Things began to change after Sept. 11, Zuñiga said, when border security became a political issue. Facing an electorate fearful about terrorism and angry about illegal immigration, Congress allocated $90 billion to border security over the next 10 years, which went toward 650 miles of new fence and, for C.B.P. agents, military hardware like drones, assault rifles and Black Hawk helicopters. The number of Border Patrol agents doubled during the second term of the George W. Bush administration, to 20,000 from 11,000. In 1995, the number of agents in C.B.P.’s Tucson sector, which includes Nogales, was roughly 400; today, it has grown to more than 4,000. There are cameras everywhere — on towers near town, on drones, on the backs of flatbed trucks driven into the desert — as well as thousands of motion-detecting sensors, many of them hidden in rocks or buried in the sand.

The fence that now bisects Ambos Nogales cost about $4.14 million per mile to build, its height varying between 18 and 30 feet. It was installed in 2011, replacing a fence made of solid steel panels. Some Border Patrol agents prefer the new slat design, because they can look through the fence and observe activity on the other side. Slick anticlimbing plates lining the top increase the difficulty of scaling the wall, but it is by no means impossible. Undocumented immigrants and drug smugglers still manage to climb it every day.

That’s why the call Zuñiga received in October 2012 was not especially remarkable. A Nogales police officer named Quinardo Garcia had arrived on the scene first and witnessed two men in camouflage pants and sweatshirts, with large taped bundles strapped to their backs, climbing the fence into the United States. ‘‘Based on my training and experience,’’ Garcia later wrote in his incident report, ‘‘I identified the bundles as marijuana and immediately called out the incident to assisting graveyard units.’’

Garcia chased the men on foot, but they disappeared into an overgrown residential yard. Fearing an ambush, Garcia decided to wait for backup. Within minutes, Zuñiga arrived, as did several Border Patrol agents. As they began to scope the area, Zuñiga spotted two men scaling the fence back into Mexico. ‘‘By the time I show up, they’re empty-handed, with nothing on their backs,’’ he told me.

Police officers and Border Patrol agents refrain from climbing onto the fence themselves, for reasons of both safety and jurisdiction. ‘‘I gave them numerous commands to climb down,’’ Zuñiga wrote in his own report. One of the men was having difficulty maintaining his grip and seemed on the verge of dropping back onto Arizona soil. ‘‘I then heard several rocks start hitting the ground,’’ Zuñiga wrote, ‘‘and I looked up, and I could see the rocks flying through the air.’’

So-called rockings are not uncommon occurrences at the border. The rocks are thrown from the Mexican side to distract agents and force them to take cover while smugglers pass contraband or make their escape. ‘‘When it’s dark out and you don’t know where they’re coming from,’’ one agent told me, ‘‘it’s a really tense situation.’’

What happened next remains contested. In their reports, Garcia and Zuñiga claimed to hear gunfire but could not say where the shooting was coming from. ‘‘I saw the rocks in the air and tried to take cover,’’ Zuñiga told me. ‘‘I heard shots fired, but I wasn’t sure who was shooting. The shots could have been from anywhere: behind me, from Mexico. I didn’t witness the actual shooting myself.’’

In the days following the incident, C.B.P. issued only a terse statement. ‘‘After verbal commands from agents to cease [assaulting the agents with rocks] were ignored, one agent then discharged his service firearm,’’ it read. ‘‘One of the subjects appeared to have been hit.’’

The subject who was hit was not one of the men who had been climbing the fence but a 16-year-old resident of Nogales, Mexico, named José Antonio Elena Rodríguez, who was on the Mexican side of the border. He had been shot 10 times from behind; an autopsy later revealed that gunshot wounds to the head, lungs and arteries killed him. He was unarmed, carrying nothing but a cellphone. He collapsed on a sidewalk on Calle Internacional, in front of a doctor’s office, below a sign reading ‘‘Emergencias Médicas.’’ Six months later, you could still see the bullet holes in the wall. Someone had outlined them with a red marker.

The morning after the shooting, James F. Tomsheck arrived at the Ronald Reagan Building in Washington, the headquarters of United States Customs and Border Protection, and made his way to the briefing held each weekday for a dozen of the agency’s top officials. Six years earlier, when Tomsheck was appointed head of the agency’s Office of Internal Affairs, it felt like the capstone of a long and distinguished career. A stolid Nebraskan with a precise, nearly affectless manner of speaking, Tomsheck had spent his entire adult life in law enforcement, first as a police officer in Omaha, his hometown, and later as a Secret Service agent. He busted counterfeiters in Detroit, worked the presidential detail under George H. W. Bush and Bill Clinton and eventually became a deputy assistant director of the entire Secret Service, where he oversaw half of its field offices. In 2006, he was recruited to C.B.P. by his former boss at the Secret Service, Ralph Basham, who had been appointed the C.B.P.’s commissioner by George W. Bush.

