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The looting in South Sudan will severely hinder efforts to help the 863,000 people who have fled their homes and the 3.7 million vulnerable people who are in desperate need of food.Geoffrey York/The Globe and Mail

The remains of a vast aid operation are scattered across the barren ground. Hundreds of empty cans and boxes are strewn in front of looted warehouses, where even the canvas walls have been chopped away and stolen.

The looting was organized and systematic, and it went on for days. Thousands of people – from soldiers and rebels to ordinary civilians – piled their booty into donkey carts and trucks, witnesses say. They stole 1,700 tonnes of food, intended for 100,000 of the poorest people in the country.

There were gasps of shock from officials of the United Nations World Food Program (WFP) on Friday when they visited the looted warehouses in Malakal, one of the hardest-hit towns in the fighting that has devastated South Sudan since mid-December.

Some said it was the worst looting they had ever seen. Others said it had become "a wasteland." The warehouses were financed by countries such as Canada, which donated $31-million to the WFP for South Sudan aid programs last year.

Since the crisis began, the WFP has lost 4,400 tonnes of food in a dozen looting attacks – some of which continued this week despite a ceasefire. The looting will hinder the world's efforts to help the 863,000 South Sudanese who have fled their homes and the 3.7 million vulnerable people who desperately need food aid. The WFP now considers that South Sudan is a "level three" emergency – the highest level, and one of only three such emergencies in the world today, along with Syria and the Central African Republic.

But the looting is just one of the signs of devastation in the eerily empty streets of Malakal, capital of Upper Nile state, which has repeatedly changed hands as rebels and soldiers fought for control of the town in January.

Entire markets in the town have been destroyed and abandoned. Normally bustling commercial streets are lifeless. Hundreds of ordinary homes, made of mud and thatched roofs, have been burned to the ground. Shops that escaped the looting are shuttered and deserted. Aside from soldiers, most residents have fled and there are no vehicles except military trucks and tanks. It has the feel of a war-ravaged ghost town.

New satellite images by a U.S.-based monitoring group, the Satellite Sentinel Project, suggest that at least 210 thatched huts were burned to the ground in one quarter of Malakal alone. "Almost every dwelling within the quarter was burned, leaving behind just charred earth," said a report by the satellite project, which was co-founded by Hollywood actor George Clooney. It suggested that the massive destruction could be evidence of war crimes.

Survivors confirm the horrors of the attacks. "There was destruction, killings and looting, and 13-year-old girls were raped and then killed," said Vito Mario, a 35-year-old South Sudanese oil technician who took refuge at a UN military base on the outskirts of the town.

"All of our property was taken. I've lost everything – my home and everything – and I have to begin again. I saw the dead bodies of my neighbour and his wife and two children. It was terrible, it's something you cannot believe."

In total, nearly 28,000 people are sheltering at the UN military base on the edge of the city. Thousands more are sleeping in the compound of the town's main hospital, and many tens of thousands have fled across the White Nile River in small boats and canoes, swelling the population of isolated villages on the far bank.

One such village is Wawshuluk, a sprawling collection of thatched huts across the river from Malakal but often inaccessible because there is no bridge. The killing and looting in Malakal has forced so many people to seek protection in this remote village that nobody has a clue of its current population. Estimates range from 40,000 to 75,000 but everyone admits they are guessing. After the fighting began, the village did not receive any food aid until a WFP helicopter finally landed on Friday, bringing emergency rations of energy biscuits for the first time.

James Othow Aba said he escaped Malakal's fighting by squeezing into a small boat with nine family members and crossing the White Nile to reach the village. "The current was very fast and some boats sank," he said. In one notorious case in mid-January, about 200 people drowned on an overloaded ferry that sank as it left Malakal during the military clashes.

The desperation of most people in Malakal has reached such proportions that many are sympathetic with those who looted the UN warehouses. "They were hungry," shrugged Mr. Mario.

Valerie Guarnieri, regional director for the WFP in Eastern and Central Africa, said the looting of the warehouses will "really slow us down" in the first part of this year. In future, she said, the WFP will reduce the number of its warehouses, putting food in only 30 to 40 main hubs – instead of 97 sites as it did last year – to reduce the risk of looting in conflict zones.

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