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.