In the early days of the Border Patrol, which was created in 1924, agentspatrolled the border (primarily the northern border) on horseback. By 2012, the increasingly militarized agency held its morning briefings in a secure, windowless room in Washington known as a Sensitive Compartmented Information Facility, or S.C.I.F., where electronic items are left at the door and classified information can be openly discussed. On Oct. 11, Tomsheck and his colleagues were informed that a teenage rock thrower had been killed by a Border Patrol agent in Nogales and that the shots had been fired in self-defense. Tomsheck told me that he was ‘‘immediately suspicious’’ of this official version of events. Border Patrol leadership, he said, had ‘‘a well-established history of intentional misinformation. Having sat through these meetings for years, after every one of these shootings, there’s an effort to spin and distort facts and obscure a clear understanding of what actually occurred.’’

Part of the problem was the many overlapping authorities. Tomsheck frequently found himself in an almost parodic bureaucratic scrum of competing government agencies. Within the Department of Homeland Security (D.H.S.), which absorbed various agencies into the newly created Customs and Border Protection agency after Sept. 11, the Office of Inspector General, known as D.H.S.-O.I.G., had right of first refusal when it came to taking the lead on investigations of officer misconduct. If D.H.S.-O.I.G. stepped away, Immigration and Customs Enforcement (ICE) was second in line to investigate. Only if ICE passed would Tomsheck’s Office of Internal Affairs be able to take the lead on an investigation. Information sharing among the offices, according to Tomsheck, was minimal.

Outside D.H.S., the F.B.I. could run its own parallel investigations of Border Patrol misconduct. According to Tomsheck, however, the bureau was regularly ‘‘being walled off’’ by D.H.S.-O.I.G., which ‘‘in many instances refused to share information and cooperate.’’ Ronald Hosko, who served as assistant director of the F.B.I.’s criminal investigative division from 2012 to 2014, described D.H.S.-O.I.G. as ‘‘a troubled place’’ that regarded ‘‘sharing information as misconduct,’’ adding that from his perspective, ‘‘they fought us at every turn. I believe it was a deliberate attempt by senior people in D.H.S. and in the inspector general’s shop to avoid cooperating with the F.B.I.’’

But Tomsheck was happy to work with the F.B.I., and his office had a dedicated liaison agent who reported to the bureau’s headquarters daily. In the wake of the Nogales shooting, Tomsheck’s agents in the Tucson field office found that the official Border Patrol report was ‘‘not consistent’’ with the information they uncovered on the ground. ‘‘That prompted discussion with the F.B.I. about how it seemed to be a problematic shooting,’’ Tomsheck says.

Within a week of the incident, Tomsheck was at F.B.I. headquarters watching footage captured by the security cameras lining the border fence. According to him, the video ‘‘very clearly’’ shows the marijuana smugglers struggling to scale the fence, while the two Nogales police officers and a Border Patrol agent look on. (The footage has never been publicly released.) ‘‘They do not appear to be displaying any concern for their safety whatsoever,’’ Tomsheck says of the officers. ‘‘There are no weapons drawn. People have their hands on their hips, standing there watching. If you were to give a title to the video up to that point, it would be: ‘It’s Another Day at the Border.’ ’’

Then a second Border Patrol agent arrives on the scene. Immediately after emerging from his vehicle, according to Tomsheck’s description of the video, the agent walks to the fence, pulls out his gun and begins firing. The agent did not interact with the other law-enforcement officers on the scene. ‘‘He fired the round in chamber, all 12 rounds in the magazine, reloaded and fired at least one additional round,’’ Tomsheck says. ‘‘They seem absolutely shocked at first. There’s no audio, but they’re clearly thinking, What does he know that we don’t?’’

Tomsheck says the footage he viewed ‘‘demonstrated that José Antonio was certainly not throwing rocks at the time he was shot.’’ He describes the shooting as ‘‘the most egregious’’ of any excessive-force cases he’d seen at C.B.P. and says he felt ‘‘angry and sickened. Even if he had been throwing rocks previously — it’s conceivable, but there’s no evidence. But this was evidence of a Border Patrol agent shooting an unarmed boy.’’ If charges weren’t brought against this agent, he thought, the message being sent would be, ‘‘It’s open season at the border.’’

