Luis Contreras, a doctor who lives and works in a building just south of the border fence that separates the United States from Mexico here, was playing a game on his computer late one night when an eruption of gunfire jolted him. He quickly turned off all the lights to avoid being hit, and, once the shooting stopped, cautiously peeked through the door. On the darkened sidewalk below, he could make out the figure of a person lying face down.

“He wasn’t moving,” Dr. Contreras recalls.

Moments later, at 11:35 p.m., a supervisor at police headquarters in Nogales, Mexico, took a call. It was someone with the US Border Patrol who said, in Spanish, that shots had been fired and rocks hurled along a stretch of the border shared with Nogales, Ariz.

“Apparently, someone is hurt on the Mexican side,” the caller said.

“How many people are there at the location?” the police supervisor asked.

“On the Mexican side, I couldn’t say,” the caller replied. “On our side, there are about five of us.”

The person on the sidewalk, José Antonio Elena Rodriguez, was 16 years old when he died that night on Oct. 10, 2012, in a hail of bullets fired, US prosecutors say, by a US Border Patrol agent from his P2000 semiautomatic pistol. At least 10 bullets struck the teen, mostly from behind, according to an autopsy conducted in Mexico.

Kelly Presnell/Arizona Daily Star/AP/File Araceli Rodriguez (above) holds a rosary in Nogales, Mexico, that belonged to her son José Antonio Elena Rodriguez, pictured behind her, who was killed by a Border Patrol agent in 2012.

Two years would pass before the name of the agent, Lonnie Swartz, was revealed in documents unsealed in federal court after José’s mother filed a civil lawsuit against him. The following year, a federal grand jury indicted Mr. Swartz for second-degree murder. Postponed seven times, his criminal trial is now set for March 20 in Tucson, Ariz., in a case with important legal and national security ramifications as well as implications for the future of US-Mexican relations.

Swartz is the first Border Patrol agent to be prosecuted by the US Department of Justice (DOJ) for killing someone on Mexican soil. The shooting raises complex jurisdictional issues. In the criminal case, a federal judge cleared the way for the trial with a ruling that the agent was standing on federal land when he fired his gun and thus could be prosecuted.

A parallel civil case tests whether the Constitution reaches beyond the nation’s borders – whether the same legal protections that apply to a US citizen apply to a Mexican standing in Mexico who might have been wronged by someone in the US. A ruling in this case could affect far more than border shootings: It could, for instance, influence whether civilians killed by US drone strikes in foreign lands could sue the US government.

“The legal issue of whether noncitizens who are not in the US are protected by the Constitution – that question applies to lots of other situations that are very different from [the Swartz case],” says Sarah Seo, an associate professor of law at the University of Iowa in Iowa City.

The criminal trial also comes at a time when the Trump administration wants to post thousands more agents along the southern border to stem illegal immigration and the flow of drugs into the US. However effective the growing law enforcement presence may be in curbing illegal activity, some experts say that it will likely lead to more border clashes.

Rodrigo Abd/AP A steel-slatted fence separates Nogales, Ariz., (on the left) from its more populated neighbor across the border, Nogales, Mexico.

To law enforcement officials, the border is already a zone of extreme danger. They portray a world in which they have to routinely deal with human traffickers and drug smugglers, many of whom are armed, not to mention legions of rock throwers. Immigrant rights groups say the Border Patrol is the villain here: They believe agents too often rough up detainees and use force – including deadly force – more frequently than they need to.

These two narratives, which in their own shadowy way are played out almost nightly somewhere along one of the world’s most porous borders, will clash in a wood-paneled courtroom in Tucson.

The border between Nogales, Ariz., and Nogales, Mexico, is an urban expanse of timeworn, densely packed neighborhoods and rolling hills stretching deep into the surrounding high desert valley. Unpretentious houses and one-story buildings line both sides of the border, just a few steps from the wall separating the two countries. The population of Nogales, Mexico, estimated at 250,000 to 300,000, dwarfs that of Nogales, Ariz., which is 20,000.

