The former Cobán military base sits six hours north of Guatemala City, in the Highlands region. Today it is known as Creompaz, and the United Nations trains peacekeepers there. At the metal front gate, soldiers stand with rifles on their shoulders. A narrow road leads over a bridge and up a hill to the low-slung, whitewashed main building. From roughly the 1970s through the 1990s, the military ran intelligence operations — and for at least some of that time, prison and torture facilities, prosecutors say — from the complex.  Archaeologists had long been prohibited from excavating on most military bases. The military rejected any talk of exhumations and refused to turn over meaningful documents from the war. Then in 2000, an organization called Famdegua, dedicated to finding the war’s missing, interviewed two witnesses (now in a witness-protection program) who saw civilians taken to the Cobán base. Local authorities initially wouldn’t approve the group’s request to find the bodies, but more than a decade later, in 2012, a judge granted a search warrant, and exhumations began.  By then, Peccerelli had gone from stumbling through his first exhumation to, five years later, heading a 44-person organization. His fluency in English meant Peccerelli could interact easily with American forensics experts and international funders. But also, like Snow, who became Peccerelli’s close friend and mentor and often flew to Guatemala to advise and work with the team, he combined ambitious ideas with an outsider’s fearlessness.  For years, the team had focused on “closed context” cases, massacres that took place in villages where witnesses could help identify bodies through dental work, childhood fractures, a distinctive piece of clothing. But without a DNA lab, identifying most of the 40,000 forcibly disappeared, like those found on military bases, was near impossible. How could the anthropologists link bones disintegrating in the ground for 30 years to Maya families, many of them illiterate, reluctant to trust outsiders and scattered in isolated mountains? After a decade spent planning a lab, training a staff and verifying results, Peccerelli’s lab produced its first genetic matches in 2010 — two years before the exhumations at Cobán began.  From February 2012, when the archaeologists first arrived at the base, until December 2013, they worked seven days a week, uncovering more brutality than they’d ever seen in one place. One grave held 64 men and boys, pressed helter-skelter into a still life of death: skulls face down, broken into pieces; a tangle of pants and legs akimbo, some with thick ropes encircling their ankles. Just yards away, in another grave, lay 41 women with 22 children under the age of 4. The work was delicate: Skulls can fracture. The earth shifts. Move the dirt too roughly, and it swallows bones into its folds and mixes them with other bodies. An errant stroke can brush away a remnant of a blindfold, a piece of rope, a cranium fragment with a bullet hole, the bullet itself: the criminal evidence needed to prosecute a murder.  The archaeologists boxed every set of remains and drove them to F.A.F.G.’s anthropology lab in Guatemala City, where an assistant would drill a small sample from the femur. That sample would then be sent to F.A.F.G.’s white nine-room DNA lab, which is protected by bulletproof doors and two armed guards out front. It could take months before one sample yielded results. A technician ground each bone to a flourlike powder, then added enzymes and other chemicals to extract and isolate strands of DNA. Next, a machine created thousands of copies of the DNA segments, and a technician ran them through a genetic analyzer. Finally, the copies were compared with DNA samples in the lab’s database — there are now 13,000 — each one given by a person searching for someone who was missing.  The rest of the bones remained in the main anthropology lab, in a modest two-story house in a residential neighborhood. There, some 2,400 boxes the size of minifridges are stacked three, four and five tall. They line the entire second floor and parts of the lab. Each one is marked with the location where the bones were discovered — Estrella Polar, Santa Avelina, San Juan Cotzal, Cobán — and an individual case number.  