White robe fluttering in the desert breeze, Moctar Sidi Yayia al-Wangari leads me down a sandy alley past donkeys, idle men and knapsack-toting children rushing off to school. It is a bright morning, my second in Timbuktu, in the geographic center of Mali, and al-Wangari is taking me to see the project that has consumed him for the past three years. We duck through a Moorish-style archway and enter his home, a two-story stone structure built around a concrete courtyard. With an iron key, he unlocks the door to a storage room. Filigrees of light stream through a filthy window. The air inside is stale, redolent of mildew and earth.

"Regardez," he says.

As my eyes adjust to the semidarkness, I take in the scene: cracked brown walls, rusting bicycles, pots, pans, burlap sacks of rice labeled PRODUCT OF VIETNAM. At my feet lie two dozen wood-and-metal chests blanketed in dust. Al-Wangari flips the lid of one of them, revealing stacks of old volumes bound in mottled leather. I pick up a book and turn the yellowing pages, gazing at elegant Arabic calligraphy and intricate geometric designs, some leafed in gold. Turquoise and red dyes are still visible inside grooved diamonds and polygons that decorate the cover.

Perusing the volumes, I draw back: the brittle leather has begun to break apart in my hands. Centuries-old pages flutter from broken bindings and crumble into scraps. Some volumes are bloated and misshapen by moisture; others are covered by white or yellow mold. I open a manuscript on astrology, with annotations carefully handwritten in minute letters in the margins: the ink on most pages has blurred into illegibility. "This one is rotten," al-Wangari mutters, setting aside a waterlogged 16th-century Koran. "I am afraid that it is destroyed completely."

In the mid-16th century, Mohammed abu Bakr al-Wangari, an Islamic scholar from the town of Djenné, migrated north to Timbuktu, then a city of perhaps 100,000 and a religious, educational and trading center, and founded the University of Sankoré, a loose affiliation of mosques and private homes that provided subsidized instruction to thousands of students. During the next 30 years, al-Wangari amassed handwritten books on subjects ranging from history to poetry to astronomy, from both Timbuktu and other parts of the Islamic world. After the scholar's death in 1594, the books passed to his seven sons, and subsequently dispersed to an ever-widening circle of family members. And there they remained until three years ago, when al-Wangari, 15 generations removed from the original collector, set out to recover his family's treasures. "It's a colossal task," says al-Wangari, 42. Slim and intense, he studied Arabic literature in Fez, Morocco, and later worked as a UNESCO consultant in Dakar, Senegal. "I'm working at this every waking minute, and I'm not even getting paid a franc."

A little later he leads me farther down the alley to a half-finished building, marked by a sign that reads AL-WANGARI LIBRARY RESTORATION PROJECT, where laborers are mortaring concrete-block walls and laying bricks to dry in the sun. We cross a courtyard, enter a gloomy interior and walk past dangling wires, stacks of marble tiles and gaping holes awaiting windows. "This will be the reading room," he tells me, gesturing to a bare cell with a dirt floor. "Over here, the workshop to repair the manuscripts." Then al-Wangari points out the centerpiece of his new creation: a vault reserved for the bones of his ancestor, Mohammed abu Bakr al-Wangari, who lived in the house that once stood on this spot. "He would be happy to know what's happening here," he says.

For centuries, manuscripts such as these remained some of Africa's best-kept secrets. Western explorers who passed through Timbuktu in the early 1800s, some disguised as Muslim pilgrims, made no mention of them. French colonizers carted off a handful to museums and libraries in Paris, but for the most part left the desert empty-handed. Even most Malians have known nothing about the writings, believing that the sole repositories of the region's history and culture were itinerant-musician-entertainers-oral historians known as griots. "We have no written history," I was assured in Bamako, Mali's capital, by Toumani Diabate, one of Mali's most famous musicians, who traces his griot lineage back 53 generations.

Lately, however, the manuscripts have begun to trickle out into the world. Local archaeologists are chasing down volumes buried in desert caves and hidden in underground chambers, and archivists are reassembling lost collections in libraries. South Africa's president, Thabo Mbeki, and Harvard professor Henry Louis Gates Jr. have lent their names and prestige to restoration projects. Foreign academics and book restorers have arrived in Timbuktu, providing expertise, money and materials to rescue the manuscripts before it is too late. Improperly stored for centuries, many of these works have already been ruined. Heat and aridity have made pages brittle, termites have devoured them, dust has caused further damage, and exposure to humidity during the rainy season has made the books vulnerable to mildew, which causes them to rot. "We are in a race against time," says Stephanie Diakité, an American based in Bamako who runs workshops in Timbuktu on book preservation.

