Essam Elya almost doesn't agree to meet. He calls in the evening, waffling, scared. Then he makes a spontaneous decision – we can meet later, at 10 p.m., at a local church. That is the only place he feels safe.

We sit in a small, dim room off the main hall. Mr. Elya's hands are trembling. As he tells his story, he stares at a spot on the wall, speaking haltingly, as if long sentences are too much effort. Elya is a young pediatrician in Naga Hammadi, a community of farmers and aluminum-plant workers in southern Egypt along the Nile River. As he drove home from his clinic one night in April, masked men stopped his car, grabbed him at gunpoint, and beat him unconscious.

They threw him in the middle of a sugar cane field, where he was hidden from the outside world by the head-high stalks and sharp-edged leaves. For five days, he says, his captors left him bound and blindfolded in the field, without food. The men – he never saw their faces – called his father to deliver the ransom demand. They beat Elya during the call, to encourage his father to act quickly.

"They threatened me with many things," says Elya. "A lot of difficult things, difficult for you to imagine."

At first, the kidnappers demanded £1.6 million (Egyptian, US$228,000). But they had miscalculated – Elya's family wasn't rich. His father scrambled to buy Elya's freedom. He sold his apartment and Elya's. He pulled his other children out of private universities. He borrowed money from friends.

When it was all over, Elya's father had paid £150,000 to the kidnappers – and another £250,000 to people who either claimed to be the abductors or promised help. Neither the local police nor federal authorities aided the family at all.

"The government didn't do anything for me," he says. "It didn't help me. But this is what happens – this is Egypt."

Elya's story takes place in a small town deep in the vast expanse of the Egypt that is usually forgotten. This is Upper Egypt, so named because it is upriver from Cairo and the delta. By the time the river that is Egypt's lifeblood reaches the capital and then the Mediterranean Sea, it has coursed north from the border with Sudan, past the cities and towns where people toil far from the political tumult of Tahrir Square, their struggles virtually invisible there.

As Egypt confronts another hinge moment in its millenniums-old history, a journey down the Nile reveals some of the reasons why political unrest once again engulfs the streets of this country and what challenges any government that ultimately emerges – however democratic – will have to face. Decades of government neglect and more recent failings since the 2011 uprising have left the economy and some of the stanchions of Egyptian society in disrepair: Schools are struggling, railways are crumbling, and social strife is rising as discrimination and sectarian violence grow.

The problems are exacerbated by a surge in kidnappings, once a rare phenomenon in Egypt, the looting of the country's historical sites, and a thriving trade in illegal weapons – signs of either a fear of personal safety or a desperation to make money in a society whose economy has atrophied. Even the country's farmers, who have been tilling the lush fields along the Nile since the birth of human civilization, are struggling to survive and produce enough food for a rapidly growing population.

When millions of Egyptians filled city squares across the country on June 30 to voice their rejection of now-deposed President Mohamed Morsi, Upper Egypt protested, too. Though the region does not usually see many protests, the sight of downtowns here brimming with demonstrators was a telling sign, particularly for the Muslim Brotherhood: Much of Upper Egypt, after all, voted for Mr. Morsi in the last elections.

In that sense, a journey down the Nile provides some insight into what the country's aspirations are as much as why it is so riven. With Morsi deposed, and the military-backed authorities suppressing the Brotherhood movement, debate swirls in Egypt about the future of political Islam and the Brotherhood's place in governance.

Yet more than anything, people along the world's longest river – one that the vast majority of Egyptians live within a few miles of – simply want a government that will invest in their lives, protect them from lawlessness, provide jobs, and allow them to live in dignity. They, like much of the rest of the world, want to know: Can Egypt find the stability and national cohesiveness to retake its historic place as one of the region's most dynamic and important powers?

* * *

Along with a Monitor photographer, I start my journey at the Aswan High Dam, the massive structure built in the 1960s under then-President Gamal Abdel Nasser. After overthrowing the Egyptian monarchy and breaking British influence over Egypt, the nationalist leader needed electricity to support industrialization and sufficient water for increased agriculture.

