Black Flags: The Rise of ISIS

by Joby Warrick

In 2002, King Abdullah II had been scolded by American officials for warning that an invasion of Iraq would “open Pandora’s box,” and he was taking no pleasure in seeing his predictions coming true. Sickened by the bombings and beheadings carried out in Allah’s name, the monarch began a series of private meetings with religious scholars to talk about a way to draw a line between Islam, the ancient faith, and the hateful takfiri creed used by Zarqawi to justify the killing of those he regarded as apostates. It was no easy assignment. Unlike Shiites or Roman Catholics, Sunni Muslims lack a centralized religious hierarchy that settles theological debates. Muftis, Sunni clerics of a certain rank, can issue religious edicts called fatwas, but any two can disagree wildly on the same topic: what is a damnable sin to one scholar may be regarded as permissible or even obligatory behavior to another. Since his arrival in Iraq, Zarqawi had become a master at exploiting the contradictions in the system, surrounding himself with like-minded clerics who issued fatwas to condone suicide bombings and the killing of Muslim innocents, actions that would be regarded as anti-Islamic under almost any reasonable interpretation of Koranic texts.

“We denounce and condemn extremism, radicalism and fanaticism today, just as our forefathers tirelessly denounced and opposed them throughout Islamic history,” al-Tamimi read. “On religious and moral grounds, we denounce the contemporary concept of terrorism that is associated with wrongful practices, whatever their form may be. Such acts are represented by aggression against human life in an oppressive form that transgresses the rulings of God.”

In any case, President Bush was adamant about keeping on schedule. Under the White House’s plan, there would be elections for a constitutional assembly, then a new Iraqi constitution, then a second round of voting for a new Parliament, and, finally, a legitimately chosen Iraqi government that would assume responsibility for the country and its myriad problems. Even a single day’s delay would mean postponing the moment when the United States could symbolically hand over the keys and move on. “The president,” Ford recalled, “would not hear of it.” On January 30, 2005, millions turned out to cast ballots in the country’s first democratic election. TV news programs showed smiling Iraqis holding up fingers dyed with purple ink to signify that they had cast their votes. True to Zarqawi’s warnings, insurgents carried out scores of attacks, mostly on polling stations in Sunni areas. At least forty-four people died. U.S. and Iraqi officials declared the election a success. Despite the violence, Zarqawi had failed in his threat to “wash the streets in blood.” Yet, by another key measure, the leader of al-Qaeda in Iraq had achieved exactly what he wanted: throughout the country, from the Syrian border to the Persian Gulf, Sunni voters stayed home. In Anbar Province, the participation rate among Sunnis was a mere 2 percent. Over the next ten months, other Iraqis would approve a draft constitution that would decide how power and oil wealth would be divided among the country’s three maj...

Zarqawi still might have been caught, but for a technical glitch that occurred at the worst possible moment for the Americans. The surveillance drone’s camera chose to reset itself just as Zarqawi was making his escape through the palms. When American soldiers arrived, they were forced to work slowly through the groves, moving carefully to avoid ambush or a booby trap. By then, the fugitives had long since disappeared, leaving the truck wedged against a date palm. Searching the truck, the soldiers made an extraordinary find. Resting on the seat was a laptop computer—Zarqawi’s computer—next to a sack containing a hundred thousand dollars in mixed currencies. The truck’s occupants had been in such a panic that they had not paused to grab even these treasures.

One file contained dozens of photographs, including a series of passport images showing Zarqawi trying on different looks and disguises, from clean-shaven businessman with wire-rimmed glasses to Arab sheikh with a mustache and checkered kaffiyah. Another held Zarqawi’s medical files, with more photos and notes about therapy for various war injuries. There were memos and e-mails laying out the terrorist group’s changing structure, in which Zarqawi carved out an “operational commander” role for himself while allowing Iraqis more visibility as the nominal leaders of al-Qaeda in Iraq. Still other folders contained long e-mails to al-Qaeda leaders, including Bin Laden himself, as well as PowerPoint presentations and priceless video recordings of meetings of Zarqawi’s leadership council, in which the Jordanian discussed strategy and plans. While a few of the individual documents were already familiar to U.S. counterterrorism experts, others were new.

fresh piece of the Zarqawi puzzle turned up in the daily cables from Baghdad. The surveillance net had snagged a singular piece of correspondence: a letter to Zarqawi from al-Qaeda’s number two leader, Ayman al-Zawahiri. Bin Laden’s deputy had authored a six-thousand-word performance appraisal that sought to express the organization’s concern about its newest subsidiary. The CIA’s acquisition of the letter was a closely guarded secret, so Bakos was only allowed to view it from inside a secure chamber that analysts call “the vault.” She read, her fascination growing with every line. The problem, which Zawahiri outlined in restrained prose, was simply this: Zarqawi’s bloodthirstiness was beginning to damage the al-Qaeda brand among Muslims. It was fine to kill Americans and Iraqi soldiers, Zawahiri wrote, but the car bombings, the attacks on Shiite mosques, and the gory execution videos were sending the wrong messages. To ordinary Muslims, images of dead Shiite children and beheaded Bulgarian truck drivers were not inspiring, they were repulsive. “The mujahed movement must avoid any action that the masses do not understand or approve,” Zawahiri warned.

