Wails echoed across what was left of the village when the ambulance arrived. Inside was the body of a 12-year-old girl, Roqia. She had died in a nearby hospital Tuesday morning, days after a devastating earthquake hit this stretch of northwestern Afghanistan and sent her mud-brick home crashing down on top of her.

The vehicle drove to the top of a nearby hill where mounds of dirt marked around 70 freshly dug graves. A crowd of men gathered and opened its back door, gently pulling out the girl, whose small frame was wrapped in a thick, white blanket.

Seeing her, her uncle, Shir Ahmad, stumbled backward. “Oh God, oh God,” he cried, gasping for breath. A man slipped his arms around his back to steady him as he sank to the ground in sobs.

“I lost four relatives,” the man said. “Don’t cry.”

Since Saturday, when the deadliest earthquakes to strike Afghanistan in decades occurred, hundreds of Afghans in one of the worst-hit districts, Zinda Jan, have been struggling to come to terms with the almost unfathomable destruction.

In a matter of minutes, a handful of entire villages — once clusters of mud-brick homes, their thick, beige walls blending into the endless desert — were transformed into mounds of dust. Nearly everyone in the area lost at least one relative when their homes crumbled. Many have lost most, if not all, of their immediate family.

The district is little more than a stretch of desert punctuated by villages where people live hand-to-mouth along Afghanistan’s western border. Most families survive by growing wheat, corn and figs in modest gardens and shepherding small livestock herds. Many men work as day laborers in neighboring Iran, earning only a few hundred dollars a month.

By Tuesday, the death toll from two 6.3-magnitude quakes had climbed to at least 1,053 people, according to the United Nations, while Taliban officials have said the true figure could be closer to 2,000. The vast majority of those dead belonged to only 11 villages, some of which lost a quarter or more of their populations in the quake. Early Wednesday, another 6.3-magnitude earthquake hit near Herat City, sending people running out of their homes for the second time in five days.

Across the hamlets struck by the earlier disasters, the grief and loss are palpable. The air is tinged with the smell of rotting flesh — whether from victims whose bodies have yet to be recovered or from livestock that were crushed under rubble, no one is quite sure. Rows upon rows of dirt mounds marking mass graves now outline the edges of villages that have been decimated. Sporadic screams and sobs pierce the quiet as waves of anguish overwhelm the few survivors.

In Seya Aab village, moments after the men lowered Roqia’s body into a grave on Tuesday afternoon, a young man whose mother had also been killed collapsed on top of her grave in tears. “Oh God, oh God, please help me,” he yelled.

Farther down the hill, now a newly dug cemetery, a grandfather let out a cry and dropped to his knees, drawing a crowd around him. Minutes later, another man howled in tears and screamed: “They are all of us! They are all of us!”

In Nayeb Rafi, a nearby village, the only building to survive the quake was a concrete school built by an aid group. Every single mud-brick home was destroyed. Residents told a visiting team of journalists from The New York Times that they estimate that of the roughly 2,000 people living there, 750 were killed.

At the edge of the hamlet, a man in his 70s sat on the edge of a pile of mud brick — what was once his home — in a daze. He had wrapped a hefty brown blanket dug from the rubble around his shoulders to protect himself from the chilly morning air. Behind him, black smoke from a small fire another survivor had lit for warmth clouded the sky.

The man, who goes by one name, Zarin, said he had just slaughtered a sheep for his family to eat on Saturday when the earth beneath him began to shake violently, throwing him to the ground. When the convulsions finally ended, he was up to his chest in crumbled mud brick. He could hear a child’s voice crying for help but could barely see anything amid clouds of white dust, he said.

When he finally pried himself free from the rubble, he began frantically digging with his hands where his house once stood. He and another villager pulled out his granddaughter, alive, then turned their attention to where they heard two women’s voices shouting for help.

“I could hear them crying: ‘Father! Uncle! Brother! Help me! I’m still alive!’” Zarin recalled. They managed to dig out one woman who was pregnant. She was bloodied and coughing up dust, but alive, he said. By the time they found the other woman, it was too late.

“Everything is gone,” he said.

Nearby, a teenage boy sat outside a bright blue makeshift tent, decorated with waves and palm trees, that an aid organization had given him the day prior. He had been walking in a nearby pasture with his family’s eight sheep when the quake struck. He abandoned the livestock and ran to his home, only to find a pile of dust — and silence. Beneath it, his mother, his father, his younger sister and two brothers had all died.