The river that had for thousands of years brought fertile silt to the Nile Valley with its seasonal floods was tamed, turned into a dependable producer of hydroelectric power and a safeguard against drought. Constructed in the face of great international attention and geopolitical tension, the project, while not the first dam at Aswan, represented the culmination of aspirations to harness the river dating back to the 11th century.

Behind the dam sprawls a massive reservoir, its deep blue fingers extending into the tawny hills and cliffs of desert. Named for Nasser, the artificial lake stretches all the way across the border into Sudan. While the project has ended up controlling the Nile's mercurial waters, and contributing to the country's modernization, it didn't fully usher in the New Egypt that many had hoped, or been promised, in the nationalistic fervor of the moment. Today, only about 10 percent of Egypt's electricity is generated by hydropower.

The pledges of state-led development have given way to decades of government indifference toward Upper Egypt on everything from sanitation to basic security. Hopes for change after the 2011 uprising were similarly dashed.

As the Nile churns out of the dam, it meanders around lush green islands, setting an idyllic scene that belies the reality. On the north side of Aswan, a small canal flows into the river. It comes from an area of squat brick apartment buildings separated only by small dirt alleys. The area has no sewage system, and the smell of raw effluent rises from the canal, whose banks are strewn with trash. The waterway's contents flow directly into the Nile, a line forming where the green-brown muck of the canal collides with the fresh blue water of the river.

As it flows north, the line eventually disappears, even if the symbolism of the scene doesn't: of an Egypt still in need of basic plumbing, in certain areas, and encumbered by the rising problem of pollution.

* * *

As night falls, a dozen men gather at a cafe on the banks of the river in Luxor, opposite the prominent hotels. The cafe is on a rooftop, but there is no breeze, and the oppressive heat weighs down in the dark. The power goes out, a common occurrence here, and the men playing backgammon shine a cellphone light on the board. The others drink tea and smoke water pipes. These days, they have plenty of time to kill.

"Before the revolution we were working five times a week," says El Tiab Ahmed, an English-language tour guide. "Now, if we're lucky, we work once every few months."

Nowhere in Upper Egypt – and much of the rest of the country – has the decline in tourism been more pronounced since the 2011 uprising and subsequent political chaos than in Luxor, often called the world's largest open air museum.

Even before you get here, on the stretch of river between Aswan and Luxor, the hundreds of cruise ships that used to carry tourists, stopping at ancient temples along the way, have dwindled to a few dozen. Once in the city, they are docked neatly in a row, empty and silent. Behind them, in the center of the city, stands the imposing Luxor Temple, built around 1400 BC. It is lit up at night. Flashing neon lights hang from the minaret of a mosque that was built long ago atop the ruins of the temple.

Luxor's monuments are proof that the now-marginalized Upper Egypt used to be the capital of an impressive kingdom for centuries, and the city's economy has long been built on welcoming foreign visitors to the stunning array of Pharaonic temples, tombs, and other sites. Yet the road along Luxor's riverfront is now lined with empty horse carriages, waiting to transport visitors, and restaurants and hotels bereft of patrons. Many of the visitors who do come to Egypt today head to the beaches instead of the country's cultural sites.

Tourism makes up more than 11 percent of Egypt's overall economy and is an important source of foreign currency. In 2010, the year before the uprising, it brought in more than $12 billion. The drop in foreign money is important because Egypt is the world's largest wheat importer, using the grain for subsidized bread, and also imports fuel for energy.

But the decline in outside visitors hits particularly hard here because tourism is one of the only major sources of employment in the area. Unlike the delta, Upper Egypt has few factories. For decades, young men have been leaving the region to search for work in Red Sea resorts, in Cairo, or the Gulf. The exodus may accelerate if job opportunities continue to decline here.

Amid the hardship, Mr. Ahmed and other tour guides say they help each other out and depend on their families or their farms to support them. But they describe the frustrations that abound with the lack of work, noting that crime, among other things, is getting worse as they say more people turn to nefarious activities to survive. Even divorce rates are rising.