The outlines of the woman’s unhappy life emerged slowly, between bouts of quiet sobbing. Rishawi came from the volatile heartland of Iraq’s Sunni tribal region, the sister of two men who had joined Zarqawi’s insurgent movement in the early weeks of the American occupation. One of her brothers had become a midlevel officer with AQI before being killed by U.S. troops in the town of Fallujah. The Americans had also killed a second brother and a brother-in-law. The woman had been distraught over their deaths, and she felt a tug of obligation: according to tribal custom, Sunni Iraqis are obliged to avenge the killings of family members. The fall of 2005 brought a painful anniversary—one year since the first brother’s death—along with the news of the first use of women as suicide bombers in the Iraqi capital. The authorities had been taken by surprise; females were usually waved through security cordons, and their loose-fitting abayas, together with Iraqi taboos against searching women, made it easy to conceal explosives.

What Abdullah meant was not entirely clear at the time, perhaps even to him. But that day marked the beginning of a shift in Jordan’s security policies. The Mukhabarat prided itself on keeping Jordanians safe, and the monarchy was seen as a reliable partner in sharing information about suspected terrorists with other countries, including the United States. But now Jordan would take a much more aggressive posture against al-Qaeda. Breaking with a long reluctance to work directly with U.S. troops, the monarchy began to deploy specially trained Mukhabarat teams to help American special-forces operators break up terrorist cells inside Iraq.

A veteran of Algeria’s grisly civil war between radical Islamists and the state, Atiyah cautioned Zarqawi against mistakes that had brought down other jihadist movements that alienated themselves from local populations. “They destroyed themselves with their own hands, with their lack of reason. Delusions. Their ignoring of people. Their alienation of them through oppression, deviance and severity, coupled with a lack of kindness, sympathy and friendliness,” he wrote. “Their enemy did not defeat them, but rather, they defeated themselves, and were consumed and fell.”

called itself the Mujahideen Shura Council. Zarqawi would take a less prominent role as a strategic adviser, a move intended “to dismiss all the differences and disagreements,” according to a statement issued by the new group in January 2006.

“In Iraq, time is now beginning to be of service to the American forces and harmful to the resistance,” Zarqawi wrote in this memo, later found in one of his safe houses. He described Iraq’s growing national army as “an enormous shield protecting the American forces,” and he lamented the toll from the mass arrests of his fighters and disruptions in the money supply from abroad. He began thinking aloud about unconventional ways to knock the Americans off balance and restore AQI’s momentum. What if the United States could be somehow drawn into a war with Iran? he wondered. Well aware of the intelligence debacles behind the U.S. decision to invade Iraq, Zarqawi mused about his chances of planting false evidence that could provoke U.S. fury against Tehran. Perhaps he could launch a terrorist attack against the West and plant evidence that would implicate Shiite agents backed by Iran. Or maybe he could disseminate “bogus messages about confessions showing that Iran is in possession of weapons of mass destruction,” he wrote. Perhaps Zarqawi understood the improbabilities of pulling off such a scheme, as there is no evidence that he ever tried.

One was to try even harder to incite sectarian conflict: between Shiites and Sunnis, Shiites and Kurds, Shiites and just about everyone.

Before dawn on February 22, 2006, five armed men in military uniforms walked into the courtyard of the thousand-year-old al-Askari Mosque, a revered shrine in the heart of the ancient Iraqi city of Samarra. The morning was moderately cool, and a crescent moon, penetrating through thin clouds, reflected off the mosque’s iconic gold dome, one of the most celebrated structures in all of Shiite Islam. Moving quietly, the gunmen managed to subdue the mosque’s guards and proceeded to plant explosive charges along the mosque’s roofline.

The bombs themselves injured no one—there would be no accusations this time that Zarqawi had murdered innocent Muslims. But destruction of the shrine touched off waves of killings and reprisal killings as rival bands of Shiites and Sunnis shot and hacked their way through the town, sometimes wiping out entire blocks. Days later, the body count at the city morgue had surpassed thirteen hundred, and the entire country appeared to be teetering. At the U.S. Embassy, the diplomat Robert Ford’s office convened a series of urgent meetings with Iraq’s political and religious leaders, pleading for calm. A confidential memo dispatched to the White House that evening bore the ominous heading “Sectarian Nerves on Edge.”