In the US, green-and-white Border Patrol SUVs constantly prowl the road along the border fence, which cuts through downtown Nogales near the official border crossing, where an abundance of people and goods flow legally every day. Floodlights, drones, ground sensors, and surveillance cameras help US authorities track illegal activity – all part of a surge in manpower and material that mostly came in after 9/11.

Indeed, one longtime lawman in the area remembers the days when just a few dozen agents guarded the largely open expanse between the two cities, known at the time as Ambos Nogales(Both Nogaleses), a name that still evokes a single community despite the wall between them. Now, some 3,700 agents roam the 262 miles of the Border Patrol’s Tucson sector, one of the country’s busiest, that includes Nogales. Nationwide, the Border Patrol grew from 9,212 agents in 2000 to a peak of 21,444 in 2011. The number has dropped slightly since then, to 19,437.

“The strong federal presence has really changed things around here,” says Tony Estrada, sheriff of Arizona’s Santa Cruz County, who has lived in the area for about 70 years.

The wall here has changed, too. It has gone from a simple chain-link fence to a solid corrugated metal barrier to what exists today: an imposing structure of steel slats topped with anticlimbing metal plates. The latest wall, which cost $11.6 million, stretches 2.8 miles and was erected in 2011, just a year before the shooting.

With a varying height of 18 to 30 feet, the barrier is meant to intimidate. Some locals believe it has helped slow down drug smuggling in the heart of the city. But it hasn’t stopped traffickers and unauthorized immigrants from trying to scale it, often successfully. Sometimes, to accomplish this feat, they rely on accomplices on the ground to distract Border Patrol agents by throwing rocks from the Mexican side.

Anita Snow/AP Crosses with the names of migrants who have died on the northbound journey to the US hang from the border fence in Nogales.

Whether José was involved in any of these activities on that fateful night in 2012 is a matter of intense dispute. The Border Patrol, long known for its secrecy, has shed little light on what led to the shooting. Instead, incident reports from Nogales, Ariz., police officers, who help agents investigate suspicious activity along the border, offer one version of what happened before the gunshots were fired.

At about 11:15 p.m., Officer Quinardo Garcia arrived at an area along the border just west of the downtown port of entry to investigate a report of nefarious activity. He saw two men in camouflage pants and sweatshirts jump from the fence into Arizona. They had large taped bundles strapped to their backs, which he suspected was marijuana.

Garcia chased the suspects on foot but soon lost sight of the men, who vanished in between the houses that line International Street, which runs along the border wall. After Garcia called for backup, Officer John Zuñiga arrived and spotted two men – one dressed in a white shirt, the other in a blue one – struggling to climb the fence to go back into Mexico. He ordered them to get down, but they ignored him.

“I then heard several rocks start hitting the ground and I looked up and I could see the rocks flying through the air,” Zuñiga wrote in his report.

He ran for cover, then heard several shots. “I saw an agent standing near the fence,” he wrote. “I advised communications that gunshots were being fired, and I was unsure where the gunshots were coming from and who was firing them.”

Nearby, still searching for suspects, Garcia also heard the shots. He soon learned that a Border Patrol agent had shot someone who had been throwing rocks in Mexico, he wrote.

Rock attacks, the Border Patrol says, pose a significant threat to agents who must decide in a matter of seconds whether to use lethal force in tense situations that can quickly turn life-threatening. Assaults against agents have been rising in recent years. They totaled 786 in fiscal 2017, compared with 454 in fiscal 2016, according to US Customs and Border Protection (CBP), the federal agency tasked with securing the nation’s borders.

“Our jobs are dangerous, and the decisions we make every day determine if we will return home safely to our families,” the National Border Patrol Council, the union that represents agents, said in a statement after Swartz’s indictment. The group has thrown its support behind Swartz, who is on indefinite suspension from the force.

