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A Niger army soldier, taken prisoner by Tuareg rebels, stands in front of the grave of a civilian he is accused of murdering in the Aïr Mountains. The deceased was the father of the Tuareg commander (foreground), who would later decide the prisoner's fate. Image by Brent Stirton. Niger, 2011.

The rebel commander, his face hidden behind a dark turban, leads the way over the soft sand, scorched black in places by exploded mortar shells and littered with detritus from a series of battles waged here, on a soccer field.

With nearly every stride, our feet crunch spent rifle cartridges, which litter the ground like the withered bodies of locusts left after a plague. “Step in my steps,” he cautions, noting that the Niger army had mined the area, where there had been a school for Tuareg children. His men removed some of the devices, but others remained lost in the shifting sands. “Maybe they are buried too deep to explode if you step on one,” he tells me.

It is late afternoon in the dry season, and the temperature has finally slipped below 100°F. The beige dunes stretching to the north begin to take on a pinkish hue, and the shadows from the steep ridges to the southwest are spreading across the valley floor. In this lonely place called Tazerzaït, where the Aïr Massif meets the great sand seas of the Sahara, the commander’s men had won the greatest victory of their two-year rebellion against the Niger government.

The rebels, all ethnic Tuareg, descend from the fierce nomads who for several centuries dominated this desolate region of North Africa. Fighting under the banner of the Movement of Nigeriens for Justice (MNJ) and supported in part by Libyan leader Muammar Qaddafi, they had captured 72 government soldiers at Tazerzaït and renewed their longstanding Tuareg demands that the government share revenue derived from another source of treasure: uranium mined on their traditional lands. In a show of goodwill the rebels released all of their prisoners—except one. “He is a war criminal,” the commander says.

But the battle had been about more than just politics. “This place is sacred to us,” the commander says. It was here, under the shadow of Mount Tamgak, one of the black granite spires that comprise the Aïr range, where for centuries Tuareg have grazed their herds of camels, goats, donkeys, and sheep. Here their elders have passed down stories about the victories their ancestors have won amidst this rugged landscape. And here they have retreated during conflict. The commander shows me an arrowhead he’d found on the school grounds. It is glistening white quartz, the size of a tooth, finely honed into a perfect point. He and his men find these everywhere, he says. They regard them as good luck charms, relics left by ancient combatants who also fought for this land.

As we walk, the commander says that local Tuareg nomads, with the help of a Canadian tourist, built the school at Tazerzaït because it is near a well central to the region’s far-flung grazing areas. Its central location allowed families to visit their children as they moved their herds. Previously, locals who wanted their children educated had to send them to distant villages and rarely saw them.

“My father only knew how to live in the desert,” the commander says. “He knew how to make the salt caravan to Bilma, how to find grazing in the desert, how to hunt antelope in the canyons and wild sheep in the mountains. And that is what I know, but the life of the desert is ending. Our children need school.”

We reach the top of a small bluff where three mud-brick classrooms stand, their walls gouged with bullet holes, their roofs missing. The chalkboards are covered with graffiti left by the Nigerien soldiers and include French profanities and cartoons depicting Tuareg having sex with animals.

Four rebels with Kalashnikovs slung over their shoulders have brought the alleged war criminal down from the cave near the summit of Tamgak where they are holding him. His posture is slumped, like a sulking teen, and he crosses and uncrosses his arms, eyes darting among the men. The sleeves of his ragged camouflage shirt are cut off and his combat boots are untied. He claims to be 27 years old, but his round face and awkward manner make him appear much younger.

It was growing late, and the rebels, clad in sun-bleached fatigues are edgy about lingering in this exposed position. The Niger army countered its last defeat here by acquiring helicopters, and the Tuareg recently were surprised by an assault from the air that killed several men, including one of their leaders. The men squint toward the horizon, and periodically everyone goes silent to listen for the sounds of rotors beating the air. “They buy helicopters to fight us, but they will not build schools or wells for us,” the commander says, as he leads the way to the edge of the school grounds. The prisoner trails behind, his head bowed, bootlaces skipping along the ground.

The commander stops at a place where stones set in the soft sand mark out three graves. “Three old men are buried here,” he says. “When the army attacked,” he points to one of the graves, “this man, who was blind, refused to flee.” He motions to the other graves as if the old men are present and listening. “These two refused to leave him.” The prisoner remains silent, trying not to look at the graves or the commander, who pauses to adjust the strap of his rifle on his shoulder and then continues his prosecutorial account of how the soldiers accused the old men of helping set land mines.

