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“Like watching a freight train coming”

Long before Syria’s civil war—before the uprising and the bloody street clashes, before the massacres, the gassings and the thousand brutal acts that followed—the government’s Military Intelligence Directorate built a large torture palace for political prisoners on the southern outskirts of Damascus. The Branch 235 headquarters was a modern building that stood nine stories tall, not counting the three underground floors where inmates were locked away in coffin-like cells. Within the city’s small dissident community, it was dubbed the “Sheraton,” although many a guest who disappeared behind its imposing outer wall was never heard from again.

The start of the war brought Branch 235 a flood of new business, and in the spring of the war’s second year, its grim practitioners were busier than ever. On the steamy morning of May 10, 2012, the line of commuters arriving to work the day shift stretched around the block, mingling with the modest sedans of teachers and families heading toward the elementary school on the same street. No one seemed to notice the young man who pulled up to the curb by the security gate at exactly 7:10 a.m., pausing for an instant before reaching for the detonator attached by wires to a large cache of explosives in the trunk.

The blast was so powerful that it flattened a section of the concrete wall and turned nearby cars into infernos. Dazed commuters abandoned their vehicles to stare at the ruined wall as police, soldiers, and rescue workers scrambled over the broken concrete to search for victims.

Then came a second explosion, vastly larger than the first. A separate car bomb, later calculated to contain at least a ton of explosives and shrapnel, cut through the crowd of bystanders and peeled off the Branch 235 building’s entire nine-story facade. It gouged a bus-sized crater in the asphalt and shook homes and offices in downtown Damascus, more than two miles away. By the evening, rescue workers had treated nearly four hundred wounded and recovered fifty-six bodies, making the attack the deadliest of the war so far.

Blame quickly coalesced around a single suspect, and the following day, May 11, the shadowy group that called itself al-Nusra Front confirmed the suspicions by taking credit for the killings in a brief video message. The video was simply a white screen with an unseen narrator reading words that appeared in Arabic characters. In the background was a recording of a nasheed, a chanted prayer in an a cappella style popular among Islamist extremists.

“We kept our promise,” the narrator said. “What is coming will be more calamitous, God willing.”

Within minutes, the warning was being translated and parsed in dozens of capitals around the world. It commanded a prominent spot in President Barack Obama’s daily intelligence briefing at the White House, and echoed through secure conference rooms at CIA headquarters in Langley, Virginia, where analysts had followed the emergence of the mysterious terrorist group with foreboding. At the Pentagon, U.S. secretary of defense Leon Panetta stopped to ponder the meaning of the twin explosions. Until now, there had been no instances in Syria of this kind of expertly timed, double suicide bombing on a crowded street at rush hour. None of Syria’s secular rebel groups had ever killed in such an indiscriminate way. These were the unmistakable hallmarks of al-Qaeda in Iraq, the bloodthirsty jihadist group that had unleashed mayhem on U.S. troops and tens of thousands of ordinary Iraqi civilians for nearly a decade. Its leader, Abu Bakr al-Baghdadi, now called his band of murderers the Islamic State, and al-Nusra Front was the group’s first official Syrian franchise.

“An al-Qaeda presence in Syria,” Panetta mused. It was an ominous sign.

Only a handful of analysts knew Baghdadi’s name, and no one in the West had fully grasped the terrorist leader’s plans for Syria. But at that moment, in a cramped office a short walk from Panetta’s suite, a small team of Pentagon analysts was beginning to grapple with a chilling possibility. The scenario had been discussed hypothetically for months. Now, in the opinion of the team’s fifty-three-year-old leader, the threat had become alarmingly real.

Andrew C. Weber was, in the spring of 2012, the Pentagon’s assistant secretary for nuclear, chemical, and biological defense programs. He was slightly built, with a receding hairline and intelligent blue eyes, and a quiet, understated demeanor that belied an adventurous past. In an earlier life, Weber had personally led operations to smuggle loose nuclear weapons components from former Soviet republics after the fall of the communist government in Moscow. What Weber was seeing now in Syria was as troubling as anything he had witnessed there.