On the day I visited, two assistant anthropologists cleaned bones with toothbrushes and water. Near them, a skull sat on a plastic lunch tray, with an army green blindfold tied around its eye sockets. Another tray held more than 50 fragments of a cranium, shattered like glass. In the back half of the room, dozens of skeletons had been carefully reconstructed, bone by bone, and lay atop 30 plastic folding tables covered in blue cloth. Few of the bodies have all their 206 bones and 32 teeth. Finger and toe bones disintegrate; bones commingle and decompose on top of one another. The goal, always, is for the anthropologists to uncover a story. How old was the person when he or she died? (One of the pelvic bones doesn’t completely fuse until between ages 20 and 23; clavicles as late as 25. And all bones start to show signs of deterioration by the early 30s.) Was the person male or female? (Men have thicker, heavier skulls; women have wider pelvises.) What was the cause of death: a bullet? (An X-ray may reveal a bullet and possibly entrance wounds.) An ax to the throat? (The cuts may reach back to the vertebrae.) A machete against the skull? (Certain fractures indicate blunt-force trauma.)  On one table lay the remains of a victim from Cobán. He had been discovered in Grave 63 with 25 other men and women — all the bodies blindfolded or with their hands bound. On another table was a teenage boy. Next to him, the reconstructed bones of a young child, or what remained: parts of a skull about the size of a fist, most of the vertebrae, one leg bone and a smattering of ribs, each no bigger than a twig.  Guatemala City is one of the most dangerous cities in the world, ravaged by drug and gang violence, much of it a direct consequence of the dirty war and its aftermath. Under the 1996 peace accord that ended the conflict, neither the military nor the guerrillas were held accountable for war crimes. Instead many of the commanders, police officers, detectives and death squads simply traded one type of power for another, becoming ringleaders in money laundering, human smuggling and extortion, along with the drug trade that has devastated Guatemala. Stop at a red light in Guatemala City and men, doubled up on motorcycles, may wield a gun and demand your cellphone, your wallet, your life. In some areas, lynchings by vigilantes replace formal policing. For the cost of a few pounds of coffee, you can buy a hit man’s services — and most likely get away with the murder. About 70 percent of murders in Guatemala City go unpunished, according to 2012 figures.  For decades, lawyers, judges, journalists and human rights workers who have tried to uncover Guatemala’s shrouded past have faced intimidation and, not so infrequently, kidnapping, torture and murder. The death threats began for Peccerelli and his staff in 2001, when a fellow anthropologist at another organization received a letter listing 11 targets, including Peccerelli and several others at F.A.F.G. “For 10 years we have known who you are and let you be,” the letter said. “Now it is time to settle accounts.” A couple of times in the field, locals — presumably military sympathizers or former collaborators — have intimidated F.A.F.G. archaeologists, throwing rocks at them and wielding machetes and canisters of gasoline, threatening to burn them alive. In 2006, the Inter-American Court of Human Rights required the Guatemalan government to protect Peccerelli and his colleagues. He has a bulletproof S.U.V. and bodyguards around the clock. They accompanied his children to school and to friends’ houses until two years ago, when Peccerelli sent his then 17-year-old daughter to college and his 16-year-old son to boarding school in the United States.  Not surprisingly, intimidation escalates during war trials in Guatemala. When Ríos Montt was prosecuted in 2013 for genocide against the Maya Ixil, the first time a former head of state faced such charges in his own country’s court, Peccerelli and his staff were among the dozens of witnesses and experts to testify. The conservative elite and former military officers wrote op-eds in newspapers denouncing the trial. Anonymous opponents of the trial also distributed a six-page circular titled, “The Faces of Infamy,” which featured photos of Peccerelli, Attorney General Claudia Paz y Paz, who prosecuted the case, and others, labeling them “traitors.” Though Ríos Montt was found guilty, the verdict was overturned 10 days later in a split decision by the constitutional court. A retrial began this spring.  In February, just weeks after Attorney General Thelma Aldana announced arrests in the Cobán case, Peccerelli told me: “I knew it would rain on me. In Guatemala, you find the truth, then you kill the messenger.” We were on a train riding from New York City to Washington. Peccerelli had come to the United States to talk to supporters about opening an American office, in order to raise money and also connect with Guatemalans here who still have missing family members. With the impending trial, the trip had instead turned into strategy sessions with lawyers and heads of nonprofits about how to best protect F.A.F.G.’s staff and the case’s evidence.  