On the morning of Oct. 11, 2012, just a few hours after Tomsheck learned of the shooting, Roberto Montiel was driving to court when he got a call from an old friend, Taide Elena. A native of Nogales, Ariz., Montiel served for 20 years as a Superior Court judge before opening a private criminal and family law practice. Elena, a Mexican immigrant like Montiel’s own parents, had worked for Montiel’s family for years as a housekeeper. ‘‘My mother basically died in her arms,’’ Montiel told me.

That morning, Elena was distraught. ‘‘I need your help,’’ she cried in Spanish. ‘‘They killed José Antonio!’’

Elena was José Antonio’s grandmother. Though she and her husband had legally immigrated to the United States over 20 years ago, her son’s family remained in Nogales, Mexico, in a barrio called La Capilla, ‘‘the Chapel,’’ about four blocks from the border. The neighborhood took its name from the white Spanish colonial church where José Antonio and his friends would play basketball. According to the boy’s family, that’s what he was doing on the night of Oct. 10. When he turned onto Calle Internacional, he was walking to meet his older brother, Diego, who worked at a nearby Oxxo convenience store.

Beyond that, Elena later told Montiel, the family had very little information. They had been informed of the death by Mexican authorities, but no one from the United States had contacted them. The incident reports released by the Nogales Police Department listed a sole injured party by name: Tesko, the police dog who arrived at the scene with Zuñiga. In his report, Zuñiga claimed Tesko was hit by a rock.

It made no sense, Elena said. Her grandson had always been a good kid. Why would he be shot by la migra? ‘‘When are they going to do something about this killing?’’ she asked.

‘‘I explained to her how complex this was, because it involved two countries,’’ Montiel recalls. He didn’t know much about the history of cross-border shootings at the time, but he promised to find out if any criminal charges were being considered. Then he asked Luis Fernando Parra, a lawyer with whom he shares office space, to help with the case. Parra specializes in immigration law, and the two occasionally collaborate on international cases involving cross-border money laundering or domestic disputes.

Parra used his connections at the Mexican Consulate to obtain autopsy and ballistics reports from investigators. The findings were startling: Even if, as C.B.P. claimed, José Antonio had been throwing rocks at the agents — not an outrageous contention on its face, considering how much control the cartels hold over barrios like La Capilla, where scouts with walkie-talkies and binoculars monitor Border Patrol activity — the autopsy showed the bullet holes were angled ‘‘from the back to the front,’’ with entry points ‘‘behind the auricle of the ear’’ and ‘‘in the posterior region’’ of the neck, torso and deltoid. In other words, the shots had struck him from behind.

Before the autopsy report was publicly released, official accounts of José Antonio’s death had already begun to unravel. A person merely had to stand at the stretch of border fence where the shooting occurred and take in the view. That particular section of fence is 20 feet tall, but it sits on a rocky cliff, and the drop into Mexico from the base of the fence is another 25 feet. From Calle Internacional, hurling rocks over the top of the fence — or through the narrow gaps between the slats, which are only three and a half inches wide — would seem to be all but impossible. ‘‘It’s abundantly clear,’’ Tomsheck, who eventually visited the site with the F.B.I., says, ‘‘that there was no potential for José Antonio to have thrown any projectile from where he stood when he was shot that could cause injury on the U.S. side of the border, not even if he were a major-league baseball pitcher.’’

In the first months after José Antonio’s death, Parra and Montiel acted primarily in an advocacy role for his family, collecting information from authorities in Mexico, where a criminal investigation remains open, and passing it along to the United States Department of Justice. No lawsuit of any kind had been filed, but Parra told me he and Montiel ‘‘absolutely’’ had hope that there would be a criminal prosecution of the Border Patrol agent in Arizona.

Border Patrol agents are generally immune from the kind of transparency required of most state and local law-enforcement departments. A 2013 investigation by The Arizona Republic found that since 2005, C.B.P. agents had killed at least 42 people, a majority of them in the United States, but most of the agents’ identities had been kept secret, and the officers faced ‘‘few, if any, public repercussions, even in cases in which the justification for the shooting seems dubious.’’ Thirteen of the cases involved American citizens; at least three involved unarmed teenagers who were shot in the back.