Bush administration officials quickly concluded that Zarqawi was to blame, and they watched in growing dismay as the toll from sectarian killings grew to surpass anything the Jordanian might have accomplished with explosive powder and shrapnel. Senior White House officials came to view the Samarra bombing as one of the tipping points of the war. Some credited Zarqawi for having “lit the match” that set the nation’s sectarian tensions fully ablaze.

There was little need for bluster; the sectarian fire that Zarqawi had tried to ignite was sweeping through Iraqi provinces on its own momentum. Within days of the hotel bombs in Amman, U.S. soldiers in Baghdad discovered a secret underground prison where Shiite police officers systematically beat and tortured Sunni detainees. Inside the converted bomb shelter, the soldiers found nearly two hundred malnourished Sunni men, many of whom later described a daily regimen of beatings and electric shocks. The bunker was located less than a block from the residence of Iraq’s Shiite interior minister, Falah al-Naqib, who would later acknowledge that “there were some mistakes made.” The discovery offered proof that the random sectarian attacks initiated by Zarqawi had prompted organized campaigns in response, supported in some cases by institutions of the Iraqi government. Even jihadists who questioned Zarqawi’s war against the Shiites began to believe that the Jordanian’s strategy was succeeding.

At the ceremonial meeting in Assad’s hilltop residence, Ford watched the Syrian leader carefully for clues about the personality behind the charcoal suit. Seated in a powder-blue chair in a reception hall, Assad was affable and charming, showing no trace of the condescension so common among the region’s palace-bred autocrats. He was tall and narrow-shouldered, with pale-blue eyes, and a trim mustache offsetting a weak chin; he spoke with the quiet self-assurance of a man who had grown into middle age without having to raise his voice. The meeting was going pleasantly enough until Ford gently broached the subject of the State Department’s most recent report on human rights, with its lengthy catalogue of Syrian abuses, including official repression, torture, and murder. No sooner were the words uttered than the host’s entire countenance changed. The volume never varied, but Assad was enraged. “The last country in the world that I’m going to take advice from is the United States,” he said in a low snarl. “Not on human rights. Not after what you’ve done in Guantánamo, Abu Ghraib, and Afghanistan.”

Instead, with brutal displays of force—nearly all of it captured on cell-phone cameras—the Syrian leader managed to unite much of the country against him. He still controlled considerable assets. Of twenty-one million Syrians, Assad could reliably depend on members of his minority Alawite sect, which controlled the country’s elite army divisions and the security services. The remaining 87 percent of the population would have to be bought off or subdued. But how long could that last? Not long. That was the consensus view of White House officials who watched Syria implode in the spring and summer of 2011. By April, Assad was deploying army troops against unarmed civilians. By May, tanks barricaded the main squares of Hama, and snipers picked off individual protesters from rooftops. The demonstrations cooled for a while, then roared back to life in the early summer, seemingly unstoppable.

The daily search started with an astonishing array of electronic sleuthing tools, capable of sweeping up every mobile-phone call, e-mail, and text message sent by anyone, anywhere in Iraq. When someone dialed a number that matched a phone in Balad’s growing terrorist database, technical teams went to work, tracking the caller’s location and movements. U.S. drones and airplanes served as mobile cell towers that could tap directly into calls made from suspicious phones. Airborne surveillance cameras gave U.S. spies enhanced capabilities to trail suspicious cars and trucks.

One of the camp’s senior managers acknowledged that the Camp Bucca of Baghdadi’s time was both dysfunctional and, from the perspective of commanders looking to quell the Sunni insurgency, counterproductive. By corralling Islamist radicals and ordinary Iraqis in a lawless desert pen, U.S. officials inadvertently created a “jihadi university” that helped inculcate Islamist ideas into a new generation of fighters, the officer said.

“Extremists mingled with moderates in every compound,” Lieutenant Commander Vasilios Tasikas, who ran legal operations at the prison, wrote in a 2009 essay in the Military Review. “Unfortunately, U.S. forces had adopted a model of detention operations that assumed that those interned were ‘all bad guys’ to be ‘warehoused’ for an indeterminate amount of time and released randomly in arbitrary groups. This approach was not only naïve and myopic, it was also dangerous; predictably, it fueled the insurgency inside the wire.”

Despite his lack of military experience, Baghdadi offered certain advantages to the group. One was the Sharia scholar’s willingness to provide religious cover for acts of brutality that clerics around the world had condemned as un-Islamic. Everything that made the group so widely reviled—the beheadings, the suicide bombings, the kidnappings, the extortion, the war against Shiites, the spilling of so much innocent Muslim blood—Baghdadi not only endorsed, but declared legally justified under Islamic law. His other great asset was his suitability for the role of caliph—symbolically important for an organization that wanted its “Islamic State” claims to be taken seriously. Baghdadi, with his genealogical and scholarly pedigrees, could aspire to heights of leadership beyond Zarqawi’s grasp. Over the years that followed, Baghdadi worked deliberately to prepare himself for the mythical role to which he had been divinely appointed, according to a U.S. official familiar with Baghdadi’s history. “He cloaked himself with all the right religious credentials, and paid close attention to imagery, to clothing, to the way he moved and talked,” the official said. “He would go to great lengths to show that he was in his rightful place.” It was in the service of that goal that Baghdadi dispatched his emissaries across the border in August 2011, seeking a Syrian launchpad for the caliphate that still languished on the ground in his native country. A successful venture, in Baghdadi’s view, wou...