“That night they tortured them behind the classrooms,” he says. “We were hiding in the mountains, just there,” he gestures to a ridgeline above us. “We could hear the old men screaming.” His voice is even and calm. “This one,” he points to the grave in the center, “is my father.”

To reach this remote corner of the world’s largest desert requires traversing a vast primordial landscape—a place defined by salt pans that take the better part of a day to cross, dune fields that rise and fall like violent seas, and mammoth outcroppings of glassy marble and obsidian that breach the sand like strange sea creatures. Occasionally, a thorn tree appears on the horizon, its trunk twisted and bowed, its gnarled branches swept downward as if begging the relentless sun and wind for a reprieve.

Since before the Middle Ages up until their conquest by the French in the early 20th century, generations of Tuareg warriors dominated this realm, demanding tribute from merchants plying the rich caravan trade in gold, spices, and slaves. Meanwhile, they raided local sedentary tribes along the Niger River for animals and slaves of their own. Guided by the proverb “Kiss the hand you cannot sever,” the Tuareg gained a reputation for brutality and treachery, often robbing the very caravans they were hired to protect and launching surprise attacks on their allies.

When the French finally defeated the Tuareg (the last West African tribe to be pacified), their lands were absorbed into parts of Niger, Mali, Algeria, and Libya. After France cast off its African colonies in the 1960s, ethnic groups that had long been the target of Tuareg raiders rose to power in the newly independent governments of Mali and Niger. These new leaders remained highly suspicious of their Tuareg minorities but generally left them to wander their desert lands with their flocks. Problems began to flare when droughts struck the region. In recent decades, by some estimates rainy seasons have shrunk from more than 60 days a year to less than 30, and Tuareg families have struggled to sustain sizable herds. “Animals are everything to a Tuareg,” an elderly nomad once explained to me. “We drink their milk, we eat their meat, we use their skin, we trade them. When the animals die, the Tuareg dies.”

With their herds decimated, many Tuareg in Niger began asking why the government wasn’t sharing the wealth derived from the rich uranium deposits that for decades have been mined from their grazing lands. During the 1990s a Tuareg militia, largely trained and armed by Qaddafi, fought the Niger army over the issue. A peace accord was signed in 1995, but most Tuareg say that little changed. Jobs remained scarce, even as production increased at the major uranium mine at Arlit. Tuareg communities in the north complained that the only government representative they encountered was the taxman, who dutifully collected annual taxes from every nomad family. If a family didn’t have money, the taxman took one of their animals. “Why do we pay taxes?” a nomad once asked me, sweeping his hand toward the endless yellow desert. “Do you see our wells, our schools, our clinics?”

By 2007, with the price of uranium rising, the Niger government was negotiating lucrative contracts with France that would make to make Niger the world’s second largest uranium producer. More deals were struck allowing companies from China, Canada, and the U.S. to explore the desert for other resources. With the nation mired in poverty and the government refusing to make meaningful investments in Tuareg areas, the nomads rebelled again.

The rebels make camp for the night in a dune field a few miles from the school, hiding their battered pickups under the low canopies of acacia trees. Several men wash their hands and faces with water from teakettles and kneel toward Mecca for evening prayers while the less religious among them unpack cooking pots and collect dead branches for kindling. Then they gather in clusters of six or seven, each group taking shelter behind a small dune and lighting a meager fire.

A few of the rebels wait for full darkness to unwind their turbans. By tradition Tuareg men cover their faces, though the women do not. The layers of cloth not only protect from the harsh sun and wind but also conceal their emotions. A Tuareg elder once told me that it was both a sign of respect not to show your nose and mouth to another man, but it was also prudent reminder, he said, “to watch everything and to speak little.” Prudent advice, it would seem, given the Tuareg predilection for treachery.

Like mummies coming back from the dead, the young rebels’ animated faces emerge in the firelight, revealing downy wisps of beard and boyish grins. Some of their cheeks are stained with indigo dye from their turbans, an age-old mark of the Tuareg that led early visitors to dub them the “blue men.”

The rebels’ medic invites me to join his group. The men tease each other and light cigarettes as they boil macaroni and brew tea. Many appear barely old enough to have undergone the traditional post-adolescent ceremony in which their uncles pronounce them ready for manhood and twist the first turban around their heads.

