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On Friday morning, January 25, 2013, fifteen jihadis entered the restoration and conservation rooms on the ground floor of the Ahmed Baba Institute in Sankoré, the government library that Al Qaeda in the Islamic Maghreb had taken over the previous April. For nearly a year, thousands of manuscripts left behind by the Ahmed Baba staff had been sitting in the open, stacked on shelves and lying on restoration tables, while the jihadis prayed, trained, ate, and slept around them.

Now, on the verge of being expelled from Timbuktu, the Al Qaeda fighters would exact their retribution. The men swept 4,202 manuscripts off lab tables and shelves, and carried them into the tiled courtyard. In an act of nihilistic vindictiveness that they had been threatening for months, the jihadis made a pyre of the ancient texts, including fourteenth- and fifteenth-century works of physics, chemistry, and mathematics, their fragile pages covered with algebraic formulas, charts of the heavens, and molecular diagrams. They doused the manuscripts in gasoline, watching in satisfaction as the liquid saturated them, and tossed in a lit match. The brittle pages and their dry leather covers ignited in a flash. The flames rose higher, licking at a concrete column around which the volumes had been arranged. In minutes, the work of some of Timbuktu’s greatest savants and scientists, preserved for centuries, hidden from the nineteenth-century jihadis and the French conquerors, survivors of floods and the pernicious effects of dust, bacteria, water, and insects, were consumed by the inferno.

Seven months later, I walked through the Sankoré neighborhood and entered the institute, a three-story labyrinth of long hallways, Moorish-style arches, and beige stucco walls made to resemble traditional mud brick. Just inside the entrance, a white-bearded septuagenarian, wearing a white turban and matching white gown, sat on the floor, one leg extended, the other propping up a cardboard box used for manuscript storage. The box was filled with charred scraps of paper. He sifted through the blackened bits, arranging them as if assembling a jigsaw puzzle. He stared intently at the remains, mumbling to himself, lost in his futile task.

“A caretaker saw smoke rising,” curator Bouya Haidara, a gnomish figure who bears no relation to Abdel Kader Haidara, told me, as he stood beside the blackened concrete pillar, the only remaining evidence, beside the charred scraps in the manuscript box, of the crime that had taken place here. The caretaker had retrieved a few scorched pages from the fire, but the rest had been destroyed. Then, leaving nothing but blackened page fragments and ashes, the jihadis followed Abou Zeid and Ghali into the desert.

And yet out of this wanton act of destruction the curators of the Ahmed Baba Institute had managed to extract a small victory. Bouya escorted me down a wide flight of stairs to the basement, leading the way by flashlight, since power had still not been restored to the city months after the occupation. He turned the key in the lock, and cast his beam over black, moisture-resistant cardboard boxes neatly arranged on dozens of metal shelves, as tidy and ordered as the stacks of a university library in the United States. During their ten months of living at the Ahmed Baba Institute, the fighters had never bothered to venture downstairs to this dark and climate-controlled storage room hidden behind a locked door. Inside were stacks containing 10,603 restored manuscripts, folios, and leather-encased volumes, among the finest works in the collection. “All of them—untouched,” Bouya Haidara said.

In Bamako, Abdel Kader Haidara saw the burning of the manuscripts as a confirmation of the jihadis’ intentions—and a vindication of his remarkable undertaking. Starting with no money besides the meager sum in his savings account, Haidara had recruited a loyal circle of volunteers, badgered and shamed the international community into funding the scheme by presenting it as an epic showdown between civilization and the forces of barbarism, raised $1 million—a tremendous sum for Timbuktu—and hired hundreds of amateur smugglers in Timbuktu and beyond.

In a low-tech operation that seemed quaintly anomalous in the second decade of the twenty-first century, he and his team had transported to safety, by river and by road, past hostile jihadi guards and suspicious Malian soldiers, past bandits, attack helicopters, and other potentially lethal obstacles, almost all of Timbuktu’s 377,000 manuscripts. Not one had been lost en route. “Abdel Kader and I experienced something I have trouble describing. Power, strength, perseverance can’t adequately articulate what it was,” Emily Brady said in her online interview via Reddit. “We kept thinking that we had to lose some manuscripts—theft, bandits, belligerents . . . combat, books in canoes on the Niger River—we had to lose some, right? Well, we didn’t. Not a single manuscript was compromised during the evacuation—nada, zero. They all made it.”

Timbuktu had been the incubator for the richness of Islam, and Islam in its perverted form had attempted to destroy it. But the original power of the culture itself, and the people, like Haidara, who had become entranced by that power, had saved the great manuscripts in the end. Haidara would often be asked in the coming months if the effort had been worth the trouble. What would have happened, interlocutors demanded, if he had sat back and done nothing? “The only response can be ‘I cannot be one-hundred-percent certain,’ ” he would respond. “But I think that if we had left them alone, if we had not acted, many more would have ended up like the manuscripts at the Ahmed Baba Institute.”