In newspapers and on social media, right-wing organizations with ties to former members of the military have denounced Peccerelli as a fake scientist and “the son of a guerrilla.” One military advocate, whose father was a commander at Cobán and who himself was kidnapped by guerrillas during the war, has filed a lawsuit against Peccerelli and his colleagues, accusing them of obstructing justice, taking bribes and abusing authority.  Several months ago, someone in the prosecutor’s office leaked F.A.F.G. an email warning that former military members were reportedly looking for hit men to kill someone in the prosecutor’s office and at the organization. Peccerelli has since told his staff to vary their work hours and their routes home and remove any personal information from their cellphones. His fiancée, Jessika Osorio (Peccerelli and the mother of his children separated years ago), who is also the head of F.A.F.G.’s investigation team, now refuses to leave the house without Peccerelli’s bodyguard. And even Peccerelli, typically unflappable, seems worn down. “It’s changed me,” he said recently. “I love exhuming; I love telling families we found their loved ones. But the justice part has meant a lot of painful things.”  These tactics are intended not only to intimidate but also to divert time and money from his work. As it is, Peccerelli has been forced to cut his staff in recent years to 63 from 150; funding has dropped to $1.9 million this year from a peak of $3.5 million in 2013, when U.S.A.I.D. was among F.A.F.G.’s supporters. The Netherlands, the biggest F.A.F.G. funder, shut its embassy in Guatemala a couple of years ago for budgetary reasons and took its financial backing with it. Although the United States’ State Department provides some money, many Guatemala experts believe the United States needs to do more. “Hundreds of millions of dollars in U.S. aid flowed to Guatemala’s military over decades,” notes Kate Doyle, director of the Guatemalan Documentation Project at the National Security Archive. “The least the United States could do today is underwrite F.A.F.G.’s efforts to repair some of that damage for the victims.”  In the past decade, though, the country has moved, in its slow and halting way, toward judicial progress. The last two attorneys general have aggressively prosecuted war crimes and corruption, aided by a 2006 deal between the United Nations and the Guatemalan government that created the International Commission Against Impunity in Guatemala, funded in part by the United States, to help repair the broken judicial system. Last spring, tens of thousands of Guatemalans began turning out for protests, demanding the resignation and prosecution of then President Otto Pérez Molina, yet another war commander, for his involvement in a major fraud scheme and to denounce other corrupt government officials. (Pérez Molina stepped down and has been indicted.) For a country that has long been defined by terror, Doyle says, it’s been “the first steps toward a real Guatemalan Spring.”  Nevertheless, Guatemala’s right wing retains fierce power. And some observers worry that because of the stakes in the Cobán case, threats against F.A.F.G. will intensify. Over the years, weary of the intimidation, a handful of lawyers, judges and human rights workers have fled Guatemala. Peccerelli has continued to hang on. “This is a guy who came of age in the U.S. and had every opportunity to do whatever he wanted,” Jo-Marie Burt, the transitional-justice expert, says. “He could have gotten up and left any time.”  I asked Peccerelli recently if he considered returning to the United States. “I contemplate leaving here every day,” he told me. “But I’m not throwing away 21 years of work. Not many people were lucky enough to get on a plane and leave during the war. This is me paying back. I want to be here to tell the story.”  In the early months of the Cobán exhumation in 2012, Delfina Xol traveled by bus for two hours from her village, Campur, in the Alta Verapaz region of the Highlands, to Cobán, with her sister-in-law and one of her daughters. Delfina had heard radio ads that aired in the two most prominent indigenous languages of the area, Poqomchi’ and Q’eqchi’, announcing that F.A.F.G. was stationed at a nearby Catholic church, taking DNA samples and interviewing anyone with missing family members in the region.  