By the fire I notice that the medic and another man bear the common ethnic features of the African interior—dark brown skin, kinky hair, and broad noses. Two men have olive complexions, smooth black hair, and sharp Mediterranean noses. The other three are a mixture of all the traits. Regardless of skin color, a surprising number have striking topaz-blue eyes. This genetic grab bag suggests one of the paradoxes of the Tuareg, who have always considered themselves a people apart yet for centuries took slaves from other desert tribes and intermarried with them. The result is an ethnic group distinguished primarily by its common language, Tamashek, which is related to Berber tongues spoken in Algeria and Morocco.

We huddle around a communal bowl, sharing spoons to dip out mouthfuls of salty macaroni seasoned with goat fat and desert herbs. The men eat hungrily but are careful to take only their portion. Between bites, the medic tells me he was a doctor’s assistant before the rebellion. His left eye, a blank, milky orb, is a casualty of shrapnel from a grenade that exploded near him during his very first battle. Next to him sits the group’s thick-shouldered machine gunner, who mans an ancient Belgian-made .50 caliber with a rusting barrel. The machine gunner refuses to give his name but says he left engineering classes at a university in Nigeria to join the rebels. “I could not study while my Tuareg brothers were fighting,” he tells me.

Hama, a lanky youth, has never gone to school. He grew up in an Aïr village, making the annual camel caravan with his father. He points to the brightest stars and describes how to use them to navigate to the Bilma oasis in the eastern desert, where they would trade onions and garlic for salt. He points to the southeast. “it is there,” he says with certainty, as if it were just behind the horizon. “Thirty days by foot,” he says, noting that the first time, he made the trip barefoot.

I ask who is the youngest, and the medic points to a painfully shy boy named Bachir. His skin is coal black and perfectly smooth. His long and delicate fingers resemble ebony twigs. It seems nearly impossible that they could manage to pull the trigger on the heavy Kalashnikov lying beside him. Almost whispering, he says he thinks he is about 17 but isn’t sure. He was tending his family’s animals in the mountains when a rebel convoy drove by, and he asked to join them. “He is good luck,” one of the men says.

After gentle prodding, Bachir recounts how soon after he joined the rebels he was riding in the back of a pickup when it struck a mine. Two men died instantly, eight suffered serious wounds, but Bachir was hurled a hundred feet away into the top of an acacia tree. “It felt like I went to sleep and woke up in the branches, and everything was silent,” he says quietly.

The rebels were searching for his body among the smoking wreckage when he walked up. “He wasn’t even scratched by the branches,” the medic says, his good eye widening. “Allah has his hand on that one.” The other men click their tongues, using the Tuareg shorthand for agreement.

I ask Bachir what he will do after the rebellion, and he replies that he would like to be a soldier. “In the Niger army?” I ask. At the end of the last Tuareg rebellion in 1995, many former rebels were brought into the Niger military as part of the peace settlement, but I still find his answer surprising. “You would join the people who have killed your friends and nearly killed you?” He shrugs: “I think it would be a good job.” Some of the others click their tongues.

After dinner the prisoner is brought to me, and we are allowed to talk privately. He is a Fulani, one of the ethnic groups that the Tuareg used to raid for slaves. He says he is Abdul Aziz, a lieutenant in the Niger army and admits to shooting one of the old men in the leg. “It was wrong of me to do this,” he says. His superiors had been angry that two of their vehicles had struck mines laid by the rebels, killing and wounding several men. To evacuate the injured, the army would have to pass through the rebel minefield again, he says, and they were convinced that the old men knew where the explosives were laid.

“The officers asked the old men to talk, but two of them refused. The one who was shot was talking, but he wasn’t giving good information. It was getting to be night. That’s when I left,” the prisoner says. “I will swear on the Koran that I did not kill any of them.”

After he and the other soldiers were captured, the senior officers conspired to make him the scapegoat, he says. He shakes his head at the remembrance of their betrayal.

One morning the rebels marched all the prisoners down Tamgak, and he and his comrades sensed that their ordeal was ending when they saw two large Mercedes transport trucks parked in the valley. But before he could climb in the back with the other prisoners for the trip to Libya where they would be released, he was held back. A detail of rebels had marched him back up the mountain. “I could see the trucks driving toward the desert,” he says. “It was very difficult for me for many days.” But he adds that his Tuareg captors have never beaten him, and at the end of Ramadan they allowed him to receive a letter from his parents via the Red Cross. “All of us are Nigeriens,” he says with resignation. “It is only Satan who creates a problem between people.”

As the night deepens, the older rebels gather at the commander’s fire, where the flames have dwindled to coals. The men stretch out on quilts and pass around cigarettes and small glasses of hot sugared tea. A rebel named Gourem asks if I want to get high. “On what?” I ask. “Ganja,” he says, “some of the nomads grow it.” I politely decline for several reasons, not least of which is that in the event of a helicopter attack I would like to be in full control of my faculties.