The manuscripts paint a portrait of Timbuktu as the Cambridge or Oxford of its day, where from the 1300s to the late 1500s, students came from as far away as the Arabian Peninsula to learn at the feet of masters of law, literature and the sciences. At a time when Europe was emerging from the Middle Ages, African historians were chronicling the rise and fall of Saharan and Sudanese kings, replete with great battles and invasions. Astronomers charted the movement of the stars, physicians provided instructions on nutrition and the therapeutic properties of desert plants, and ethicists debated such issues as polygamy and the smoking of tobacco. Says Tal Tamari, a historian at the National Center for Scientific Research in Paris, who recently visited Timbuktu: "[These discoveries are] going to revolutionize what one thinks about West Africa."

Some scholars believe that the works might even help to bridge the widening gap between the West and the Islamic world. Sixteenth-century Islamic scholars advocate expanding the rights of women, explore methods of conflict resolution and debate how best to incorporate non-Muslims into an Islamic society. One of the later manuscripts discovered, an 1853 epistle by Sheik al-Bakkay al-Kounti, a spiritual leader in Timbuktu, asks the reigning monarch, the Sultan of Masina, to spare the life of German explorer Heinrich Barth. The sultan had ordered Barth's execution because non-Muslims were barred from entering the city, but al-Bakkay argued in an eloquent letter that Islamic law forbade the killing. "He is a human being, and he has not made war against us," al-Bakkay wrote. Barth remained under the protection of al-Bakkay and eventually made it back to Europe unscathed. "The manuscripts show that Islam is a religion of tolerance," says Abdel Kader Haidara, who owns one of the largest private collections of manuscripts in Timbuktu, including the letter from al-Bakkay. Haidara is raising funds to translate some of them into English and French. "We need to change people's minds about Islam," he says. "We need to show them the truth."

The last time I'd visited Timbuktu, in 1995, there were only three ways to get there: a three-day journey upriver by a motorized pirogue, or canoe, from the trading town of Mopti; a chartered plane; or a flight on the notoriously unreliable government airline, Air Mali, mockingly known as Air Maybe. But when I returned last February, at the end of the cool, dry season, to check on the city's cultural revival, I flew from Bamako on a commercial flight operated by a new private airline, Mali Air Express—one of four flights to Timbuktu each week. The Russian-made turboprop, with a South African crew, followed the course of the Niger River, a sinuous strand of silver that wound through a pancake-flat, desolate landscape. After two hours we banked low over flat-roofed, dun-colored buildings a few miles east of the river and touched down at Timbuktu's tarmac airstrip. Outside a tiny terminal, a fleet of four-wheel-drive taxis waited to ferry tourists down a newly constructed asphalt road to town. I climbed into a Toyota Land Cruiser and directed the driver, Baba, a young Tuareg who spoke excellent French and a few words of English, to the Hotel Colombe, one of several hotels that have opened in the past three years to cater to a rapidly expanding tourist trade.

At first glance, little had changed in the decade that I'd been away. The place still felt like the proverbial back of beyond. Under a blazing late winter sun, locals drifted through sandy alleys lined by mud-walled and concrete-block huts, the only shade provided by the thorny branches of acacia trees. The few splashes of color that brightened the otherwise monochromatic landscape came from the fiery red jerseys of a soccer team practicing in a sandy field, the lime green facade of a grocery store and the peacock blue bubus, or traditional robes, of the local Tuareg men. The city petered out into a haphazard collection of domed Tuareg tents and piles of trash that goats were feeding on.

Yet Timbuktu's isolation has become a bit less oppressive. Ikatel, a private cellular phone network, came to town two years ago, as their ubiquitous billboards and phone-card booths testify. I noticed a white-robed imam talking emphatically on his Nokia in front of the Djingareyber Mosque, a massive mud fortress built in the 1320s that rises in the town center. Three Internet cafés have opened. Hammering, sawing and bricklaying are going on all over town, as new libraries prepare to open to the public. The day I arrived, a delegation of imams from Morocco, several researchers from Paris, a team of preservationists from the University of Oslo and a pair of radio reporters from Germany were on hand to look at manuscripts.