José’s shooting compounded rising criticism over agents’ use of deadly force rather than a less lethal response in rock attacks and other confrontations. An investigation by The Arizona Republic newspaper found that CBP agents killed at least 42 people – with few repercussions – between 2005 and 2013. At least 13 were Americans. Here in Nogales, a small, hand-drawn mural along the border depicts José, another teenage boy, and four men who were standing on Mexican soil when agents shot them dead between 2010 and 2012.

“There are more than 50 people that have died since 2010 at the hands of the Border Patrol, and no one has been held accountable for it,” says Hiram Soto of the Southern Border Communities Coalition, a group of more than 60 organizations that seeks to strengthen oversight of CBP.

In May 2014, under intense pressure from outside groups, CBP, which oversees the Border Patrol, released a year-old report it had commissioned on its use-of-force policy. After reviewing 67 cases, the Police Executive Research Forum, an outside research group hired to conduct the study, criticized the agency for incidents in which agents opted to shoot at moving vehicles and rock throwers rather than avoid conflict.

The group recommended training that focuses on keeping agents out of the path of vehicles. It also said agents “should be prohibited from using deadly force against subjects throwing objects not capable of causing serious physical injury or death.”

CBP has made public revised rules that emphasize de-escalation tactics and the use of nonlethal devices. In early February, the agency released figures showing a 69 percent drop in use-of-force cases involving firearms, from 55 in 2012 to 17 in 2017.

Daylight had turned to dusk when José’s mother, Araceli Rodriguez, recently turned the corner onto Calle Internacional, the street that runs along the border wall just inside Mexico. She knelt on the sidewalk where her youngest son died, now marked by a shrine, and lit a candle. It’s something she has done on the 10th day of each month since he was killed.

On this night, family members and a dozen friends from the US joined her at the monthly vigil to sing and pray before a white metal cross with a photo of José in the center. Her hair pulled back in a ponytail, Ms. Rodriguez looked weary. Though she’s waited for more than five years for the agent accused of shooting her son to be tried, she knows justice can be elusive.

“It’s taken so long just to get to this point, to decide if the man is guilty or innocent,” says Rodriguez, a single mother. “The truth is that, whatever the circumstances, he killed my son.”

The family lives at the end of a steep cobblestone street, across from an elementary school. Growing up, José played with toy cars and followed his older brother, Diego, everywhere. The two often played basketball with friends at a church just up the hill. His grandmother, Taide Elena, says José was shooting hoops just hours before he was killed.

José was cared for by Ms. Elena and his aunts and uncles after his mother, following a separation from her husband, moved 370 miles away to Navojoa, her hometown, taking her two younger daughters with her.

The day José was shot, Elena says, the two had spent time together in the living room of the hilltop house. They chatted about a variety of topics, including his upcoming transfer to a new high school. José later walked his grandmother to the border crossing so she could return to Nogales, Ariz., where she lives. It was the last time she saw him alive.

The teen never went home that night. The next morning, searching for José, Diego and his aunt saw a photo in a newspaper of someone who’d been shot 30 feet from the border the night before. He was wearing a gray T-shirt, jeans, and gray sneakers that looked just like the ones José’s aunt had recently bought for him.

After José’s death, his mother returned to Nogales, Mexico, and stayed. Since then, she’s led marches, protests, and vigils in a call for justice. Frustrated with the silence surrounding the case, she filed the civil suit in US District Court in Tucson, initially charging the unnamed agents with using “unreasonable and excessive force.” Luis Parra, one of her lawyers on the civil case team, says the DOJ’s subsequent decision to prosecute Swartz represents a vindication for the family.

In August 2014, US and Mexican investigators swarmed the block where José was killed. They cordoned off the crime scene with yellow tape and carefully inspected the sidewalk where the youth had lain nearly two years earlier.

They also took note of the still-visible bullet marks on the walls of the abutting medical building and a nearby surveillance camera posted along the border, on the US side, that had recorded the activity on the night of the shooting.