From a legal perspective, the complexity of cross-border shootings confounded José Antonio’s case even further. Had the Border Patrol agent been in Mexico when he shot the teenager, he could have been arrested and tried by Mexican authorities; likewise, had José Antonio been standing on American soil, most legal scholars agree, he would have had constitutional rights. But the presence of the border fence created a strange extralegal limbo. A similar cross-border shooting took place in Texas in 2010, in which a Border Patrol agent named Jesus Mesa Jr. shot and killed a 15-year-old boy, Sergio Adrián Hernández Güereca, who was accused of throwing rocks across the Rio Grande from Ciudad Juárez. In that case, the Fifth Circuit Court of Appeals ruled that Hernández’s family had no grounds for a lawsuit because he was a Mexican citizen standing on Mexican soil and therefore not protected by the United States Constitution.

Lee Gelernt, an attorney at the American Civil Liberties Union who would eventually work with José Antonio’s family, notes that the Nogales shooting raises ‘‘very, very big questions about the Constitution that the courts will have to resolve.’’ It also raises even broader questions about what, exactly, our borders signify. From the beginning, the story upended the typical mysteries that surround a killing. José Antonio’s death was not the sort of whodunit that involved a search for a murder weapon, or poring over C.S.I. reports, or a hunt for an unknown perpetrator. Most of the important facts, including the identity of the Border Patrol agent who shot José Antonio, were known in the immediate aftermath of the shooting, at least by the authorities. Rather, the mysteries inherent in the case were territorial, jurisdictional and, ultimately, philosophical.

At Internal Affairs, Tomsheck’s duties included determining security clearances and investigating administrative misconduct. But he soon discovered that when it came to more serious infractions, particularly involving excessive use of force, his office held little real power. ‘‘We had a mandate to hold the Border Patrol accountable but were given very few to no authorities to do that job,’’ he told me. ‘‘From Day 1, they aggressively resisted every effort.’’

Increasingly, Tomsheck found himself making better headway working with the F.B.I., where his work primarily involved corruption cases, assisting the bureau with investigations that eventually could be passed on to the Department of Justice. In 2007, working with the bureau, Tomsheck helped make a case against a Border Patrol agent named Eric Macias, who, using his badge to bypass airport security, boarded a domestic flight with five kilos of cocaine in his carry-on luggage. He eventually pleaded guilty to accepting bribes from drug smugglers and received a six-year prison sentence.

Tomsheck told me that he gave David Agui­lar, then chief of the Border Patrol, a courtesy call to let him know Macias was going to be arrested. He expected appreciation, but Agui­lar was furious. ‘‘He said, ‘You don’t get this! We don’t do what you’re doing! We manage these problems.’ He told me that making these kinds of arrests causes embarrassment for the families of agents who’ve died in the field.’’ (Aguilar declined to comment through a spokesman.)

By 2011, the sheer number of C.B.P. misconduct cases had become so glaring — an average of one C.B.P. officer was arrested every day between 2005 and 2012, 144 of them for corruption-level offenses — that C.B.P. redefined the way in which misconduct was categorized, Tomsheck said. Certain misconduct cases would be deemed ‘‘mission-compromising’’ and others ‘‘non-mission-compromising’’; only the former would have to be reported to Congress.

John Sandweg, who joined Homeland Security in 2009, serving as senior counselor and acting general counsel under Secretary Janet Napolitano and later as acting director of ICE, confirms Tomsheck’s accounts of intra-agency jostling. ‘‘A big source of tension,’’ Sandweg said, was D.H.S.-O.I.G.’s ‘‘strong belief’’ that C.B.P. Internal Affairs was violating protocol by passing leads to the F.B.I. instead of to the inspector general’s office, adding that a massive backlog of corruption cases at D.H.S.-O.I.G. was a major concern for Napolitano. The backlog was inevitable, Sandweg says, after ‘‘Congress doubled the size of the Border Patrol but never properly resourced D.H.S.-O.I.G. with enough investigators or funding.’’ But Sandweg pushes back strongly against Tomsheck’s contention that he was stymied for political reasons. ‘‘That’s a ridiculous allegation,’’ he says. ‘‘We were focused on ferreting out corruption cases, period.’’

Tomsheck was also concerned about the pace of the Border Patrol’s expansion. He believes it became impossible to properly screen all the new hires. ‘‘When you double the size of an agency so quickly, you will get people who are minimally qualified,’’ he says. I spoke with a former C.B.P. Internal Affairs investigator, E., who spent nearly two decades as a Border Patrol field agent in Texas and now works in corporate security. (He requested anonymity because his current position sometimes requires the help of old contacts at C.B.P.) E. also linked the hiring surge to problems at C.B.P.: ‘‘I’d see these chiefs I’d known all my career, and they’d say, ‘We’ve got to take what they send us.’ ’’ He continued, ‘‘A lot of stuff was bypassed during the hiring surge. They were mandated to fill those numbers. And Border Patrol, being Border Patrol, said, ‘O.K., bring it on.’ ’’ In 2010, testifying before a Senate Homeland Security subcommittee, Tom­sheck reported a staggering internal study: 60 percent of a pool of Border Patrol agents and customs inspectors who had been administered polygraph tests were deemed unsuitable for service.