disappeared, as stories circulated about sectarian killings and assaults. In her mostly Sunni neighborhood, flyers began appearing in doorways, warning of coming attacks from Alawite death squads. At the same time, al-Ameer’s Alawite friends were getting similar warnings about Sunnis. Meanwhile, the regime’s notorious goon squads—hired gangs called shabiha or “ghosts”—snatched women and children from the streets and then returned them, sometimes dead, other times beaten and tortured, with tales about being brutalized by Alawite thugs. By late 2011, a new chant was added to the repertoire at the daily protests: “Christians to Beirut, Alawites to their coffins.” Then it was al-Ameer’s turn to be caught. She was on her way to a visit with her mother when police officers pulled her off a public bus and brought her to one of the intelligence service’s special interrogation centers in Damascus. Again she believed she would die. Instead, her captors locked her in a cell and forced her to listen as they beat and tortured one of her friends. When al-Ameer still refused to break, the officers strapped her into a chair and attached electrodes to her temples and chest. The pain shot through her body like liquid fire as her captors laughed to see if she would cry out. “We’re going to exterminate all of you, you Sunnis!” one of the officers said, using epithets that al-Ameer, years later, could not bring herself to repeat. After she had spent eighty-five days in prison, family members w...

“We hereby bring the Islamic nation the glad tidings of a long-awaited event,” said Abu Mohammad al-Julani, the man dispatched into Syria five months earlier by the Islamic State’s central branch in Iraq. A call for help had been heard, Julani said, and “what else could we do but answer the call?” By the time the video aired, Julani’s band had been offering its brand of assistance for at least three months. A few weeks earlier, a pair of perfectly synchronized car bombs had exploded outside one of the Assad regime’s security offices in Damascus, killing forty-four people and serving notice that a new type of combatant had entered the fray. The al-Nusra Front later claimed responsibility; terrorism experts had already concluded that the culprit was likely al-Qaeda or someone trained in the group’s methods.

Kuwait, one of the biggest providers of private funding, a preacher named Hajjaj al-Ajmi, launched a Twitter campaign to persuade his 250,000 followers to donate money to special bank accounts set up to help the rebels. “Give your money to the ones who will spend it on jihad, not aid,” al-Ajmi exhorted donors in a video pitch posted to YouTube in 2012. Other supporters held Twitter “auctions” to sell off cars, boats, vacation properties—anything that could be exchanged for cash to help the Syrian rebels. A few wealthy donors—sometimes called “angel investors” by those who benefitted—arranged visits to the battlefield to hand-deliver suitcases full of cash, and were sometimes rewarded by having a rebel brigade rename itself in the patron’s honor.

“Where are these revolutions going to stop?” he asked one day during a private chat with one of his Gulf counterparts. “I hope these revolutions continue in the Middle East,” said the other sovereign, a man who has publicly acknowledged sharing many of the Islamists’ religious views. “I’ve paid for the support of these groups, and they owe allegiance to me.” “That’s not how it works,” Abdullah snapped. “You have moved yourself down on the menu. But eventually they’re going to come after you.” The flow of money and weapons into Syria continued unabated. In private talks with his aides, Abdullah could see the possible pathways that history might take. One possibility—that Assad, backed by Iran and Russia, would emerge victorious through brute force—now seemed unlikely. An alternate path would see the “loonies”—radical Islamists—seize control in Damascus, though that also seemed remote. A third possibility, if the region were exceedingly lucky, would be a negotiated settlement in which Assad would be forced to surrender power to a Syrian unity government, one that would oversee elections while leaving essential institutions in place to ensure order and safety for Syria’s citizens. There was, however, yet a fourth possible outcome: prolonged violence with no clear resolution. In this scenario, the country known as Syria would disintegrate in a maelstrom that slowly consumed other countries in its wake, destabilizing the region for decades to come. Abdullah, in his discussions ...

“We weren’t convinced that al-Nusra was coming for us next week, but we were worried about all these trained jihadis coming back to Europe and having a passport,” the senior adviser said. “This is when the mood music in the Situation Room started to change.” From the CIA to the Pentagon, the concerns were given voice in official reports. The State Department’s Syria team, which included Ford and other refugees from the now closed U.S. Embassy in Damascus, put together a document for Undersecretary of State William J. Burns that sought to put the latest events and trends in context. The classified report was never made public, but the point, as Ford recalled afterward, was that Syria had drifted into a kind of lawlessness that dangerous groups were beginning to exploit.