"People working in tourism used to spend more money," says Yasser Amin, another tour guide. "It's not only us who are suffering, but so many people."

Majdi Riadh is one of those who is struggling. He lives with his wife, young son, and his parents in one apartment. They used to live in the village of Hijaza, outside Luxor, where Mr. Riadh worked in a shop that produced wooden figurines sold to tourists. But when the foreigners stopped coming after the uprising, his work evaporated.

He moved to Luxor to take a job at a cheese factory. He earns less, and they live in a much smaller apartment now. As his parents sit in the simple living room, scolding his toddler son, Riadh holds up an example of his previous work – a carved wooden elephant.

"My house in Hijaza was the one I set up for my wife and I after we were married. It was our home," he says. "This" – he gestures to the cramped apartment – "doesn't feel like home."

* * *

As the Nile arcs and ambles northward, it passes the town of Naga Hammadi, whose dun-colored streets and buildings are dirty and shabby, with a notable exception: the colorful juice bars. Naga Hammadi is known for its sugar cane, and the juice shops are marked by bright wood shavings on the ground, spread to absorb spilled drinks, and tepees of dried cane stalks out front.

In the heart of the town lies the Reform Center, so named because it is owned by the government authority set up under Nasser to redistribute Egypt's agricultural land as part of one of his socialist-nationalist reforms: taking plots from wealthy landowners and distributing them to peasants. Though that task was long ago completed, the authority still exists, and now oversees the garishly decorated collection of shops, restaurants, a wedding hall, and hotel. We watch families come to have tea or eat dinner in the open-air restaurant on the ground floor, sitting under blue and red neon lights while the music from the wedding hall thumps in the background.

Famous for its aluminum factory, Naga Hammadi is also now known among the Christian community in Upper Egypt for something more sinister: kidnappings. Activists estimate that about 30 Christians, including Elya, have been abducted for ransom since the 2011 uprising. There are even more cases of attempted kidnappings and extortion, with some people paying protection money to avoid being taken.

The activists say the kidnappers target Christians not because they are motivated by hate, but by opportunity – Christians are vulnerable, and a number of them in this community are wealthy. Many of the Muslim inhabitants of Naga Hammadi and the surrounding areas have large – and well-armed – families and tribes who retaliate if one of their members is harmed. "Copts are the weakest link in the chain," says Hana Haseeb, a local writer and activist. "We don't believe in vengeance, and we don't have weapons. So how can they make money? From the weakest class, the Christians, who are not protected by the state."

Mr. Haseeb and George Sobhi, a local lawyer who tallies the cases, say police rarely intervene, even when families file reports. And few victims do report their cases now, because of both inaction by authorities and a fear of retaliation by the kidnappers. Police say they can do nothing if the cases aren't reported. Kidnappings of Christians are also widespread in Minya, a city to the north, and spreading to places such as Sohag and Assiut.

As the abductions rise, families here and in surrounding areas are living in fear. Doctors and pharmacists, who are often targeted, speak of wondering "who's next?" They don't go out late at night anymore.

"I think if I can't protect myself, how can I protect my family?" says Hani Abdel Malak, one of the few who was kidnapped and later reported his case to police. (There have been no arrests.) "I lost confidence in the police, in the state, in everything around me. I feel at any second, anything could happen."

Many fathers shuttle their children to and from schools instead of sending them in buses or taxis. One pharmacist, whose 11-year-old son was abducted for two weeks last December, now refuses to allow the boy to go out of the house alone. "We're living in terror," he says.

* * *

Along a small canal north of Naga Hammadi, we hear the staccato beat of water pumps that support an activity Egyptians have carried out in this area for thousands of years: tilling the land. The pumps draw water from one of the numerous canals that branch off the Nile and channel it into small irrigation ditches that trickle through lush fields of corn, wheat, sesame, and other crops.