“I don’t even know what happened to the sheep,” the boy, Khan Mohammad, 18, said, staring blankly at the horizon.

Hours after the quake hit on Saturday, volunteers from the nearby Herat City and government workers made their way through the desert dunes and rough roads to the village, helping residents pull their loved ones from the rubble and shuttling injured people to a nearby hospital.

But by Tuesday, efforts to rescue people had ended. Instead, volunteer crews armed with shovels and excavators knew their task had become more somber: Recovering the remains of those missing, any hope they might still be alive gone.

One man, Sirajuddin, 45, worked alongside his brother and uncle with a shovel and pickax to recover what they could: a bag of flour here, a pan there.

“Where is Wais?” he asked his uncle, Naeem, 58, who had just returned from visiting injured relatives in the hospital in Herat City that morning.

“He was with his daughter, she’s OK,” he replied.

“What about Zahra?” Sirajuddin, who goes by one name, asked. Naeem shrugged, the cousin’s fate unknown.

Explaining what was once their close-knit community, the men rattled off the names of their neighbors, and the loss each one of them just incurred.

There was Jan Mohammad, a farmer, whose wife and two daughters died. Next door to him was Nazar, a man in his 60s who died alongside his 5-year-old and 2-year-old grandsons. Further down was Gafar, whose daughter was killed; Sataar, whose brother and two sons were killed; and a widow, Maryam, whose 18-year-old daughter died. And then there was Ahmad’s family of five. Only his daughter and son survived.

As Sirajuddin dug, a forest green police vehicle roared through town, an officer calling through its loudspeaker for people to go to the edge of the city to help improve a mass gravesite where around 300 people were buried the night before.

There, hundreds of men — mostly volunteers from villages across the province — picked up shovels and began tossing dirt on top of six rows of graves. Every two or three feet they placed a stone, an imprecise but symbolic way to differentiate each person buried in the ditches.

One volunteer, Abdi Mohammadi, 45, paused to look over the gravesite. Then he shook his head.

“This place has seen the wrath of God,” he said.

The magnitude-6.3 temblor struck northwestern Afghanistan at 5:22 a.m. at a depth of about six miles, according to the U.S. Geological Survey. The epicenter was just outside Herat City, the provincial capital and one of the country’s cultural and economic hubs.

At least 120 people were injured in the quake on Wednesday and one was killed, according to Dr. Mohammad Asif Kabir, head of Herat Province’s

“When my body started shaking I realized it was another quake,” said Nadar, 52, who goes by one name and who had been sleeping in his yard. “Everyone sleeping outside was shouting and screaming.”

Inside the Arg Hotel, a team of New York Times journalists felt the walls shake violently and the building sway. Bright lights illuminating the hallway flickered and went dark as guests ran out of the building. When the shaking subsided, parts of the concrete walls had broken off, and pieces of the ceiling in some rooms had crashed to the floor.

“I thought that it was all over,” said Mr. Reza, 28. When he woke to the walls shaking, he sprinted from the house barefoot, through the yard and to the alley outside.

“I was so scared and shocked, now I feel dizzy and I’m just throwing up,” he added.

The Saturday quakes, both of which were also 6.3 magnitude, caused mud-brick homes in several districts to come crashing down. At least seven tremors followed.

There was optimism that the Wednesday quake would be less destructive. The buildings in Herat City are mostly made from concrete — not mud-brick, as in districts that saw the worst devastation on Saturday — and many people were sleeping outside.

But the historic city, which once served as a center of medieval Islamic culture, home to poets, scholars and painters, the ruins of ancient architecture did not survive the quake unscathed.

At the Musalla of Gawhar Shah, a 15th-century Islamic religious complex, the top of one of five minarets still standing was partially damaged by the quake, according to Farid Ahmad Ayoubi, the director of information for Herat Province. The Great Mosque of Herat, one of the oldest mosques in the region, widely considered a masterpiece of Islamic architecture and recognizable by its vibrant blue minarets, was also damaged, he said.

At Herat’s regional public hospital, ambulances raced in and out of the gate Wednesday morning carrying dozens of injured people.

Outside the intensive care unit, dozens of doctors and nurses stood at a makeshift triage station and swarmed the ambulances as each new wave of patients arrived. They bandaged bloodied arms and legs, rolled out IVs on rickety metal stands and tried to calm people crying with fear as their loved ones were treated.