Timbuktu is also no longer immune to the ideological contagions that have plagued the wider world. On the southeast edge of town, Baba pointed out a bright yellow concrete mosque, by far the best constructed new building in town, built by Saudi Wahhabis who have tried, without much success, to export their hard-line brand of Islam to the Sahara. Not far from the Wahhabis' haunt, on the terrace of the Hotel Bouctou, I ran across five clean-cut young U.S. Special Forces troops, dispatched to train the Malian Army in counterterrorism. Joint military operations have become common in the Sahel since an Algerian Islamic terrorist cell, the Salafist Group for Preaching and Combat, seized dozens of European hostages on the border between Algeria and Mali three years ago and held them for six months in the Malian desert.

Most historians believe that Timbuktu was founded in the 1100s by a Tuareg woman named Bouctou, who ran a rest stop for camel caravans on a tributary of the Niger River. ("Tin Bouctou" means "the well of Bouctou.") The city reached its peak in the early 16th century, during the reign of King Askia Mohammed, who united West Africa in the Songhai Empire and ruled for 35 prosperous years. The Tariqh al-Sudan, a history of Timbuktu written in the 17th century, described the city in its heyday as "a refuge of scholarly and righteous folk, a haunt of saints and ascetics, and a meeting place for caravans and boats." In 1509, Mohammed al-Wazzan al-Zayati, a 16-year-old student from Fez, arrived by camel with his uncle, a diplomat, and found a bustling commercial crossroads. Timber, gold and slave traders from Ghana, salt sellers from the Sahara, and Arab scholars and merchants from the Levant mingled in bazaars packed with spices, fabrics and foodstuffs, and conducted transactions with cowrie shells and nuggets of gold. "In the middle of the town there is a temple built of masoned stones and limestone mortar...and a large palace where the king stays," al-Zayati wrote in an account published in 1526 under the name Leo Africanus. "There are numerous artisans' workshops, merchants, and weavers of cotton cloths. The cloths of Europe reach Timbuktu, brought by Barbary merchants."

Al-Zayati was astonished by the scholarship that he discovered in Timbuktu. (Despite his encouragement of education, the emperor himself was not known for his open-mindedness. "The king is an inveterate enemy of the Jews," al-Zayati noted. "He does not wish any to live in his town. If he hears it said that a Barbary merchant...does business with them, he confiscates his goods.") Al-Zayati was most impressed by the flourishing trade in books that he observed in Timbuktu's markets. Handwritten in classical Arabic, the books were made of linen-based paper purchased from traders who crossed the desert from Morocco and Algeria. Ink and dyes were extracted from desert plants, and covers were made from the skins of goats and sheep. "Many manuscripts...are sold," he noted. "Such sales are more profitable than any other goods."

Eighty-two years after al-Zayati's visit, the armies of the Moroccan sultan entered the city, killed scholars who urged resistance and carried off the rest to the royal court in Marrakesh. The forced exodus ended the city's days as a center of scholasticism. (Timbuktu soon faded as a commercial center as well, after slave traders and other merchants from Europe landed in West Africa and set up ocean networks to compete with the desert routes.) For the most part, the volumes of history, poetry, medicine, astronomy and other subjects that were bought and sold by the thousands in Timbuktu's bazaars vanished into the desert. And there they remained, hidden in rusting trunks in musty storage rooms, stashed in mountain caves or buried in holes in the Saharan sands to protect them from conquerors and colonizers, most recently the French, who left in 1960.

The campaign to rescue Mali's manuscripts began in 1964, four years after Mali won its independence. That year, UNESCO representatives met in Timbuktu and resolved to create a handful of centers to collect and preserve the region's lost writings. It took another nine years before the government opened the Centre Ahmed Baba, named after a famed Islamic teacher who was carried to exile in Marrakesh in 1591. With funding from the United Nations and several Islamic countries, including Kuwait and Saudi Arabia, the center dispatched staff members into the countryside to forage for lost manuscripts. One collector was Mohammed Haidara, an Islamic scholar and manuscript maker from Bamba, a village midway between Timbuktu and the village of Gao. Haidara helped build a collection of 2,500 volumes. Soon after his death in 1981, the center's director turned to Haidara's son, Abdel Kader, then in his 20s, and asked him to take over his father's job.