Haidara often chose such moments to portray Timbuktu as a paragon of moderation and intellectual ferment that had fallen victim to a once-in-a-millennium conflagration. The reality, of course, is more complex and less flattering to the city’s reputation. Timbuktu had witnessed the killings of scholars by the Emperor Sunni Ali in the 1300s, the rise of the anti-Semitic preacher Muhammed Al Maghili in the 1490s, the edicts of King Askia Mohammed banning and imprisoning Jews during that same decade, and the implementation of Shariah law in Timbuktu by the jihadis in the early and mid-1800s. The city seemed to be in a constant state of flux, periods of openness and liberalism followed by waves of intolerance and repression. “These Wahhabis who came to Timbuktu in 2012 represented something entirely new,” Haidara always insisted, though it was clear that similar strains of anti-intellectualism, religious purification, and barbarism had coursed through the city repeatedly over the preceding five centuries.

As Abou Zeid was fleeing Timbuktu and his comrades were destroying whatever manuscripts they could lay their hands on, I boarded a flight from Algiers to Bamako to piece together for The New York Review of Books the story of the jihadis’ 2012 conquest and to report on the French military effort to bring them down. The country was in turmoil, elated by the sudden French intervention, yet fearful that AQIM and Ansar Dine could inflict a last burst of savage violence. On my first morning in the capital, I paid a call on Imam Chérit Ousmane Mandani Haidara, no relation to Abdel Kader, a charismatic Sufi preacher who was much admired in Mali for being the first Muslim leader to denounce jihadi rule in the north. The Mawloud festival had begun in Bamako, and pilgrims crammed the courtyard of Imam Haidara’s green-domed Sufi mosque on a sealed-off street in the capital, protected by metal detectors and a battalion of red-bereted private guards. The imam received me in a dusty room above his mosque, furnished with gold-painted wingback chairs and sofas and blood-red carpets. Jihadi sympathizers had infiltrated the capital, he told me. He was fearful of assassination, too terrified to leave his compound. What’s more, his moderate Islamic organization, Ansar Dine, a Sufi group with one million followers and branches across West and Central Africa, had been tainted by Iyad Ag Ghali’s appropriation of the name. His followers were being harrassed by the police and army in several African countries, accused of being terrorists. “Iyad Ag Ghali is a Wahhabi, his Ansar Dine is not the same as my Ansar Dine, I am a pacifist,” insisted the imam, a tall and imposing figure in his fifties, swathed in a golden boubou and a green wool scarf. “They created Ansar Dine only to make trouble for me.” The Mawloud Festival at Haidara’s mosque went off without any trouble, but the imam’s fears of jihadist infiltration in the capital would be realized some time later, when Al Qaeda terrorists threw grenades and sprayed automatic-weapons fire at La Terrasse, a popular bar-restaurant frequented by expatriates in Bamako, killing two Westerners and three Malians.

I set out the next day for the north in a hired Toyota Land Cruiser. The tarmac quickly turned to dirt, and my driver fell in behind a half-mile-long French military convoy heading to Timbuktu. In 1994 I had traveled with the French army during Operation Turquoise in Rwanda, and the scenes were vividly familiar. French flags hung from mud-brick huts, jeeps and trucks kicked up clouds of dust, and children waved from the roadside. The French intervention in Rwanda had been cloaked in ambiguity: though French president François Mitterrand had presented it to the world as a humanitarian campaign to save Tutsis from genocide, its real intent seemed to be to carve out a safe haven for the Hutu génocidaires, and prevent Paul Kagame’s Anglophone Rwandan Patriotic Front from seizing control of the country. The mission in Mali, however, was far more straightforward and was moving ahead with what seemed like near-universal approval.

From time to time on the journey north I found myself thinking about my old acquaintance Abdel Kader, whom I had not spoken to since before the jihadi occupation began, and speculating on the fate of his manuscripts. I had imagined that Haidara and his colleagues might have buried them in the desert, as people had done during French colonial times. I had no idea that at that moment a fleet of boats was heading upriver from Timbuktu, bearing seven hundred footlockers toward safe havens in Bamako.

After ten hours and 380 miles, I pulled into Mopti, a Niger River port once favored by backpackers and other adventurous travelers, and a jumping-off point to visit the Dogon people, an animist tribe that dwelled in the nearby falaise, or cliffs. Now hotels, travel agencies, and once popular cafés such as the Restaurant Bar Bozo—noted for its views of sunset over the river—all stood deserted, having shut down following the kidnappings and killings of Westerners. Here the Niger River came into view for the first time since we had left Bamako; the handful of pinasses that I saw motoring slowly upstream might well have been loaded with Haidara’s precious cargo, though I had no awareness of the boatlift that was then in progress.