His office, at the end of a long corridor on the Pentagon’s third floor, was adorned with oversized windows that looked out onto a courtyard. Weber kept the shades drawn at all times because of the highly sensitive intelligence he kept there. There were paper maps, delivered every morning with the day’s classified briefing materials, and special computers from which the most restricted electronic files could be accessed. From his reading, Weber had come to appreciate the exquisite detail contained in page after page of secret memos from the CIA’s files on Syria’s chemical weapons program. Thanks to the dead spy, the agency knew all about Syria’s 1,300-ton stockpile, including where it was made and how it was kept. Tens of thousands of gallons of binary sarin and VX lay scattered across nearly two dozen military bases and storage depots, nominally controlled by an embattled Syrian regime that, in the estimation of every leading intelligence agency in the world, was on the verge of collapse. If the consensus view was correct, Syria’s dictator could topple within weeks, perhaps even days. What would happen to all those weapons then?

Weber had followed the events in Syria since the earliest days of the uprising, with a single-minded focus on the security of the regime’s arsenal of poisons. What had begun as civil protests had become a true civil war, with government troops fighting pitched battles against an army of its own citizens. If President Bashar al-Assad’s government truly began to falter, he reasoned, things could go bad very quickly. A desperate Assad might decide to use his weapons or give them to Iran or another ally. The government might lose control of a few liters of sarin, or the entire stockpile. For such deadly weapons to go missing in the Middle East would be a crisis without parallel in modern history. Of all the reasons to worry about Syria, Weber believed, none posed a more urgent threat to Americans than this.

There are multiple potential disasters, Weber thought. And on top of all of it, now you have al-Nusra.

With the bombings in Damascus, the thought of terrorists hauling tankers of liquid sarin through Turkey and into the heart of Europe did not seem far-fetched. In the weeks after the attack, Weber sat with his staff in a small conference room to study the maps and ponder the awful possibilities. If al-Nusra could penetrate the most secure corners of Syria’s capital, what else was within the group’s reach? In the hills just east of Damascus, in places where fighting now raged, lay the underground storage bunkers and production halls the CIA’s “chemist” spy had helped commission some fifteen years earlier. There, too, were the mixing trucks designed to turn binary sarin into its lethal, final form. How hard would it be for al-Nusra to blast its way into one of the hidden sites and run off with the lethal ingredients for a massive terrorist strike against the West—one that could make the plotters of the September 11, 2001, attacks on New York and Washington seem like amateurs?

“It was like watching a freight train coming,” said a former intelligence official who attended many of the classified briefing sessions on Syria in Weber’s office. “The real nightmare scenario for us then was al-Nusra. Already they were knocking over convoys, garrisons, storage depots. You had the potential for a bunch of very bad stuff getting out and ending up in places where it could have an impact on the world stage. They might not even know what they have, and just get lucky. Then it’s ‘Hold on, look what we’ve got.’ ”

Weber was convinced that the theft would be deliberate. Baghdadi possessed the capability and the will to pull off such an act. Sooner or later, the allure of the weapons would prove irresistible.

“Here was a well-organized al-Qaeda affiliate, capable of striking right in the very heart of Damascus,” Weber said, recalling his thinking on that May morning as the reports of the twin bombing trickled in. “I thought, My God. This is a nightmare.”

The dream was nearly as old as al-Qaeda itself. It was the subject of fervent discussion and wistful scheming long before Osama bin Laden and his followers thought of the idea of flying airliners into buildings. Bin Laden once went so far as to declare the acquisition of nuclear, biological, and chemical weapons a sacred quest: “a religious duty,” he said in 1998. He had tried multiple times and failed just as often. But if offered a chance to plunder Bashar al-Assad’s chemical stockpile, there could be little doubt that al-Qaeda, or its jihadist rivals, would do it.

The diligence with which al-Qaeda pursued chemical weapons has been amply described, including in accounts by former members of the terrorist group. One of them, a Saudi-born operative named Aimen Dean, worked for a time in an Afghan training camp where different combinations of poisons were tried on rabbits, dogs, and other animals. The camp’s chief “scientist,” Abu Khabab al-Masri, had concluded that nuclear and biological terrorism were too technically challenging for amateurs. But chemical weapons were different. “They are within our reach,” he told Dean.

One day Dean walked into al-Qaeda’s crude lab as Masri was attempting an experiment with hydrogen cyanide gas, a substance that was used as a chemical weapon during World War I. As Dean watched, the gas was pumped into an aquarium in which Masri had placed a live rabbit.