In the State Department’s analysis, the “extremists” consisted mainly of the al-Nusra Front, which was looking increasingly dangerous as the year 2012 neared its end. Not only was the group indisputably linked to al-Qaeda terrorists, but it also was emerging among the rebels as one of their most effective military organizations, as well as a preferred destination for many of the incoming foreign fighters. Even al-Nusra’s relatively moderate—by al-Qaeda’s standards—behavior was cause for alarm. Though its leaders insisted on imposing strict Sharia law in villages they “liberated,” they largely avoided violence against Muslim civilians. Some al-Nusra units actually made a show of picking up trash and delivering food and water to battered neighborhoods, acts that won them respect and even admiration. What would happen, analysts wondered, if this new brand of “jihadist lite” truly caught hold? What if Syria—a neighbor to Israel, and a true linchpin of the Middle East—were to become the first of the Arab Spring dominoes to fall to a government that was al-Qaeda in all but name?

Since the beginning of the uprising, the White House’s entire national security team had been unanimous in opposing direct U.S. interference in Syria’s internal conflicts. By the late summer of 2012, the prevailing view had shifted in one significant respect: Key members of President Obama’s inner circle now regarded the notion of arming Syria’s moderate rebels as undesirable yet necessary—the least objectionable out of a list of exceedingly bad options.

At the time, the White House stuck to its policy of providing nonlethal support to the opposition while using diplomatic pressure to bring about Assad’s resignation and a new interim government. But the results had been frustrating at best. Kofi Annan, the former UN secretary-general in charge of peace negotiations, resigned in disgust over the summer after repeated setbacks, including Russia’s insistent blocking of any measure before the world body that might pressure Assad into stepping down. On the ground, the fighting intensified, and yet neither side could gain a decisive advantage. The Syrian president replenished his weary forces with Hezbollah fighters from Lebanon and used his air force to bomb and strafe rebel positions. Turkey and the Persian Gulf countries sent fresh torrents of cash and weapons to back a rebel force increasingly dominated by Islamists. For the Americans, as Hillary Clinton would later acknowledge, “every option appears worse than the next.”

Clinton began privately pushing for what she would call a “carefully vetted and trained force of moderate rebels who could be trusted” with American weapons. As she described the events in her book Hard Choices, she invited then CIA director David Petraeus to her house for lunch in July 2012 to brainstorm about ways to recruit and build such a force. If America “was willing finally to get in the game, we could be much more effective in isolating the extremists and empowering the moderates inside Syria,” she wrote. By late summer, following extensive meetings with NATO counterparts and rebel leaders, Clinton was “reasonably confident” that an effective strategy could be put in place, she said. Petraeus’s CIA put together a plan for building, training, and arming a moderate rebel army that could eventually overthrow the regime and establish authority in provinces now effectively controlled by Islamists. The plan was presented to President Obama at a White House meeting in late August, and Panetta was among the core group of senior advisers to argue for its acceptance. “We’re outside the game,” Panetta would argue. “We don’t have any credibility with [Syrian moderates]. We’re giving them nonlethal assistance and they’re dying.” Panetta was not naïve about the risks. Even the most carefully vetted rebel group might decide to switch sides, or commit a massacre using American-supplied guns. Arms given to friendly fighters could easily end up in the wrong hands. “There’s always a...

In the end, Obama, who had been elected on a promise to end America’s involvement in Middle East wars, rejected the CIA plan. The situation could change in the future, the president allowed, particularly if Assad crossed the administration’s “red line” of using or transferring his stocks of chemical weapons. But for the moment, there would be no shipments of U.S. military hardware to Syria’s rebels. The debate would erupt again, but an opportunity had passed. Clinton, disappointed, plunged back into the task of seeking the elusive diplomatic accord that would end the conflict. She also secured an agreement for increasing humanitarian aid—more blankets, food, computers, phones—for Syria’s opposition.

In explaining the change, Baghdadi recounted a history of the group’s previous incarnations, starting with the early days under Zarqawi, the founder and esteemed “mujahid sheikh.” He told a story of how Zarqawi, when he first swore allegiance to Osama bin Laden, explained privately to his followers that he did so for strategic reasons, and not out of some genuine devotion or need. “I swear by Allah, I didn’t need from him money or weapons or men, but I saw in him a symbol,” Baghdadi quoted Zarqawi as saying. Now, in a similar vein, it had become strategically important for the Syrian offshoot organization to unite symbolically with its parent, he said. “Al-Nusra Front was only an expansion of the Islamic State of Iraq, and part of it,” Baghdadi said. “So we declare, keeping our trust in Allah, the abolishing of the name of the Islamic State of Iraq and the abolishing of the name of al-Nusra Front, and joining them under one name—the Islamic State in Iraq and al-Sham—and also uniting the banner, which is the banner of the Islamic State.”