The lawyer for Swartz says José was hurling rocks at the agents that night and was likely involved in drug smuggling. Rodriguez’s family says the youth was an innocent bystander gunned down while simply walking by, probably on his way to a convenience store.

In the area, the border wall sits on top of a small cliff, about 25 feet high. Throwing rocks over the elevated fence would require someone to make a long, arcing toss, something that supporters of the family say wouldn’t likely hurt anyone on the other side. The rocks that rained down that night hit, but didn’t injure, a dog named Tesko, according to a police report. Yet it is also possible to throw rocks through the slatted openings in the barrier. This is how the bullets were able to travel through the wall.

Witnesses on the Mexican side told DOJ investigators that José was walking down the street, and that other individuals ran past him when the shots were fired, suggesting to them that he wasn’t involved in any reckless activity. For prosecutors, the case isn’t about rock attacks or drugs but comes down to one overarching argument: that the agent wasn’t justified in using deadly force.

The defense, for its part, doesn’t deny the agent shot José, but contends he did so in self-defense. They argue that he felt threatened, and, in the tense circumstances of the moment, made a decision that was justified to protect himself.

In June 2010, a Border Patrol agent shot and killed 15-year-old Sergio Hernandez Guereca while he played with friends on the Mexican side of a culvert between Ciudad Juárez, Mexico, and El Paso, Texas. In a disputed account, Jesus Mesa Jr. said he fired his gun after being pelted with rocks. No charges were filed against him.

Sergio’s family filed a civil suit against Mr. Mesa, and the Fifth Circuit Court of Appeals ruled that no legal claim could be pursued against the agent because the youth was a Mexican citizen in Mexico when he was shot. In Jose’s case, a federal judge in Tucson ruled just the opposite – that the case could go forward.

The US Supreme Court then took up the Hernandez case. In June 2017, the high court sent the Texas case back to the lower court without addressing the more profound question of whether constitutional protections extend to foreign nationals outside the US. Instead, the Supreme Court asked the lower court to consider whether the plaintiffs can rely on a landmark 1971 decision, Bivens v. Six Unknown Named Agents of Federal Bureau of Narcotics, that granted individuals whose rights were violated the right to sue federal officials. But the Bivens precedent has never been used in a case beyond US borders.

The potential implications for foreign policy and national security may be one reason the high court avoided the question of constitutional rights for people in other countries, according to Ms. Seo of the University of Iowa law school.

Brian Skoloff/AP US Border Patrol Agent Kevin Hecht discusses a new technology in the drug war – a wireless, camera-equipped robot – in Nogales, Ariz. Between 2006 and 2014 (the year the robot debuted), agents discovered 75 drug-smuggling tunnels along the US-Mexican border.

“The situation that a lot of law professors have written about is drone strikes,” she says. “A lot of drones are controlled in the US but are flying in Afghanistan. So if an innocent person in Afghanistan dies from a drone strike and a button was pressed in the US, can somebody in Afghanistan who’s not a US citizen, halfway around the world, sue the US government for damages?”

Paul Bender, a constitutional law professor at Arizona State University in Tempe, says a conviction in the criminal case could help Rodriguez’s civil suit. The Ninth Circuit Court of Appeals will decide if it can go forward. But “I would assume what’s going to happen is if he’s convicted, then they’ll settle the civil case,” he says.

Back at the medical building where Contreras, the doctor, tends to his patients, the bullet holes that long pockmarked the facade have now been patched. In February, a construction worker slathered a skim coat of cement on the wall. He covered the memorial cross to keep it free of debris while he worked.

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Inside the building, Contreras sits at his desk. He has watched the endless legal maneuverings over the shooting closely, as have many people on both sides of the border, including in Mexico City and Washington, D.C. Mexico’s government decried José’s killing when it happened. Various authorities from Nogales, Mexico, are expected to testify at the trial – a first in a fatal cross-border shooting.

Contreras leans back in his chair and tilts his head toward the border fence. “We’ll see what kind of justice is done on the American side,” he says. ρ