“Within seconds the poor creature started furiously licking its lips,” Dean later recalled. “Its breathing quickened and it started scratching furiously at the side of the tank before losing muscle control, rolling onto its back and convulsing. Finally, it was dead. The whole process had lasted a minute.”

The experiment was impressive in a macabre way, and some of bin Laden’s deputies began to see chemical weapons as a potential game-changer, although the group had not yet devised a method for dispersing them. Dean was sure his comrades would find one, and he became so troubled by the prospects of a large-scale chemical attack that he eventually left the group and became an informant for the British spy service MI6.

“The question that lurked at the back of my mind was how soon such a weapon might spread deadly gas in a cinema in London or in the Paris Metro,” he later wrote.

It very nearly happened. A little more than a year after the group’s September 11, 2001, attack, al-Qaeda developed a device for dispersing hydrogen cyanide, and its operatives were just weeks away from a planned mission to place it in the New York subway system, according to accounts by several former al-Qaeda members. The crude machine, dubbed mubtakkar al-farid—Arabic for “unique invention”—was operated remotely by cell phone and designed to release its lethal contents through a vent. A target date was set for early 2003.

Preparations for the attack were well under way when Ayman al-Zawahiri, then al-Qaeda’s number two leader, got cold feet. At the time, the George W. Bush administration was inching closer to a threatened invasion of Iraq, and the Egyptian terrorist worried that a chemical attack in New York would become a pretext for war. Zawahiri postponed the attack, but by then it was probably too late anyway: Bahraini police, alerted by Britain’s MI6 spy service and its secret informant, nabbed an al-Qaeda operative who was transporting blueprints for the mubtakkar on his laptop. Weeks later, the CIA built and tested a replica of the machine, and agency officials were so alarmed by the results that they brought the device to the White House to brief the president in person, according to author Ron Suskind, who first described the incident in his book The One Percent Doctrine.

“The prototype confirmed their worst fears,” Suskind wrote of the intelligence agency’s internal assessment. “In the world of terrorist weaponry, this was the equivalent of splitting the atom.”

Al-Qaeda’s Afghan laboratory was destroyed by U.S. troops in 2002, and many of its top weapons experts, including Masri, were later tracked and killed in CIA drone strikes. Whether the mubtakkar blueprints survived is unclear. But the jihadists’ interest in chemical weapons most certainly did.

In the same period, in a mountain hideout on the border between Iraq and Iran, Jordanian terrorist Abu Musab al-Zarqawi and his disciples also carried out experiments using dogs and rabbits as test subjects, taking video of the grisly results. By late 2002 the militants were beginning to sketch out ideas and enlist recruits for a future chemical attack in Europe. Those plans were shoved aside when U.S. troops invaded Iraq and Zarqawi saw an opportunity to move to Baghdad to start an insurgency. He called his organization “al-Qaeda in Iraq.” It would later call itself the Islamic State.

Like bin Laden and his followers, ISIS dreamed of a mass-casualty terrorist attack involving chemical weapons. In 2004, Zarqawi sent operatives to his native Jordan to carry out a plan to release a cloud of poison gas over the capital city, Amman. The bombmaker picked for the job had gathered the ingredients and chosen his target when Jordanian intelligence officials learned of the plot and killed or captured the ringleaders in a dramatic shootout. Later, after Zarqawi’s death in 2006, his followers terrorized central Iraq with a string of chemical bombings that released chlorine, a common industrial chemical that can kill or injure if inhaled. In less than a year, U.S. officials recorded thirteen such attacks, including several that wounded American service members. In the deadliest single incident, in May 2007, a chlorine bomb detonated in a crowded marketplace in Diyala Province, leaving, between blast wounds and asphyxiation, thirty-two people dead and at least fifty injured.

Yet chlorine was a weak substitute for the poisons ISIS wanted most. To deliver a blow that would truly shock the world, Zarqawi’s men needed something more powerful: a nerve agent. These could be obtained either by buying or stealing sarin or VX that had been made by someone else; or by acquiring enough real estate, equipment, and technical know-how to start a homegrown manufacturing operation.

For years, both routes remained beyond the terrorists’ reach. In Syria’s war-ravaged provinces, that was about to change.