Tomsheck thought many of the problems at C.B.P. could be attributed to the hiring of agents who had no law-enforcement experience. The new agents, Tomsheck says, ‘‘were assured they were not law enforcement but part of a military agency tasked with securing the border. I heard people internally use the word ‘cop’ in a derogatory way, which I took offense to. By the time I came to C.B.P., I had over 30 years of law-enforcement experience. I was a cop. But that’s not what C.B.P. leadership led these people to believe. They came to believe they were not subject to the same constraints as the rest of law enforcement in the United States.’’

E. has deep familiarity with the Arevalo case, including professional ties to members of the boat patrol, and he told me, ‘‘Knowing the details — seven rounds, that distance, with no justifiable cause — it’s intent.’’ He continued: ‘‘Even if he could’ve hurled that rock at that distance, for the agent to say he feared imminent bodily injury? If he did, he could have done something very simple: sat down.’’ In E.’s estimation, ‘‘He was executed.’’

James Wong, who served under Tomsheck as deputy assistant commissioner of Internal Affairs from 2008 to 2011, previously worked as a state police officer in Louisiana. He not only confirmed Tomsheck’s recollections of the pushback against Internal Affairs investigations but also shares Tomsheck’s view that the militarization of the Border Patrol has taken officers into dangerous territory. ‘‘When I started in law enforcement back in the early ’70s,’’ Wong told me, ‘‘we learned very early on that you don’t shoot a fleeing felon in the back, unless they’re shooting back over their shoulder or firing indiscriminately in front of them. To use deadly force just to prevent escape is illegal. The Border Patrol, on the other hand, has a viewpoint where they are on the front line defending the U.S. I have heard several Border Patrol agents say, ‘We will never surrender a foot of U.S. soil’ — essentially, ‘I’ll never retreat.’ If you have that mind-set, that sets up potentially deadly confrontations.’’ When he questioned agents about the use of deadly force in response to rockings, he said, the typical response was, ‘‘ ‘You’ve never worn green, so you don’t understand.’ The Border Patrol likened themselves to the Marine Corps. No offense — my son-in-law is a Marine. But if you’re a law-enforcement agency, that’s not what you should be modeling yourself after.’’

One afternoon last September, I visited the block of International Street where the shooting took place. A dog in front of a run-down house furiously tested its chain. Several of the fence’s bars had been tagged with stickers, each one about twice the size of a baseball card and illustrated, Shepard Fairey-style, with a portrait of José Antonio. The artist had painted the boy’s skin yellow, the shade of a butterscotch candy.

I’d been standing at the fence for approximately 20 seconds when the first Border Patrol car drove slowly past me. About a minute later, a second Border Patrol vehicle pulled up nearby. An agent emerged, wearing a stiff green uniform, a flak jacket and a sidearm. ‘‘You’re not allowed to pass anything through the fence,’’ he told me. I held up my notebook and identified myself as a reporter. Looking dubious, he replied, ‘‘If I see you doing anything, I’m going to have to do something about it.’’ I said O.K., and he returned to his truck, where he sat and watched me.

As I walked back to my rental car, the agent waved me over and asked what I was writing about. He was familiar with the case. ‘‘Sad story,’’ he said. Lowering his voice in a conspiratorial way, he added: ‘‘Thing is? It was totally legit.’’ He meant the shots. He wouldn’t elaborate, only to say that he’d had rocks thrown at him and that it was ‘‘some scary [expletive].’’ Then he pointed out a section of fence down the street that he said was a popular climbing spot. Sure enough, when I went over to take a look, the rust color of the bars had been worn away by overuse, leaving vitiligous blotches of white.

Just beyond that section of fence, José Antonio lived in one of the older barrios of Nogales. When I visited the site of his death, at the corner of Calle Ingenieros (Engineers Street) and Calle Internacional, the bullet holes in the wall of the doctor’s office had been filled in, but posters featuring images of José Antonio’s face and the word JUSTICIA! were pasted to the wall. Though it was after 8 p.m., a group of kids wearing uniforms came walking past on their way home from school. (Because of overcrowding, students attend school in Nogales and other parts of Mexico in shifts.) One boy was holding a basketball; a girl strummed a ukulele.