Abdel Kader Haidara spent the next decade traveling on foot and by camel throughout Mali, and taking pirogues along the Niger River and its tributaries. "I went looking for manuscripts in all the villages," he told me. A tall, ebullient man with a Falstaffian goatee and tufts of black curly hair framing a shiny, bald pate, Haidara is widely considered the most important figure in Timbuktu's renaissance. "Everybody knew my father. They all said, ‘Ah, you are his son,' but the work was difficult," he said. Many villagers were deeply distrustful of an interloper trying to take away possessions that had been in their families for generations. "People said, ‘He's dangerous. What does he want with these manuscripts? Maybe he wants to destroy them. Maybe he wants to bring us a new religion.'" Others drove hard bargains. One village chief demanded that Haidara build a mosque for his village in exchange for his collection of ancient books; after construction was finished, he extracted a renovation for the local madrasa (Islamic religious school) and a new house as well. Some chiefs wanted cash, others settled for livestock. But Haidara negotiated hard—he had grown up around ancient manuscripts and had developed a keen sense of each book's worth. "I gave out a lot of cows," he said.

In 1993, Haidara decided to leave the center and venture out on his own. "I had a lot of my own manuscripts, but my family said it was not permitted to sell them. So I told the Ahmed Baba director, ‘I want to create a private library for them,' and he said, ‘fine.'" For three years, Haidara searched for financing with no success. Then, in 1997, Henry Louis Gates Jr. stopped in Timbuktu while making a television series about Africa. Haidara showed his manuscripts to the Harvard scholar, who had known little about black Africa's written history. "Gates was moved," Haidara says. "He cried, and he said, ‘I'm going to try to help you.'" With Gates' endorsement, Haidara got a grant from the Andrew Mellon Foundation, which allowed him to continue searching for family books and to construct a library to house them. The Bibliothèque Mamma Haidara opened in Timbuktu in 2000; today the collection contains 9,000 volumes.

In 1996 a foundation that Haidara established, Savama-DCI, to encourage others with access to family collections to follow in his footsteps, received a $600,000 grant from the Ford Foundation to construct two new libraries in Timbuktu, the Bibliothèque al-Wangari and the Bibliothèque Allimam Ben Essayouti. The funds will also allow Haidara to renovate his own library and to purchase computers to digitize the works, hire experts to restore damaged books and give instruction to local archivists. Haidara has become the driving force behind manuscript preservation in the Sahara. "We want people to be able to touch and read these manuscripts," he told me. "We want to make them accessible. But first, they must be protected."

The work is gaining momentum. After meeting with Haidara, I visited the Centre Ahmed Baba, a handsome complex of stone buildings with Moorish archways set around a sand courtyard planted with date palms and desert acacias. Director Mohamed Gallah Dicko escorted me into the atelier. Fourteen workers were making storage boxes and carefully wrapping crumbling manuscript pages in transparent Japanese paper called kitikata. "This will protect them for at least 100 years," he said. A total of 6,538 manuscripts at the center have been "dedusted," wrapped in acid-free paper and placed in boxes, Gallah Dicko said; there are another 19,000 to go. The workers have flown to workshops in Cape Town and Pretoria paid for by South Africa's National Archive, part of a program that the South African government initiated after President Mbeki visited Timbuktu in 2002. In an airless room across the courtyard, a dozen archivists huddle over Epson and Canon scanners, creating digital images of the works, page by page. The manuscript collection is growing so fast that the staff can't keep up. "We're expanding our search to the northwest and the northeast," Gallah Dicko tells me. "There are hundreds of thousands of manuscripts still out there."

Yet placing the books in Timbuktu's libraries under the care of experts doesn't guarantee their protection. Seven years ago, heavy rains caused the Niger to overflow its banks. The worst flood in decades swept through Timbuktu, destroying 200 houses and many valuable works. Only rapid salvaging prevented the ruin of 7,025 manuscripts at the Spanish-funded Bibliothèque Fondo Kati, whose treasures include a priceless illuminated Koran made in Ceuta, Andalusia, in 1198. "We put bags of sand around the house, and we saved it from collapse," I was told by the library's creator, Ismael Diadie Haidara (no relation to Abdel Kader Haidara), whose paternal ancestor fled Toledo in 1468 and brought hundreds of manuscripts, including the Ceuta Koran, to Africa. "We could have lost everything."

