On a stifling day in August 2013, a police photographer with chiseled features and a military bearing moved hurriedly about his office in Damascus. For two years, as Syria’s civil war became ever more deadly, he lived a double life: regime bureaucrat by day, opposition spy by night. Now he had to flee. Having downloaded thousands of high-resolution photographs [see second set of images below] onto flash drives, he snuck into the empty office of his boss and took cell-phone pictures of the papers on the man’s desk. Among them were execution orders and directives to falsify death certificates and dispose of bodies. Armed with as much evidence as he could safely carry, the photographer—code-named Caesar—fled the country.

Since then, the images that Caesar secreted out of Syria have received wide circulation, having been touted by Western officials and others as clear evidence of war crimes. The pictures, most of them taken in Syrian military hospitals, show corpses photographed at close range—one at a time as well as in small groupings. Virtually all of the bodies—thousands of them—betray signs of torture: gouged eyes; mangled genitals; bruises and dried blood from beatings; acid and electric burns; emaciation; and marks from strangulation. Caesar took a number of these pictures, working with roughly a dozen other photographers assigned to the same military-police unit.

But Caesar himself, like the intelligence operation of which he became a part, has remained in the shadows. He appeared only once in public, last summer, before the House Foreign Affairs Committee, where he wore a hood and spoke through a translator. He spoke briefly, and in a restricted setting, though I have been able to obtain a copy of his complete testimony. He sought and was granted asylum in a Western European country whose name Vanity Fair has agreed not to disclose, for his personal safety.

Since going into exile, Caesar has turned inward, according to several of his closest associates. He has stopped talking with some of his key supporters and will not speak with journalists. He has postponed several meetings with prosecutors in the U.K. and Spain, who would like to use his information to bring war-crimes charges against Syrian officials. But Vanity Fair, in an exhaustive investigation, has managed to piece together Caesar’s story with the help of his lawyer and confidantes, including members of Syrian opposition groups, war-crimes investigators, intelligence operatives, and Obama-administration insiders. All of these people have their own agendas, but their accounts reinforce one another. These individuals have also helped to furnish documents and provide entrée to medical-staff members who worked in the hospitals where Ceasar photographed—on the very wards that are at the center of the Assad regime’s brutally repressive machinery.

Here, then, is Caesar’s tale, revealed in detail for the first time: equal parts Kafka, Ian Fleming, and The Killing Fields.

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From its perch atop Mount Mezzeh, Syria’s presidential palace offers sweeping vistas of Damascus. Bashar al-Assad, the 49-year-old ophthalmologist who has ruled Syria since 2000, has an unobstructed view of Mezzeh military hospital, an unprepossessing structure located at the foot of the hill. Mezzeh, in turn, lies several miles from a sprawling complex called Tishreen, which happens to be where Assad did his residency. Both Mezzeh and Tishreen are run by Syria’s Military Medical Services and are supposed to provide in-patient and emergency treatment for soldiers and civilians. In truth, however, the hospitals are way stations in a sadistic assembly line. They are black sites where enemies of the state—protesters, opposition figures, and ordinary citizens who, often for capricious reasons, have fallen out of favor with the regime—are tortured, executed, or simply deposited after being killed off-site. “These are not hospitals,” one survivor, now a refugee in Turkey, told me during a recent trip I made to the region. “They are slaughterhouses.”

U.S. and European officials allege that Assad’s regime has committed war crimes on an industrial scale. They contend that rarely in the annals of international justice has the evidence of such actions been as voluminous. For reasons perhaps known only to Assad and his inner circle, hospital functionaries, working closely with Syrian intelligence agents, have been carefully documenting the regime’s handiwork, using a distinctive numbering scheme to track victims and keep records of the killings that contain fictitious death certificates.