José Antonio lived a short walk from the corner, at the top of a hill and across the street from a primary school. His family’s home, surrounded by a variety of ramshackle dwellings, sits on a rocky outcropping, a couple of feet of which must be scaled to reach the yard, which is partly surrounded by a half-built cinder-block wall. Inside, in a modestly decorated living room with cracked plaster walls, a shrine had been erected atop an end table: a framed photograph of José Antonio at 15 surrounded by ceramic angels, flowers and religious candles. The photograph was the original image used by the poster artists. José Antonio seemed impossibly young, a crew-neck T-shirt visible beneath his striped polo shirt and a placid, searching expression on his face.

Araceli Rodríguez, José Antonio’s mother, was wearing a red blouse and jeans when I visited. (José Antonio’s family members all spoke in Spanish.) Her hair was pulled back, and her mouth remained fixed in a melancholy, anxious smile. She grew up in Navojoa, a small city not far from the Gulf of California coast. At 18, she moved to Nogales to join her brother’s family and soon met her future husband, Román Elena Zojo. She didn’t want to talk much about him: They had four children together, but he was convicted in 1999 for his part in a kidnapping incident in which the victim died, and he spent 10 years in prison. The couple separated during this period. Not long after his release, he was found dead in Nogales, Mexico, a plastic bag over his head and a cardboard sign attached to his body referring to los bajadores of the area, ‘‘the workers.’’ News articles at the time of his death said he had been smuggling drugs and undocumented immigrants into the United States.

José Antonio was 13 when his father was murdered. He had visited him in prison on occasion but never got to know him very well. Supporting her four children as a single mother, Araceli had taken a job cleaning a bank in Navojoa, a nine-hour bus ride from Nogales. The two youngest children, both girls, lived with their mother, while the boys remained at the house in Nogales, looked after by Taide Elena and an aunt. Araceli said she spoke with her sons constantly and visited as often as she could.

José Antonio’s brother, Diego, 22, is tall and slender, with a wispy goatee. He sat on a kitchen chair, beneath a crooked door frame. Norteño music drifted up from the street below, through the tight mesh of a metal screen door pocked with larger holes. When I asked Diego what sorts of things he and his brother did for fun, his face reddened, and he began to weep.

It was six months after José Antonio’s death before a pair of assistant United States attorneys from the Department of Justice finally arranged to speak with Araceli and Diego. Parra said the interviews took place in a room at the main border-crossing station in Nogales. (Despite living so close to the fence and having family on the other side, none of the family members had ever been granted a visa or visited the United States.) ‘‘It was pretty hard-nosed questioning,’’ Parra, who was at the interview, said, ‘‘but the family is absolutely sure José Antonio wasn’t involved in anything.’’

The D.O.J. also interviewed witnesses in Mexico. A 34-year-old security guard named Isidro Alvarado told investigators he was walking along Calle Internacional about 20 feet behind José Antonio when two young people came racing past them and turned onto a side street. Seconds later, multiple shots rang out, and José Antonio fell to the ground.

Another witness, a local restaurant owner who lived across the street from the doctor’s office where José Antonio collapsed, was pulling into his driveway when he heard a commotion near the fence. He told investigators that he saw the smugglers trying to climb back into Mexico. Then, he said, four men on the Mexican side of the border threw rocks toward the fence and ran past his house. After that, he heard multiple shots. When the gunfire stopped, he went outside and saw José Antonio’s body.

After their interview, the Rodríguez family received no further word from the Justice Department. Parra and Montiel couldn’t get any information, either — not about the status of the D.O.J.’s investigation or even if a criminal case would ever be brought against the agent.

Unknown to José Antonio’s family, whose grief had been magnified by the silence of the United States government, the incident had roiled the Border Patrol. By late 2012, news reports about the shooting of José Antonio had increased scrutiny of the agency. Tomsheck had also been telling the acting deputy C.B.P. commissioner, Thomas Winkowski, that there was a ‘‘use-of-force problem’’ within the agency. In response to these external pressures, C.B.P. commissioned a study by the independent, nonprofit Police Executive Research Forum (PERF), which reviewed every incident between January 2010 and October 2012 in which a Border Patrol agent had used deadly force: 67 cases in all, 19 resulting in deaths.

The damning report, which was leaked in February 2014, described agents ‘‘who intentionally put themselves into the exit path’’ of suspects fleeing in vehicles, ‘‘thereby . . . creating justification for the use of deadly force’’; in the case of rockings, the authors noted that ‘‘too many cases do not appear to meet the test of objective reasonableness with regard to the use of deadly force.’’ They recommended that C.B.P. ‘‘train agents to de-escalate these encounters by taking cover, moving out of range and/or using less lethal weapons.’’ The report also recommended that ‘‘officers/agents should be prohibited from using deadly force against subjects throwing objects not capable of causing serious physical injury or death.’’