The air is cool and sweet, and the dunes glow under the oval moon. One man produces a guitar. The lowest bass string was broken and replaced with a motorcycle brake cable, giving certain chords a resonant buzz. “Do you know Tinariwen?” the guitar player asks, referring to a Tuareg band whose founders had trained together in Libyan military camps during the 1980s. He begins to play one of their songs. “It is about the Tuareg struggle,” another rebel says.

A few at the fire had trained in the Libyan camps. As teenagers they had heard radio broadcasts of Qaddafi sympathizing with the plight of the Tuareg and exhorting them to come to Libya, where he would help them fight for their rights. But soon after joining one of his training camps, they realized the Libyan dictator was using them. Some were sent to fight in Lebanon; others saw action when Libya invaded Chad.

“We also used Qaddafi,” one rebel says, noting that Tuareg from Mali and Niger had smuggled weapons from the camps to fight their governments at home. In recent years Qaddafi sent millions in economic aid to leaders in Mali and Niger while funneling support to Tuareg groups fighting against them. “Our leader is in Tripoli now,” the commander says, referring to Aghali Alambo, the MNJ’s president.

I ask the commander about the Niger government’s recent charges that the rebels are an ally of al Qaeda and involved in drug smuggling—two growing threats in the Sahara. He motions at his bedraggled platoon. “Do we look like rich smugglers?” The other men click their tongues.

I mention the prisoner’s claims that his fellow soldiers framed him for the murders of the old men. “He killed them,” the commander replies in a quiet, certain voice. I ask what he plans to do with the young man. “Sometimes, I think I will kill him,” he says bluntly. “It would be justice.” And then as an afterthought then adds, “What do you think I should do?” He presents the question in such a way that it feels like a test as much as a consultation. Caught off-guard, I stutter out an ill-informed suggestion about seeking an international war crimes prosecution and pronounce that such a move would show the world that the MNJ is merciful and interested in justice. But even as I speak the words, I realize I have no clue how such a plan might actually work. The commander listens patiently and after a moment says only, “Perhaps.” The other men are silent.

The music continues, more glasses of tea are poured, and the men begin telling stories. Some recount their exploits from the first rebellion in the 1990s. “We were so hungry,” recalls one rebel, whose long gray beard features gives him a passing resemblance to Osama bin Laden, “that we used to hope the army would attack so we could take their food.” Some of the others nod. Another describes a spectacularly successful daylight attack on a small outpost that was timed to coincide with the radio broadcast of a Niger’s national soccer team playing an international match. “The soldiers were so surprised that they all surrendered right away, but they asked if they could listen to the rest of the match,” Gourem remembers.

One rebel offers me a cigarette and quietly confides that the men are suspicious of their leader, Alambo. “There are rumors he has a villa in Tripoli,” the man says between puffs. “We have strong vehicles and many weapons. We want to fight, but when we make a plan to attack, Alambo always says no. No one understands what he is waiting for.”

The next day I am to travel farther into the mountains to join another group of Tuareg rebels. “You will see,” the man says. “The Tuareg there will say bad things about us—that we are not fighting, that we will betray them, that our leaders are corrupt.” He sighs. “There is always disagreement among the Tuareg. It is our curse.”

Several weeks after I left the Aïr, the commander released the prisoner. In the ensuing months the rebels and the government announced a cease-fire, and not long afterward the Niger army overthrew the country’s strongman president, Mamadou Tandja, and held free elections. Last February, with democracy protests mounting in Tripoli, Qaddafi sent recruiters to Niger and Mali with offers, reportedly as high as a thousand dollars a day, to any Tuareg who would come fight for his regime in Libya. Tuareg sources in Niger say that some former members of the MNJ have taken the offer.

Upon hearing this news, I recalled one of my last conversations with the rebel commander. He had driven me to a place in the desert where I would depart from his territory. He gave me some dried sheep’s cheese, a Tuareg delicacy, and said he wanted to send me with the message that if the world wanted to stop the growing threats of al Qaeda and drug smuggling in the Sahara, they needed to enlist the Tuareg. “The desert has no secrets from the Tuareg,” he said, repeating a favorite local aphorism. “We know how to fight here better than anyone.” Yes, I said, but given the Tuareg history of betrayal and infighting, could the West trust them? He answered with a click of his tongue. I couldn’t gauge his expression because his face was completely obscured by his turban.

A shorter version of this story was published as Lost Lords of the Sahara in National Geographic’s September issue.

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