It had been more than two decades since her husband, Roberto, disappeared from the village where he grew up and where he and Delfina fell in love as teenagers. They had four children together, and Delfina was pregnant with their fifth when he vanished. Roberto owned a small store; he helped build a local school. He was outgoing, an affectionate dad who loved taking his kids to the river and playing soccer with friends.  On July 13, 1988, Roberto Xol awoke at 5 a.m., skipped breakfast and dressed in the clothes his 11-year-old daughter, Filomena, had picked out, as she often did: jeans, a Coca-Cola T-shirt, a pressed button-up shirt. He was walking toward the bus stop to get supplies for his store when a man wearing sunglasses and driving a white car stopped him in the street. The car, a witness later said, looked like a jeep. Darkened windows, no license plate. The driver motioned to Roberto: Get in.  That afternoon, his younger children ran back and forth to the bus stop waiting for their father to return, while Filomena tended to the store. By nightfall, Delfina feared the worst: She knew what had happened to men in her town. Roberto’s cousin had disappeared, as had at least 40 others in the community.  When he didn’t come home after a couple of days, Delfina gathered her children and traveled by bus to the military base in Cobán. Had he been arrested? Forced into service? A soldier at the front entrance gave her no information, just a warning: “Don’t return here again, or you will die here.” She went to morgues, jails, hospitals. Without his income, the family — once well-off by local standards — soon lost everything. Delfina had to sell the store, the house and Roberto’s construction tools, one by one. She cut corn and picked coffee beans, but it wasn’t enough. She couldn’t afford the books and uniforms required for her children to attend school. They begged on the street. For weeks at a time, the family lived on tortillas.  Over the years, Delfina hoped that somehow Roberto would return. She never remarried. She dreamed about him often. Perhaps he was living as a refugee in Mexico, like some who escaped Guatemala’s civil war. Or he had amnesia and would recover soon. Rumors had circulated in the Highlands about a large house where the military imprisoned the disappeared.  At the Cobán church, an investigator asked Delfina if Roberto had distinguishing marks that might help identify him — dental work, bone fractures. Next, he took swabs from inside the cheeks of one of Roberto’s daughters and his sister, and sent them off to the DNA lab.  A year later, two F.A.F.G. investigators, Freddy Muñoz and Diane Manuela Xiloj Cuin, arrived in Campur with news for the family. The lab, they said, had a potential match. But they would need samples from the other daughters before they could confirm it. Months went by; the lab had an enormous backlog of cases. Then, one day in July 2014, Muñoz and Xiloj Cuin told the family they were returning to Campur with more information. Filomena walked three hours from her village, which is inaccessible by car and has no cellphone service, to join her mother and her sisters. As they gathered in the youngest daughter’s living room, Xiloj Cuin explained how the DNA process works. Muñoz then told them F.A.F.G. had been able to match the daughters’ DNA to a skeleton found in Grave 45, known as case No. 1433-XLV-1, one of the more than 560 bodies exhumed at Cobán.  Delfina and all her daughters were weeping by then. Roberto hadn’t run off to start a new family. He hadn’t moved to Mexico. Instead, he was kidnapped by the military, possibly tortured. He was murdered and dumped into a hole in the ground on a base just 30 miles away. And he lay there, alone in the cold earth, for more than 20 years.  Four months later, Peccerelli headed from Guatemala City to Campur for Roberto Xol’s funeral. As dawn broke on the drive into the Highlands, the air smelled of dew and wood smoke from open-fire cooking. Mist clung to the mountains. For several hours, the road wound past one-story houses of adobe, concrete or wood, many with tin roofs, no plumbing, no electricity. Pickup trucks stuffed with men, women, children — a Highlands version of public transportation — shared the narrow dirt roads with women walking to markets and men and young boys descending from the mountains, hunched because of the stacks of wood on their backs, almost as big as their thin bodies.
In the face of death threats, a forensic anthropologist has spent two decades exhuming the victims of a “dirty” civil war. Now his work might help bring justice for their murders.