The report did not cite specific details, but certain of the fatal Border Patrol shootings covered by the investigators had long been public — and troubling. In 2010, Miguel Torres Vasquez, a Border Patrol agent in Douglas, Ariz., shot and killed a fleeing undocumented migrant named Jorge Alfredo Solis Palma; Vasquez claimed Palma had been throwing rocks. That same year, in Eagle Pass, Tex., a Border Patrol agent named Taylor Poitevent chased down a pickup truck being driven by Juan Mendez Jr., an 18-year-old American citizen. Mendez had been trying to drive away with 320 pounds of marijuana that had been smuggled across the Rio Grande; Poitevent fatally shot Mendez in the back after the pair came to blows on a residential lawn. The following summer, a Border Patrol agent, Dorian Diaz, shot and killed Jesus Yañez Reyes, an undocumented migrant; Diaz claimed Reyes was throwing rocks from a tree on the Mexican side of the fence, near the Tijuana-San Diego border. No criminal charges were ever brought against any of the agents.

By the time the report was leaked, Tomsheck had had a copy for a year. Many within the agency had dismissed it. ‘‘The Border Patrol perspective was that many of the recommendations were not appropriate or valid,’’ Tom­sheck told me. ‘‘I saw this as another example of the Border Patrol attempting to advance a pattern and practice that departed significantly from use-of-force policies common throughout U.S. law enforcement.’’ But in May 2014, three months after the report leaked, a new C.B.P. commissioner, Gil Kerlikowske, released a revised use-of-force policy that incorporated a number of the report’s recommendations.

The following month, Tomsheck received a letter from Kerlikowske that he says is known, colloquially, as a ‘‘3R.’’ It forced him to resign, retire or accept a reassignment. He had had an inkling that he was going to be removed from his post at Internal Affairs. His constant clashes with C.B.P. leadership had made him deeply unpopular, and the PERF report had leaked after he had provided a copy, against the wishes of C.B.P. leadership, to D.H.S.-O.I.G. (Congress had been requesting copies from C.B.P. since the previous fall but had been given only summaries.)

 As the two-year anniversary of José Antonio’s death approached, the lawyers advised his family to move ahead with their only other recourse for justice: filing a lawsuit against the Border Patrol agent who shot him. The case had to be filed as a John Doe suit, because the agent was still anonymous; C.B.P. had not even indicated if the agent had been removed from his post or disciplined at all.

 Parra and Montiel asked the A.C.L.U. for help with the lawsuit, eventually partnering with Gelernt, who has been a human-rights observer at Guantánamo Bay and has argued before the Supreme Court. ‘‘The constitutional question José Antonio’s case is raising — about the extent to which the Constitution applies extraterritorially — is one that the A.C.L.U. institutionally has been working on in various contexts,’’ Gelernt told me. ‘‘At some level, it’s just common sense and basic fairness that the law has to allow his family to bring this lawsuit. It can’t be that a U.S. agent is going to put his gun through the hole in the fence and shoot at Mexican kids, 20 feet away, and there’ll be no ramifications. In a town where people are just necessarily walking along the border, there has to be some reciprocity of the rule of law. There can’t be just a situation where everybody who lives in a border town, in Canada or Mexico, runs the risk of being shot, without any ability to vindicate their rights.’’

Because of the failure of the previous lawsuit filed in Texas by the family of Sergio Adrián Hernández Güereca (which is being appealed), Gelernt understood that the case would be difficult — but also that, if a judge in the federal Court of Appeals allowed the lawsuit to move forward, it could set up a Supreme Court case, because two circuit courts of equal stature would have ruled in opposition on the same constitutional question. Rodríguez v. John Does was filed on July 29, 2014. ‘‘At the time of the shooting, the agents and/or officers were not under threat by [José Antonio] or anyone else standing near him,’’ the complaint read. ‘‘J.A.’s death was senseless and unjustified.’’

That November, José Antonio’s family members scored their first legal victory in the lawsuit when Raner Collins, a federal district judge in Arizona, ordered that the name of the Border Patrol agent be unsealed and released to the public. The agent’s name was Lonnie Ray Swartz. No other information, not even a photograph, was released, and Swartz did not appear in court. Nor did Araceli or Diego Rodríguez, who were still not allowed to enter the United States.