The message cut a fresh trough of despair across Western capitals. Analysts had long assumed that the al-Nusra Front was an Islamic State offshoot, though one that had at least temporarily decided to soften its image. Now Baghdadi was asserting publicly that the two organizations were one and the same. Moreover, the more fearsome Iraqi side was taking charge. But the most emphatic response came from a surprising source: Baghdadi’s presumed partner in the merger. No one had bothered to secure the consent of the al-Nusra Front, which, as it turned out, had no intention of fading away. The al-Nusra leader, Abu Mohammad al-Julani, fired back two days later with an audiotaped message repudiating everything Baghdadi had said. “Al-Nusra Front’s banner will remain, nothing will be changed in it,” said Baghdadi’s old comrade and former friend.

Julani then appealed to the world’s preeminent jihadist, al-Qaeda’s leader, Ayman al-Zawahiri, to settle the dispute. The longtime deputy of Osama bin Laden had famously quarreled with Zarqawi over beheadings and other shock-theater tactics, and the old Egyptian had been equally unhappy with Zarqawi’s successors. On June 9, 2013, Zawahiri published an open letter, ordering a halt to the merger and scolding Baghdadi for attempting such a thing without consulting with him first. In an astonishing rebuke, he decreed that Baghdadi would be on probation for a year as leader of t...

Finally, to ensure that no fighting erupted between the groups, Zawahiri said he was sending a personal emissary, an al-Qaeda elder statesman named Abu Khalid al-Suri, into Syria to mediate any future disputes. “Muslim...

It was a remarkable, and strikingly public, feud between branches of the al-Qaeda network, one that not only contained echoes of the dispute between Zarqawi and Bin Laden but also evoked the earlier rift between Zarqawi and his one-time mentor, Abu Muhammad al-Maqdisi. The squabbling continued to play out for months, with Islamist scholars and pundits around the world taking sides in Internet forums and chat rooms, arguing over which leader best represented the movement’s future. Baghdadi dealt with al-Qaeda’s advice just as Zarqawi did: he ignored it. He issued one additional statement, claiming that he was merely following orders from a higher authority. “I prefer the command of Allah over the command that contravenes it,” he said. And then he proceeded to launch his unified Islamic State of Iraq and al-Sham as though the al-Nusra Front did not exist. Throughout 2013, bands of ISIS fighters would fan out across nearly every part of Syria, from the lawless eastern desert to the populated corridors along the Turkish and Jordanian borders and to the very suburbs of Damascus. But before the assault began in earnest, Baghdadi had a few matters of business to attend to inside Iraq. He first commenced an organizational overhaul, appointing regional governors, Sharia advisers, and military commanders to oversee operations locally throughout Iraq and Syria. The Islamic State would function like a real government, with flow charts for acquiring approvals and special departments in...

Abu Ibrahim vividly remembered ISIS’s triumphant entry into the city. The prelude was a week of heavy street fighting that left scores of bodies lying in the streets and most of the city’s civilians trapped in their houses, afraid to venture out for fear of being hit by sniper fire. Stores and bakeries closed, and many families ran out of food. “If you had bread, it was like having a million dollars,” he recalled. “These were the hardest days.” The fighting gradually waned, as militiamen opposed to ISIS either fled or switched sides. Then, all at once, columns of foreign fighters—mostly Iraqis, Abu Ibrahim later learned—appeared in the streets. ISIS’s men raised their black flags over the main government buildings and claimed Raqqa as the new capital of the Islamic State. “They walked around with their weapons, saying everything was going to be good now,” he said. “They even began removing the bodies that had been lying around in the streets.” Many in Raqqa initially did not know what to make of the newcomers, Abu Ibrahim said. Some were relieved at least to see the fighting come to an end. Shops reopened and the city began to feel safe again. But then the executions started. The first one witnessed by Abu Ibrahaim involved a young man that ISIS commanders described as a criminal, though the man’s offense was never made clear. The condemned man was forced to stand in Raqqa’s main plaza, where his sentence was publicly read. Then he was shot in the head as a small crowd loo...

In Raqqa’s downtown markets, bearded, rifle-toting foreigners seemed at times to outnumber locals as the ISIS occupation took on a look of permanence. The group’s coffers were fattening quickly, between the fees and bribes assessed to businesses and the sale of more than forty thousand barrels of crude oil per day from oil wells captured by ISIS in its march across the Syrian desert. The jihadists who had been so anxious to capture Raqqa a few months earlier seemed in no hurry now to push on to further conquests, Abu Ibrahim noted. The Islamic State’s men would turn aggressive whenever there were punishments to mete out, but between executions and floggings, Abu Ibrahim would see them relaxing in restaurants, gawking at Western Web sites in Internet cafés, or buying knockoff Viagra from the drugstores.

