in retaliation for recent battlefield losses. Most in the village, including Yakida’s family, had already fled to Uganda; Yakida was on his way when the troops arrested him.

The soldiers watched as Yakida carved out a knee-deep hole. The commander ordered him to roll the corpse into the pit and cover it with soil. Famished, thirsty, and exhausted, Yakida complied. Once the work was done, the soldiers tied him to a wooden pole, the remnants of a rudimentary hut.

“Where is the headman of the village?” the commander barked. “Where is Abu Sala?”

Abu Sala is what people in Bamurye called Alex Kajoba, a night watchman at the local medical dispensary who was known for advocating on behalf of villagers who had been detained at the barracks. It wasn’t a question but a threat; both men knew exactly where Abu Sala was and why he wouldn’t be coming to Yakida’s aid.

Eventually, the soldiers—members of the Sudan People’s Liberation Army (S.P.L.A.)—untied Yakida and ordered him to sit on top of the fresh grave. They bound his hands and ankles. One of the soldiers offered a salute, then cocked his weapon. The commander ordered him to fire, and he pulled the trigger.

Yet two days later, Yakida stood before me, wearing a gray polo shirt with marks & spencer emblazoned on it and ill-fitting jeans that read bing boss. We were in Laufori, a Ugandan border town with dusty dirt roads and wooden stalls where you could buy cheap flip-flops and warm Cokes. Yakida was living beneath an immense mango tree, still separated from his family. His lean arms bore the marks from where the rope had dug into them.

Tears spilled down his drawn cheeks as he told me about his failed execution. A bullet passed through his oversize shirt, just beneath his left armpit. On the second and third attempts, the rifle jammed. After an argument among the troops, a soldier allowed him to leave, and Yakida joined the tide of refugees pouring out of Bamurye and dozens of other South Sudanese villages. He seemed broken by the ordeal.

After Yakida told me his story, I asked if he had any questions for me. “These are government soldiers. They’re supposed to be protecting civilians, but they’re the ones who are killing us,” he replied. “Why are they killing the people they’re supposed to be protecting?”

One afternoon this February, I stood on the side of a dirt track that led from South Sudan to Uganda. It was the worst time to travel, with the midday sun baking the road, but at least one refugee crossed the border every minute, coated in a mix of sweat and dust from the rust-colored earth. For a week, I staked out trails like this, in an attempt to understand what has become the fastest-growing refugee crisis on the planet: a wave of ethnic cleansing that experts warn may tip into genocide.

There were three other roads nearby with refugees making the same trek. Many had run with only the clothes they were wearing—threadbare dresses and long colorful skirts, blouses held together by safety pins, a soiled ted nugent: body count T-shirt, a pair of dress pants several sizes too big belted around a diminishing waist with twine, an aqua-blue sandal on one foot and a battered brown loafer on the other.

The current conflict has deep roots. From 1983 to 2005, southern Sudanese fought a civil war against Sudan’s government. In 2011, the South gained its independence, becoming the world’s newest nation. Salva Kiir, a member of the largest of the country’s sixty-four ethnic groups, the Dinka, became the first president of the Texas-size nation of 12 million...................

 

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Berhane