Judge Collins rejected Swartz’s immunity claim seven months later, a ruling that directly contradicted the Fifth Circuit Court of Appeals, which had found, in the Hernández case, that the boy’s family had no constitutional grounds for a lawsuit. Collins, in his decision, noted that José Antonio ‘‘was not suspected of, charged with or convicted of violating any law’’; that he was ‘‘visible and not hiding’’; that witnesses ‘‘stated that he did not pose a threat, but was peacefully walking down the street’’; that he was ‘‘not a citizen of a country with which the United States are at war’’; and that ‘‘upon information and belief, Swartz did not issue any verbal warnings before opening fire.’’ Swartz has appealed the ruling.

Just as the civil case appeared to be moving forward, there was another surprise, one that many of the interested parties had nearly stopped expecting: In September, it was announced that Swartz had been indicted by a federal grand jury in Tucson for second-degree murder. According to the indictment, Swartz ‘‘did with malice aforethought, and while armed with a P2000 semiautomatic pistol, unlawfully kill’’ José Antonio. On Oct. 9, 2015 — the day before the third anniversary of the boy’s death — Swartz appeared in a Tucson courtroom for the first time, the first Border Patrol agent to be prosecuted by the Department of Justice for a cross-border shooting. The Arizona Republic described him as a ‘‘tall man with crew-cut red hair and a light red mustache.’’ A Border Patrol union representative revealed that Swartz had been transferred to Nevada and that, in the wake of the indictment, he had been put on administrative leave.

Why now? Tomsheck, for one, had seen the evidence gathered by the F.B.I. — the videos, the autopsy report, the interview transcripts — in the immediate months after the shooting, all of which had been handed over to the Department of Justice. ‘‘I don’t understand why it took three years to indict,’’ Tomsheck says. Collins’s ruling, its toughness, may have ultimately played a role. ‘‘He made it very clear that the civil case needs to proceed, but he went beyond just saying that, using very strong language to indicate this is clearly excessive use of force,’’ Tomsheck said. ‘‘At the end of the day, it might have created a scenario where, if they didn’t criminally charge Swartz, there would have been a lot of explaining to do on the part of the Department of Justice.’’

The Border Patrol union released a statement saying it supported Swartz ‘‘100 percent.’’ Swartz has pleaded not guilty. Collins has placed a protective order on the trial evidence, meaning that for now, the thousands of pages of documents and videos of José Antonio’s shooting submitted by the United States attorney’s office will not be made public.

José Antonio’s family was elated by the indictment. Diego called the claims of rock throwing ‘‘a bunch of lies.’’ Elena said, ‘‘That’s always an excuse that they use. He wasn’t a hoodlum.’’

Elena would cross into Mexico regularly to visit her grandsons. The night before José Antonio died, he walked her back to the border checkpoint. ‘‘He was a good kid,’’ she said. ‘‘He was focused. He had goals.’’ She had already bought him the oversize watch he wanted for Christmas, even though it was only October. She ended up placing it inside his coffin.

Araceli and her children were given permission to attend the indictment, and they entered the United States for the first time. In court, seeing Swartz, Araceli said she was struck by his size. ‘‘He was a massive, large man,’’ she said. She couldn’t understand how a man that size could have felt endangered by her son. She didn’t look him directly in the face, and he never looked in the family’s direction. She doesn’t want to see any of the video or photographic evidence of her son’s death. ‘‘I want to remember my son as he was when he was alive,’’ she said. She plans to attend all the future hearings, ‘‘anything that requires the presence of that man in court.’’ The next hearing is scheduled for this month.

Wiping away tears, Araceli had told me when I visited her at her home: ‘‘There are times when we’re bad and we start thinking about José Antonio, and we kind of make believe that he’s still around. Because it’s unreal that he’s not.’’

It must be difficult to be asked to conjure a portrait of a lost child, to fix in time a person on the verge of growing up; inevitably, such efforts will feel woefully incomplete. According to his family, José Antonio was reserved. He preferred cloudy days. Diego used to tease him for crying during ‘‘The Lion King.’’ José Antonio knew his brother could be squeamish and a bit of a hypochondriac, and once tricked him into climbing out of a swimming hole by saying, ‘‘It looks like your eyes are about to pop out! How long have you been in there?’’ He had a girlfriend. He chided his brother for having his arm tattooed and refused to get any ink himself, out of fear it might hurt his chances to join the military when he turned 18, a plan he had made with a group of friends. For the same reason, he was determined to finish high school. He had been forced to temporarily drop out because his family couldn’t afford to pay tuition. The Monday after his death, he was scheduled to return to class.

Source: http://www.nytimes.com/2016/03/06/magazine/10-shots-across-the-border.html?_r=1