One man in a dirt-covered orange salwar kameez, a traditional loosefitting garment, carried a young boy to the triage station and laid him down on the pavement. After the initial quake Saturday morning, they had come from Nawabad village, on the outskirts of Herat, in an Army Ranger vehicle.

As doctors inserted an IV into the boy, the man stood up in tears and let out a shriek.

“There’s nothing left!” he cried, before pleading with hospital staff members to let him check the morgue for other relatives who were still missing from the weekend disaster, which leveled homes in his village.

“Please,” he begged. “Just let me go and check the dead bodies.”

For many in Herat, the quake on Wednesday was a terrifying reminder of the unease that continues to plague the city after the initial quake last weekend.

Along the grassy median of a main road running through the city, dozens of people lay inside makeshift tents they had constructed with clothes, rugs and string. Many had slept there since Saturday, fearing the aftershocks that have rolled through the city.

Mohammadi Yasin, 22, set up his campsite with his siblings and other relatives on Saturday afternoon, heeding the advice of his neighbors, who warned about possible tremors after the initial quakes.

“It’s not the safest place, but it’s the only one that we could find,” Mr. Yasin said, his 11-month-old nephew asleep in the shade of a tree next to him. “We don’t have a yard, and we couldn’t stay in alleys outside our house — there were big buildings around it; we were afraid they would fall down,” he added.

His family had returned to their two-story home nearby on Tuesday night, thinking the crisis was finally over. Then, early Wednesday morning, they were jolted awake as the ground shook violently beneath them. His two sisters screamed in fear as they fled the house for the alleyway, their drinking glasses tumbling off the shelves of their kitchen and smashing onto the ground.

Now, he said, his family plans to stay on the median for at least a week.

“We are not feeling safe; the earthquakes are happening all around us,” he said. “It might happen again.”

Andrés R. Martínez contributed reporting.

Hundreds of police officers flooded into a Karachi slum around midnight, surrounding the homes of Afghan migrants and pounding at their doors. Under the harsh glare of floodlights, the police told women to stand to one side of their homes and demanded the men present immigration papers proving they were living in Pakistan legally. Those without documents were lined up in the street, some shaking with fear for what was to come: Detention in a Pakistani prison and deportation to Taliban-controlled Afghanistan.

The police raid on Friday in Karachi, Pakistan’s largest city, followed an abrupt decision by the Pakistani authorities last week to deport the more than one million Afghan migrants living illegally in the country.

“Police entered every house without warning,” said Abdul Bashar, an Afghan migrant whose two cousins were among the 51 people who the police said were arrested during the neighborhood sweep. “The fear has left us restless, making it difficult for us to sleep peacefully at night.”

On Tuesday, Pakistan’s Interior Ministry announced that migrants residing illegally in the country had 28 days to leave voluntarily, and it offered a “reward” for information leading to their arrests once that deadline passed.

While Afghans have faced harassment in Pakistan for decades, this announcement was the government’s most far-reaching and explicit action affecting Afghan migrants. It was widely seen as a sign of the increasing hostility between the Pakistani government and the Taliban authorities in neighboring Afghanistan as they clash over extremist groups operating across their borders.

Over the past year, Pakistan has experienced a surge in terrorist attacks, both by militant groups that have found haven in Afghanistan under the Taliban administration and by others whose fighters have been pushed into Pakistan following a brutal Taliban-led crackdown on their ranks. Some former Taliban fighters have also migrated to Pakistan to wage jihad against the Pakistani government.

For months, the Pakistani authorities have pleaded with the Taliban to rein in extremist violence stemming from Afghan soil. But Taliban officials have rebuffed those calls, instead offering to mediate talks between the Pakistani authorities and the militants.

The growing animosity between the two countries has threatened to further destabilize a region that is already a political tinderbox.

On the other is nuclear-armed Pakistan, which has struggled with military coups, volatile politics and waves of sectarian violence since its founding 75 years ago.

Caught in between are the roughly 1.7 million Afghans living in Pakistan illegally, according to Pakistani officials. Among them are around 600,000 people — including journalists, activists and former policemen, soldiers and former officials with the toppled U.S.-backed government — who fled after the Taliban seized power, according to United Nations estimates.

