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It was a blazing Saturday in October, and the crowd had been waiting for hours. Cousins, brothers, wives and daughters stood sweating under a few big mango trees on the banks of the Nile in Juba, South Sudan's new capital. Kids coaxed the unripe fruit out of the branches with sticks, getting the green orbs to the dirt with a plunk. The hot smell of charcoal wafted out from a makeshift tea stand, where a woman heaped spoons of sugar into small glass cups. At last, the barge appeared, first a dark smudge on the wide, brown river, and soon enough, a teeming, cheering vessel carrying hundreds of South Sudanese on the last leg of their very long journey home.

"Juba!" a man onboard called out from a megaphone. "Juba! We bring you good news!" As the boat pulled into port, passengers stood on the roof and hung over its railings, spotting their relatives onshore and waving wildly across the narrowing gap of water. On land, men yelped and women let out long, high-pitched trills. Somebody unfurled a government banner bearing the portrait President Salva Kiir in his signature black cowboy hat bearing the slogan "Return in safety and dignity."

It's a stirring scene that has been playing out for months now in the world's newest nation, as South Sudanese who left the country during the long years of war are going home. The government estimates 4 million southerners were displaced both internally and externally during the decades-long civil war. As a result of a 2005 peace deal that ended the north-south fighting and paved the way for the south's secession, the fledgling government promised a home to southerners who wanted to repatriate, an offer that has become particularly appealing to the hundreds of thousands who have been living in the increasingly inhospitable environs of Khartoum. Since October 2010, three months before the south voted to become independent, more than 360,000 southerners have returned from the north by train, bus and barge, most of them taking everything they owned with them — and great expectations of a fresh start in the country they had left decades before.

That's a lot of baggage for any government to handle, let alone a months-old administration grappling with building a war-traumatized country nearly from scratch. Getting people back home, a process that has been largely paid for by the International Organization for Migration, has been complicated, to say the least. Because the government promised that the move would be paid for in full, many returnees, as they're called there, left little but memories behind, arriving with beds, pots, clothes, trunks, armoires, scooters and stacks of plastic chairs in tow. For every barge of returnees that has creaked into Juba, at least one more barge of their belongings has gone with it. "I dream at night of luggage falling on my head," laments William Chan Achuil, the chairperson of the South Sudan Relief and Rehabilitation Commission (SSRRC), the government body charged with overseeing the returns. "It has not gone well."

Flaring tensions between the north and south have not helped. This summer, after fighting broke out along the border between Sudanese forces and rebels aligned with the south during the civil war, the movement of people and goods from north to south ground to a near halt. What overland routes were still available passed through the conflict zones and were deemed too dangerous to use. As a result, tens of thousands of returnees — and their luggage — have been stuck for months in swelling camps on both sides of the border, waiting to make the two-week trip down the Nile on the crowded barges. In Renk, a remote town in South Sudan where thousands of returnees are waiting for passage, food is scarce and sanitary conditions are poor, with only a few international aid agencies scrambling to try to provide some services to an increasingly frustrated crowd. "The national government has made a political decision to evacuate people from Sudan and bring them south as quickly as possible without guaranteeing the practical consequences of that decision," says Peter Orr, a senior advocate for Refugees International. "Now they're turning to the humanitarian community and saying, You have to help these people."

Once they do get home, the afterglow can fade fast. Getting off the barge in Juba, passengers are emotional and enthusiastic, relieved that their months-long wait has ended. But a few paces away from where families reunite with hugs and handshakes, a settlement has sprung up amid the pools of stagnant rainwater, plastic water bottles, feces and garbage. Land is scarce in Juba, and, as in several state capitals, authorities have not been able to secure space for returnees who want to settle near a city rather than go back to the countryside they left decades ago. Instead, returnees to the capital have been instructed to find a place with friends and relatives, but for people like John Soroba, who left for Khartoum 35 years ago, those connections no longer exist. In October, his family and dozens of others had camped out around the port for weeks, waiting for somebody to tell them where to go. "No transport, no money, no food," Soroba says, brushing his hands together to indicate everything is gone. "Why am I even here?"

Indeed, finding a place for returnees to call home has become a problem throughout the nation. In Renk, in addition to the thousands who are waiting to get on a barge, another 12,000 to 13,000 southerners have camped out in the city for months with no intention of leaving, putting pressure on the local government to find a solution to a problem the national government has created. "For the people who didn't leave, you can understand why there is some reluctance to give away land to people coming from the north," says Orr. "It's a very tricky situation." And it's likely to get worse before it gets better. After the south declared independence on July 9, the legal status of southerners living in the north was revoked, and Khartoum gave southerners nine months to either go home or wait and see if their legal status would be renewed at the end of the year. "Between now and December, a lot of returnees will come," says Achuil, the SSRRC chairperson in Juba. "If they find that services are not available, there will be conflict — over land, over food, over water."

Still, for some, the sheer relief of being home outweighs the problems they face once they get there. At an abandoned aid compound in Bentiu, the capital of Unity state, a group of 470 people had been sharing three small, stuffy huts for over a month in mid-October, waiting to get to their homes nearby. The long, heavy rainy season rendered the dirt roads home impassable, and several deadly land-mine explosions in the region in the past few months slowed things down even more. "We have some rations, but we don't have enough," says Cirillo Mayik, one of the elders of the group who moved to Khartoum during the war in 1974. "There's no oil, no lentils, nothing." Still, Mayik says, after years of feeling like an outsider in Khartoum, he's happy to back — come what may. He grabs the branch of a tree he's standing next to and gives it a shake. "Even if I'm not given a home, I'll be given a tree, and I can sit underneath that."

Produced in association with the International Reporting Project.

• Krista Mahr / Juba
• As soon as it was clear that Juba would be independent of Khartoum, the exiles began to return. But is there room for them as the country figures out its future?