For Moustafa, now two years into his job and more deeply engaged in Syria’s struggle than he could ever have imagined, it was another ominous turn. By early 2013, Moustafa had all but despaired of the possibility of a major U.S. intervention in the conflict. Now he spent most of his time looking for practical ways to improve the lives of Syrians in areas of the country outside Assad’s control. But for every forward step, there were steps back: infighting among rebel groups; widespread corruption, sometimes fueled by suitcases of cash from Arab governments; a growing sectarian divide that hampered cooperation and sometimes led to reprisal killings. Soon the ISIS problem—the presence of heavily armed extremists at war with everyone else, their replacement of existing courts and police departments with their own system of justice—would eclipse all others, further complicating the efforts by moderate rebels to win Western support for the opposition. Moustafa’s perspective on Syria’s unraveling now came at close range. He traveled to Syria constantly, often venturing within a few miles of the ever-changing front lines. He spoke and met regularly with rebel commanders, part of a growing personal network that also included journalists, international relief workers, foreign diplomats, and wealthy donors. After the U.S. Embassy in Damascus closed, Moustafa’s reports from Syria became a useful window into parts of the country the Americans could no longer monitor directly. When alle...

In late summer, the Assad regime’s chemical-weapons attack on civilians in Ghouta, a Damascus suburb, briefly raised expectations of a Western military response. After U.S. intelligence agencies released evidence showing that Assad’s army had fired canisters of sarin gas into residential neighborhoods on August 21, Obama signaled his intention to punish Assad for crossing America’s one clear “red line.” Yet, despite widespread outrage over the deaths, the White House could not muster the political support for a military strike. Congress blocked a vote on a resolution authorizing air strikes against Assad, and the Parliament in Britain—a country presumed to be a key ally in any military campaign—rejected a similar proposal by Prime Minister David Cameron’s Tory government. President Obama managed to secure a deal, with Russia’s help, to remove all chemical weapons from Syrian territory, and the prospect of military intervention was again pushed aside. Among Syria’s opposition leaders, the collapse, in their view, of Western resolve after the Ghouta attack was a tougher psychological blow than the chemical attacks themselves, Moustafa said. Some rebel groups that had previously aligned themselves with the moderate Free Syrian Army simply gave up and joined the Islamists, who at least paid better salaries. “People had been ecstatic when they believed the U.S. was finally going to act,” Moustafa said. “It was one of those moments when everyone remembers exactly where they were...

At the root of the spring’s dramatic events was a conflict between Iraq’s Shiite government and one Sunni tribe, the Dulaims. It happened to be the familial clan of Zaydan al-Jabiri, the Ramadi sheikh and rancher who had been caught up in the fight against Zarqawi nearly a decade earlier. Zaydan had first watched his fellow tribesmen take up arms against the Americans in 2004, amid soaring anger over the occupation. He had then been a key participant in the anti-Zarqawi backlash known as the Anbar Awakening, when tribal militias helped drive insurgents out of their villages. Now the currents had shifted again, and Zaydan would watch with approval as his entire tribe rose up against an Iraqi government that many Dulaims saw as a greater threat than Zarqawi had ever been.

“The ones who are leading now were thieves, bandits, and sectarian religious parties,” Zaydan said, referring to the cohort in power since Prime Minister Nouri al-Maliki’s narrow election in 2010. “Even with all the bad things the Americans did in Anbar, they didn’t kill people in mosques, and they respected our religion. Those who are with the Iranians do not. They want to get rid of everything called ‘Sunni.’ I’m not saying the Americans were great, but they were better than these.”

Then, beginning in late 2012, Sunni relations with the central government turned sharply worse. On December 21, government security forces raided the home of Rafi al-Issawi, a popular Sunni politician and a former Iraqi finance minister who had been outspoken in his criticism of the Maliki government. Thousands of Dulaims took to the streets in Fallujah, some of them carrying banners that read “Resistance Is Still in Our Veins.” The rally eventually grew into a weekly pan-Sunni protest that spread to multiple cities and continued for month after month. After more than a year of such protests, Maliki had finally had enough. On December 30, 2013, he sent security forces into Ramadi to shut down the demonstrations and break up a tent city that had sprouted in one of the city’s plazas. Clashes broke out, and on New Year’s Day 2014, protesters set fire to four Ramadi police stations. On January 2, rioting spread to neighboring Fallujah. On January 3, a convoy of armed ISIS militants rolled into town. The jihadists joined tribal militias in street battles with outmatched police and troops, inflicting more than one hundred casualties. Finally, on January 4, the remnants of Fallujah’s government evacuated the town, and Islamic fighters raised the black flag of ISIS over the city’s administration building.

The Dulaimi-ISIS alliance quickly drew support from other Sunni tribes as well as from a shadowy organization of former Baathists known as the Naqshbandi Order. The Sunni pact waged seesaw battles with army troops for several weeks for control of Ramadi and five other cities, but an uneasy truce settled over Fallujah, with ISIS firmly in charge of the center of t...

