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.