The sugar cane is knee high, but the corn is tall, and the tassels are beginning to turn golden brown. Piles of clothes sit atop the small bridges that cross the canal, left by the boys splashing in the murky water to cool off. In the village of Awlad Yehia, Momen Fahmy Ali oversees his workers as they harvest cattle feed. On his plot, about two acres, he grows corn, cucumbers, tomatoes, wheat, sesame, and fava beans.

He, like many growers, has struggled in recent years with a variety of challenges – water shortages, fertilizer shortages, gas and diesel shortages. These problems have put pressure on farmers in almost every way in Upper Egypt, where agriculture is a key source of employment and income. "We only have the land of our fathers," said one farmer. "No factories, no businesses, no jobs."

The dearth of diesel and gasoline, which has been widespread throughout the country in the past year, means farmers have trouble finding fuel to operate their irrigation pumps. Mr. Ali says he often has to buy fuel on the black market, for double the price. "The plants have to have their water, no matter the price of the fuel," he says. "We have to irrigate at special times – we can't be late."

Similarly, Ali buys fertilizer on the underground market for £150 a bag because the government, which sells subsidized fertilizer for £75 a bag, doesn't give him enough.

Water has become increasingly scarce since 2011. According to tribal leader Ahmed Mokhtar, one reason is the frequent power outages that halt the large irrigation pumps on the canals. Another is that some towns are taking advantage of the chaotic security situation and damming the canals to make sure they have enough water for themselves. That leaves downstream areas dry. In the province of Qena, some canals have turned to a trickle.

Before 2011, problems like this would happen once a year, and be resolved within days, says Mr. Mokhtar. Now, water shortages can last as long as two months. "Can you imagine a farm without water for 60 days?" he says. "As a farmer, my bread, and my income for my children, is burning in the sun in front of me."

All this partly explains why many in Upper Egypt turned against Morsi. "Their bread is being threatened," says Mokhtar. "There's no bigger reason to protest than that."

* * *

When we arrive in Assiut, one of the biggest cities in Upper Egypt, the police presence is immediately more noticeable. But authorities still struggle to control the lawlessness that has increased since the uprising, aided by weapons flowing into Egypt from neighboring Libya and Sudan. The proliferation of guns is now a problem all over the country, but especially in Upper Egypt. Though residents of this rural area have always had guns, they're armed with more of them now – and more substantial ones. In some places, residents tell of warring tribes brandishing RPGs and truck-mounted machine guns.

A high-ranking police officer who asked to remain anonymous says criminals are more confident since 2011 and harder to confront now that they are better armed. "They stand in our faces," he says, using an Arabic turn of phrase. He complains that the police don't have the equipment, the training, or the manpower needed to restore security. Villages known for their gun dealers, where people can buy automatic weapons, lie just across the river from the police station here.

In the 1970s and '80s, Assiut was one of the strongholds of the Gamaa Islamiya, a formerly militant Islamist organization that began in the universities of Upper Egypt. We traveled to the nearby town of Manfalut to meet Ahmed Abdel Salam, who was imprisoned for more than 15 years for his role in planning murders as part of the group's armed wing.

Mr. Abdel Salam, a large man whose affability belies his former role, has the beard and shortened trousers typical of conservative Muslims. He says he grew up in a deeply religious home, and joined Gamaa Islamiya when he was a student at Assiut University in the mid-1970s, assisting the group in its aim of establishing an Islamic state by "enforcing morality and banning immorality." They started, he says, by informing students of their idea of religious duties, like prayer, segregation of the sexes, and, for women, wearing of the veil. But when words weren't enough, they turned to force. "We used to go into the auditorium and separate the boys from the girls," he says, noting that they used sticks and weapons and "beatings" if necessary.

He eventually joined the unit that planned assassinations and attacks and received military training. In the 1990s, the group waged a violent insurgency against the state, targeting police officers, government officials, Christians, and tourists. The militants killed more than 1,000 people. In 1993 Abdel Salam was convicted for his role in the violence and was imprisoned until 2007.