ISIS seized the moment to fire off a stream of propaganda images on Twitter, showing its victorious troops parading around the center of the same city from which U.S. marines had ousted Zarqawi’s men a decade earlier. Among the fighters posing for photographs was Abu Wahib al-Dulaimi, the flamboyant, publicity-obsessed ISIS commander for Anbar Province who had shot the three Syrian truck drivers on an Anbar highway the previous spring. In one frame, he grimaces, rifle in hand, next to a burning police car, wearing a black overcoat and boots like a Western gunslinger. In another, he walks through one of the captured police stations carrying a stack of files, like some kind of doomsday office clerk. Iraqis who saw the images might have noticed the familiar last name: Abu Wahib’s surname identifies him as a member of the Dulaim tribe, making him a kinsman to the men who had organized the Fallujah protests. Enemies before, they were now officially on the same side. At the White House, President Obama’s security advisers viewed the same images with dismay. Administration officials quickly announced plans to speed up the delivery of promised military aid to the Maliki government, incl...

In fact, ISIS already was moving to settle scores in Anbar neighborhoods that had welcomed the group’s arrival. Abdalrazzaq al-Suleiman, a Sunni tribal sheikh and one of Zaydan’s Ramadi neighbors, happened to be away on business when a truck filled with black-clad fighters drove up to his farm. The jihadists shot several of Suleiman’s bodyguards, destroyed his cars, and then leveled his house with explosive charges. Suleiman’s offense: Eight years earlier he had been a leader of the Anbar Awakening movement that cooperated with U.S. troops in driving Zarqawi’s followers out of the province. “They stole everything that was in my house before they blew it up,” said Suleiman, who moved to Jordan for safety. “It was my duty and honor to work with the Americans as a tribal leader fighting terrorism. But now it feels like we’ve been abandoned. We were left in the middle of the road.”

But ISIS also was clearly learning and adapting, gaining new capabilities under Baghdadi’s oversight, Flynn explained. Baghdadi was a more careful planner, and he was willing to be both patient and strategic in building alliances and support networks. In short, ISIS’s recent gains in Iraq had been no accident. “They got better because they saw how they were defeated,” Flynn said. “Zarqawi was trying to create a civil war immediately to turn the situation in Iraq to his advantage. But the one big mistake he made was that he did not gain enough favor with the tribes in Anbar Province. He stole authority from them and then really abused it, because he was a vicious guy. This new crowd realizes that and they’re operating differently.” Slowly, Baghdadi had repaired relations with the Sunni tribes, Flynn said, echoing the assessment made by Zaydan and other tribesmen. The ISIS leader exploited Syria’s uprising to rebuild his finances while bringing in fresh recruits and a renewed sense of purpose. And he also had built an organizational structure made up of subject experts in fields as diverse as housing and transportation and strategic messaging.

At 4:30 p.m. came the decisive blow. A large water truck packed with explosives barreled into the hotel, exploding in flames and killing or injuring many of the Iraqi force’s senior officers. “The sound shook the whole of Mosul,” said Obeidi, whose leg was torn open by the blast. The rest of the army’s defenses collapsed soon after that. By evening, police and army troops were discarding their uniforms and fleeing the battlefield in civilian clothes. Those who were caught were lined up in groups and shot. By noon on June 10, just four days after the start of the offensive, the jihadists controlled Mosul’s airport and most of the town’s central district. They emptied the cash reserves from downtown banks and stripped an Iraqi military base of millions of dollars’ worth of U.S.-made weapons and equipment. Then they seized control of Mosul’s main prison, releasing the Sunni inmates and summarily executing the others—about 670 Shiites, Kurds, and Christians. By the end of the day, Mosul, Iraq’s second-largest city, was fully under ISIS’s control. Iraq’s army eventually regrouped and launched a counteroffensive that stopped ISIS from advancing into Baghdad, even as ISIS continued to gain ground in other parts of the country. By late June, the terrorist group’s total land holdings, from western Syria to central Iraq, was greater than the areas of Israel and Lebanon combined. The man who presided over this expanse now controlled more than just real estate. He owned oil wells, ref...

Some Iraqis, particularly the descendants of the East Bank tribes, such as Zaydan al-Jabiri, had been willing to cut a deal with ISIS in order to free themselves from repressive Shiite rule. But the Islamists who seized control of Fallujah and Mosul turned out to be every bit as brutal as their Raqqa counterparts. Captured Iraqi soldiers were paraded before cameras and then gunned down in open pits. Suspected apostates were murdered in the streets, and priceless Babylonian artifacts—a source of cultural pride for generations of Iraqis—were smashed into powder. Such acts were welcomed by small numbers of religious conservatives whose views aligned with those of the Islamists. But among the Iraqis who had welcomed the Islamist guns, few were interested in Islamist rule. Now it was too late to rescind the invitation.