Shortly after dawn the next morning, under a slate-gray sky, my driver took me toward Konna. Our plan was to follow the French army all the way to Timbuktu and, if our timing was fortuitous, observe the moment of liberation from jihadi rule. But Malian soldiers at a roadblock just past the airport at Sévaré had other ideas. Blocked from advancing by the surly troops, we parked on the roadside, beside a pancake-flat sea of thorny acacias and desert grass, and over the next hour another twenty vehicles filled with film crews and newspaper and newsmagazine reporters took their place along the shoulder. The morning dragged on, the sun rising higher in the now cobalt-blue sky, temperature soaring into the low one hundreds, journalists kicking the dirt in frustration, the soldiers gruffly refusing repeated entreaties to let the convoy through.

A French paratroop officer roared up in a jeep and tried to intervene on our behalf, eventually directing us back down the road to the airport. Outside the front gate, a Malian colonel in crisp fatigues and Ray-Bans curtly informed the pack of journalists that he made the rules, not the French, and the “theater of operations” would remain sealed off to the press. French TV had reported that day that Malian government soldiers had murdered eleven suspected Islamists and thrown their bodies down a well in Sévaré, and some speculated that the soldiers’ obstinance toward the press may have stemmed from that unsavory revelation.

At the Hotel Kanaga on the river in Mopti—the only functioning hotel for Westerners in the city—I sat at the poolside bar that night beside a handful of other reporters and aid workers, swatting away mosquitoes in the tropical heat, and listened to French radio reports of a hostage drama across the border that served as a reminder of the spillover effect of the Malian war and the potential for further turbulence in North Africa. Forty Islamic militants had seized dozens of Western employees at the In Amenas gasworks in the Algerian Sahara. Algerian security forces had attacked the terrorists, and thirty-eight hostages—including three Americans—and twenty-nine Islamists had been killed in the crossfire. The militant who had orchestrated the attack from a secret enclave in the desert was identified as none other than Mokhtar Belmokhtar, the one-eyed cigarette smuggler turned emir of Gao, on the run from French forces, and seeking revenge for the routing of his fighters in northern Mali.

In the months leading up to the French invasion, Belmokhtar’s independent streak had led to ugly quarrels with his masters in the Algerian mountains, a dispute that had apparently culminated in this monumental act of terror. In October 2012 the fourteen members of AQIM’s Shura Council had rebuked him in a pointed letter, later discovered by an Associated Press reporter in an abandoned Al Qaeda barracks in Timbuktu. The Council chastised him for failing to stage “spectacular attacks” in the Sahara, in contrast to his chief rival, Abou Zeid; making only a feeble effort to acquire weapons; and “poorly” managing the kidnapping of the Canadian diplomats in 2008, “trading the weightiest case (Canadian diplomats!) for the most meager price (700,000 euros)!” Most egregiously, Belmokhtar had, it seemed, aired the organization’s “dirty laundry” and revealed closely guarded information to rival militant groups. “Did he not intentionally depict [himself] as the great leader in the field while depicting the organization’s leadership as a failure?” the council asked. “If not for God’s grace, he would have splashed out secrets to the whole world and the heavens above.”

With the officious and mundane language of a performance review at a law firm or a bank, the Shura Council further rebuked him for refusing to take his superiors’ phone calls, ignoring summonses to meetings, and neglecting to file expense reports. Such behavior could have “destructive effects for the entity of the organisation and would tear it apart,” wrote the secretary of the Shura Council, which was dominated by former senior members of the GIA, the Islamist radicals who had murdered tens of thousands of civilians during Algeria’s civil war, and the GSPC, the Salafi spinoff that kidnapped Westerners for ransom and bombed embassies and other facilities in north Africa in the early 2000s. “Why do the successive emirs of the region only have difficulties with you?” they challenged Belmokhtar. As their final insult, the council announced that they had “suspended” him from his command.

In December 2012, Belmokhtar had issued his response: he split from Al Qaeda and formed a new organization, Al Mouwakoune Bi-Dima, Arabic for “Those Who Sign with Blood,” taking the name from an Islamist rebel cell in the 1990s Algerian civil war. The January 2013 carnage at the Saharan gasworks, prefaced by demands for the release of one hundred prisoners from Algeria’s jails, might well have been Belmokhtar’s grotesque effort to upstage his bosses, and to show that he could be every bit as ruthless and murderous toward Western hostages as the fanatic Abou Zeid.

Gao fell on January 26, and on the evening of the 27th, while I was still sitting by the roadblock at Sévaré, waiting to cross into former jihadi territory, a French armored column, supported by Tiger attack helicopters and a battalion of parachutists, entered Timbuktu without firing a shot. Mohammed Touré, Haidara’s right-hand man, was one of thousands of residents who rode in cars, trucks, and motorcycles through the dusty streets, honking their horns in celebration.

“Merci François Hollande, Merci,” one ecstatic young man, draped in a French tricolor, chanted over and over as jeep-loads of French soldiers roared past. At the radio station, the manager patched together equipment and returned to the air, playing the first music that had been heard in Timbuktu in nine months. And hundreds of jihadis headed north, to the remote mountain sanctuary that some of them knew well. There they would make their final stand against the French army.