Two days after our meeting, Abdel Kader Haidara arranges for me to travel to the Tuareg village of Ber, 40 miles east of Timbuktu. It is one of a handful of remote Saharan settlements where Islamic scholars and others, under Haidara's tutelage, have begun building their own manuscript collections. The sun is just rising when we depart Timbuktu, and a chill wind whips through the open windows of our battered Land Cruiser. Baba steers the vehicle over an undulating sand track, passing encampments of nomads who have pitched tents on the city's outskirts to sell jewelry and offer camel rides to Western tourists. Then we're in the heart of the Sahara, fishtailing past dunes and scraggly acacias.

Fida ag Mohammed, the collection's curator, fiddles with a set of prayer beads in the rear seat. A gaunt man in his late 40s or early 50s with wispy sideburns that blow outward in the breeze, Mohammed was initially reluctant to take me, a stranger, to Ber. But Haidara reassured him that I was a journalist, not a spy, and he finally consented. "There are evil people out there who want to steal from us our traditions, our history," he explains as Baba swerves to avoid a speeding pickup truck packed with blue-robed, white-scarved Tuaregs. "We have to be careful."

After two hours we reach Ber, a shadeless collection of mud-brick huts and tents scattered across a saddle between two low desert ridges. There is a veterinary clinic, a health center and a primary school, but few other signs of permanence. Mohammed leads us to his two-room house, where we sit on mats on the dirt floor. He disappears into his kitchen and returns with a pot filled with something dark and smelly: minced gazelle, Baba whispers. Nervously, I taste a few spoonfuls of the meat, finding it gamy and gristly, and decline the warm camel milk that Mohammed offers as a digestif.

Ber once had 15,000 manuscripts dating as far back as the 15th century, the men tell me. Most of these were in the possession of village marabouts, or "knowledge men," often the only individuals who know how to read and write. But in the early 1990s, after a period of droughts and neglect by the government, the Tuaregs launched a violent rebellion. Tuareg villages were attacked, looted and sometimes burned by government troops and mercenaries from other desert tribes. (Ber was spared.) Before the Tuaregs and the government concluded a peace deal in 1996, Ber's inhabitants dispersed all but a few hundred manuscripts to settlements deep in the Sahara, or buried them in the sand. It was a modern-day version of a story that has played out in Mali for centuries, a story of war, depredation and loss. "I'm starting to locate the manuscripts again," Mohammed tells me. "But it takes time."

We cross a sandy field and enter a tin-roofed shack, Mohammed's "Centre de Recherche." Mohammed opens a trunk at my feet and begins to take out dozens of volumes, the remains of Ber's original collection, along with a few he has recovered. He touches them reverently, delicately. "Dust is the enemy of these manuscripts," he murmurs, shaking his head. "Dust eats away at them and destroys them over time." I pick up a miniature Koran from the 15th century, thumb through it and stare in amazement at an illustration of the Great Mosque of Medina. It's the only drawing, besides geometrical patterns, that I've seen in four days of looking at manuscripts: a minutely rendered, pen-and-ink depiction by an anonymous artist of Saudi Arabia's stone-walled fortress, two pencil-thin minarets rising over the central golden dome, date palm trees at the fringes of the mosque and desert mountains in the distance. "You are one of the first outsiders to see this," he tells me.

After an hour inspecting the works, Mohammed brings out a guest register, a thin, grade-school composition book, and asks me to sign it. A total of six visitors have registered since 2002, including a former U.S. ambassador to Mali. "The next time you come to Ber, I'll take you into the desert for a week," Mohammed tells me before we part. "I'll show you where they buried the books, deep in the ground, so that nobody can find them." They are still out there, thousands of them, guarded by fearful villagers, disintegrating slowly in the heat and dust. But thanks to Mohammed, Haidara, al-Wangari and others like them, the desert has at last begun to surrender its secrets.

Writer Joshua Hammer lives in Cape Town, South Africa. Photographer Alyssa Banta is based in Fort Worth, Texas.