The group's leaders renounced violence while he was in prison; after the 2011 uprising, Gamaa Islamiya formed a political party and ran candidates in elections. Abdel Salam says he became convinced that violence was not the way before he went to prison, when he saw how the incarceration of thousands of Gamaa Islamiya members left families without support. He leads a quieter life since his release, working in his civil engineering company and running a charity – a nursery and Quranic recitation school – from his home. I asked Abdel Salam if he regrets participating in violence. "I don't regret it, but I feel things could have been done in a better way," he says.

The military coup against Morsi, Egypt's first Islamist president, has many worried that some Islamists who embraced democracy as a better way to transform society than violence may change their minds. If Islamists are blocked from political participation, they fear, violence may regain its appeal.

That is unlikely to be the case for Abdel Salam, even if it is for others. "Arms are not the solution, because the government will always have more than us," he says. "The best way for the country and the revolution now is the democratic way, through the ballot box."

* * *

In our next stop, Mallawi, as in much of Upper Egypt, illegal building on agricultural land is rampant – and may eventually affect the nation's ability to feed itself. To the left of a road outside the village, cornfields stretch into the distance, their stalks bending in the breeze. To the right, new buildings, built of brick and limestone, loom where crops once flourished.

One of the buildings belongs to Omar Kamel, a small man with a shy smile. It serves both as a home for his family and a space for his wedding dress rental shop and his wife's hair salon.

Mr. Kamel's grandfather received this small plot under Nasser's land redistribution program, allowing him to earn a living farming corn and sugar cane, and he passed it on to his son. But with the costs of farming rising, Kamel no longer wants to earn a marginal income cultivating the tiny plot. Instead, he used the land to build a new house, one five times larger than the cramped apartment he and his family inhabited in the village.

Egyptian law prohibits most building on agricultural land, an effort to protect the nation's food production. A rapidly growing population and increasing urbanization are eating into the tiny percentage of arable land left in this desert country, threatening to make Egypt even more reliant on food imports than it already is.

Landowners say that before the uprising, police would often demolish illegally built structures. Now people are developing land virtually unhindered, simply paying a fine after the building is finished. With the lax enforcement, illegal structures have been popping up all over Upper Egypt for the past two years, and experts say the trend could have an alarming effect on agricultural output in the future.

"What are we going to do? Agriculture doesn't pay anymore," says Kamel. "Everything is more expensive. We have a big family. I'm building a future for my children."

Nearby, past the cluster of newly built structures, green farmland stretches for about a mile before running into the brick buildings of the village. "Within five years, all that land will be built on," says Kamel, making a sweeping gesture toward the fields.

* * *

Egypt's lax security has consequences not only for its present, but also for the protection of its past. North of Mallawi, on the opposite bank of the Nile, lies Sheikh Ibada, a small village built on the edge of the ancient Roman city of Antinopolis. It's also the site of a former Pharaonic temple and contains artifacts from Egypt's Christian period. Since the uprising, it's been regularly looted – an outgrowth of hard economic times and insecurity that endangers some of Egypt's, and the world's, most treasured antiquities.

As we drive into the site, there are few signs of its spectacular history in the mostly barren landscape. We pass mounds of ancient pottery shards, and a few toppled pillars and capitals. But when we round a corner, we see a group of people in the distance, the puffs of rising sand a sign of their digging. As we approach, they scatter and hide in a nearby cemetery.

Eventually, satisfied we are not police, they return. The group of seven mostly teenagers sift the sand with round sieves in hopes of finding small artifacts – ancient coins, small statues, and what they call "glass masks." Most of what they find sells for a few hundred pounds, but occasionally they find an artifact worth thousands.

Ahmed, a friendly teenager, says the area is an ancient trash heap: They are just digging through their ancestors' garbage to make a living. "Everyone from the town comes here to dig," says Ahmed. "Whoever saves a bit of money buys weapons in this bad time, or puts the money toward his marriage."