Many of those migrants face a stark choice: Either return to Afghanistan, where they fear persecution by the Taliban, or remain in Pakistan and face harassment from the Pakistani authorities.

“We have been left in the lurch,” said Mahmood Kochai, an Afghan journalist who fled to Pakistan with his wife and six children after the Taliban seized power.

Like many Afghan migrants in the capital, Islamabad, Mr. Kochai arrived in Pakistan on a temporary visa, anticipating an asylum decision from Western embassies in Islamabad. Soon after arriving, he applied for sanctuary in the United States under a refugee program for Afghans who worked with the U.S. government or U.S.-funded organizations.

But since he applied more than a year ago, he has not heard anything back, Mr. Kochai said. Now, he is concerned about the expiration of their Pakistani visas in two months.

In Karachi, home to a sizable population of Afghan migrants, news of migrants’ getting arrested at security checkpoints on roads and in markets during routine outings has stoked panic.

Ali, a former Afghan security official who would give only his first name because of his immigrant status in Pakistan, said he and his neighbors — also Afghan migrants — had barely gone outside for two weeks, fearing getting arrested and being sent back to Afghanistan. If he is deported, he worries he faces arrest — or worse — because of his affiliation with the U.S.-backed government.

The new policy has in fact drawn criticism from human rights groups, which say deporting Afghans could put them at risk in Afghanistan. Despite the Taliban’s policy of blanket amnesty for Afghans who worked with the U.S.-backed government, human rights monitors have documented hundreds of abuses against former government officials since the Taliban seized power.

Pakistani officials have defended the policy as necessary to protect Pakistan from extremist violence. In a news conference on Tuesday, the Pakistani caretaker government’s interior minister, Sarfraz Bugti, asserted that Afghans were involved in 14 of the 24 major terrorist attacks in Pakistan this year.

“There are attacks on us from Afghanistan, and Afghan nationals are involved in those attacks,” he said. Taliban officials denied those claims.

The aggressive approach echoes similar crackdowns on Afghan migrants in years past, observers say. After a string of major terrorist attacks in 2016, the Pakistani authorities began a sweeping campaign to uproot Afghan migrants, forcing around 600,000 back to Afghanistan. Human Rights Watch characterized Pakistan’s actions as the world’s “largest unlawful mass forced return of refugees” in recent times.

“Afghans always get stuck when foreign relations break down between Afghanistan and Pakistan,” said Sanaa Alimia, researcher and author of “Refugee Cities: How Afghans Changed Urban Pakistan.”

“That usually manifests itself as harassment of ordinary Afghans in the country and those getting harassed are usually in the lowest income groups, they are an easy target,” she added.

Pakistan has not signed the 1951 Geneva Convention and its 1967 protocol covering the status of refugees, which protects people seeking asylum. Instead, Pakistan’s Foreigners’ Act grants the authorities the right to apprehend, detain and expel foreigners — including refugees and asylum seekers — who lack valid documentation.

After previous crackdowns, many Afghans have either remained in Pakistan or returned after being deported — underlining the limit of the Pakistani government’s ability to repatriate Afghans, experts say.

Now, with the government facing dueling economic and political crises, it is unclear how the Pakistani authorities would repatriate such a large number of refugees, a deportation campaign requiring substantial personnel as well as military and intelligence resources.

Maulvi Abdul Jabbar Takhari, the Taliban’s consul general in Karachi, said that many Afghans who had been arrested possess legal documents allowing them to live in Pakistan and that Taliban officials had been trying to secure their release.

Mr. Takhari, who lived as a refugee in Karachi for several years, urged Pakistan’s government “to provide a specific time frame for undocumented refugees so that they can peacefully and respectfully wind up their businesses and return to their homeland.”

But for Afghan migrants, the wave of arrests has been a chilling reminder of their precarious status in Pakistan. Many arrived in the country decades ago, after the Soviet Union’s invasion of Afghanistan in 1979 and after the civil war that followed the Soviet withdrawal.

Abdullah Bukhari, 51, came to Karachi in 1980 from Kunduz Province fleeing violence during the Soviet-Afghan war. The notion of uprooting his life in less than a month feels absurd and heartbreaking.

“How can they uproot everything in such a short period?” Mr. Bukhari asked. “We’ve spent our lives as refugees and amid conflict, but our biggest concern is for our children. They have never experienced Afghanistan even for a day.”