They sell the artifacts to "traders" from outside the village, and the income is enough to keep them coming back. As we talk, more men come to dig, their faces covered with scarves to hide their identities as well as shield themselves from the grit-filled wind.

Archaeologists say looting is going on at cultural sites throughout Upper Egypt and even near Cairo. An inspector responsible for protecting this site says the police know it's happening but do nothing to stop it, while the government ministry responsible for antiquities ignores requests for more security. "It's a tragedy, all this damage of our history and heritage," he says. "In my opinion, the revolution destroyed our heritage."

* * *

It began over something as mundane as the construction of a speed bump. By the time it was over, it had escalated into sectarian mob violence, with two Muslims being killed and dozens of Christian homes and shops being torched and looted. The incident, which occurred in April 2011 in the village of Abu Qurqas, the last stop on our journey, is a reminder that religious tensions still persist in Egypt – and remain a major challenge for a nation in search of an inclusive and functional democracy.

Abu Qurqas is located in the province of Minya, which has a large Christian population and a history of attacks on Christians. Throughout Egypt, sectarian violence was on the rise even during the last years of President Hosni Mubarak's rule and continued to escalate after the 2011 uprising. It has intensified again since the ouster of Morsi, with aggrieved Islamists attacking individual Christians and their churches. Abu Qurqas provides a window into the current mood.

When the fighting first broke out here in early 2011, representatives from both the Christian and Muslim communities tried to quell the violence. But angry crowds quickly gathered in front of Christian homes, and some of the occupants fired guns from their rooftops. Later, the mobs burned Christian homes and businesses.

Maria Dawoud was at her family's home when the structure was set on fire. "We didn't know where we would go. We were just running, so scared," she says. Crowds looted everything in the home.

Authorities arrested 20 people, and a state security court convicted all 12 Christians, sentencing them to life in prison, while acquitting the eight Muslims on trial. That verdict has since been annulled and the 12 released, though a retrial is ongoing.

Mrs. Dawoud's son, Fanous Nadi Ibrahim, was one of those arrested. A cattle trader, he says he was in another town on business when the violence broke out and had nothing to do with it. Since his release from prison, he lives in a new home with his wife, children, and extended family. It's unfinished – the walls are raw concrete – and barely furnished, unlike their previous home. The loss of all the family's possessions, along with money in the house that was not his and had to be repaid, "has set me back 10 years," he says.

Abu Qurqas looks peaceful – it's full of small alleyways where children sit on front steps, and in the evenings farmers come in from the fields, herding their oxen ahead of them through the streets. But the village is roughly divided into Christian and Muslim areas, and residents say that divide has grown sharper since the events.

Christians say they rarely go to the Muslim areas now and express fear at the prospect of doing so. They talk about the Muslim side as if the two areas are far apart, when the reality is it's just around a corner. "Even those Christians who were not imprisoned sold their houses in [the Muslim] area," he says. "It's because of the discrimination, the name-calling, the insults. There's injustice toward Christians everywhere now. All we want is God's justice."

* * *

But justice is hard to find. The journey from Aswan to Abu Qurqas shows that Egyptians are still struggling with the same challenges of injustice and inequality that pushed people to overthrow Mr. Mubarak.

The defining chant of the 2011 protests – bread, freedom, and social justice – showed that what Egyptians wanted wasn't just free elections, but a government that would address the entrenched issues that were pushing the country down. The rulers who came after Mubarak, both the military junta and Morsi, never solved those problems. They never attempted to reform police and create security forces that could protect people without the rampant abuse and torture that exists now. They ignored the civil strife that is deepening in dangerous ways, failing to protect Egypt's minorities. They didn't address the inequality and growing economic crisis leaving millions of Egyptians without jobs and options.

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The protests on June 30, while partly a rejection of Morsi's autocratic ruling style and the perception that he was serving the interests of the Muslim Brotherhood instead of Egypt, were also about these same unfulfilled demands. In a way, they're a warning to Egypt's future leaders – that as long as these problems are ignored, instability may continue.

• This project was supported by a grant from the Ford Foundation.