Nazario sat in a cell in a private prison in San Diego, weeping. His 5-year-old daughter had been taken away by U.S. border agents. Filomena had been by his side almost every day of her life. Now he had no idea where she was, whether she was all right, and when he would see her again.

The 32-year-old peasant farmer had left his village in the western highlands of Guatemala and traveled all the way across Mexico with Filomena. He was fleeing a local gang that had threatened to kill him. (Out of concern for the family’s safety, KQED is not using their last names.)

Nazario and Filomena reached the California border on May 16 and, a little after 6 p.m., crossed with a couple of other travelers into the hills of eastern San Diego County. This is their story gathered from Nazario’s public defender, court documents and conversations with Nazario’s wife in Guatemala.

A Border Patrol affidavit describes what happened next: “Agent Sparks encountered four individuals walking the border road toward him.” The agent arrested the four, who told him they were citizens of Guatemala. Nazario acknowledged that he had entered the United States illegally, the agent said. Nazario said that he had come to the U.S. to ask for asylum, according to a legal declaration he dictated later to his court-appointed criminal defense lawyer.

At the Border Patrol station in Campo, California, Nazario was told he would be sent to jail. He was to be prosecuted in federal court for the misdemeanor offense of illegally entering the country.

Scared, Filomena clung to him, Nazario said in his declaration. And then: “Two Border Patrol Agents grabbed her out of my arms. ... My daughter was screaming and crying. And so was I.”

Officials with U.S. Customs and Border Protection, which oversees the Border Patrol, did not respond to repeated requests for comment.

Nazario said the agents told him he would be in jail for two or three days and then would be returned to his daughter, who would stay at the Border Patrol station. But that’s not what happened at all.

Caught in the Policy Crossfire

Nazario and his daughter walked into the United States in the midst of a dramatic reworking of how this country handles unauthorized immigrants -- including those seeking asylum and those traveling with children. Thousands of children like Filomena have been removed from their parents and placed into a confusing system of institutional care that is stretched beyond its maximum capacity. Government directives have shifted repeatedly in recent days, leading to confusion and lack of communication among agencies.

For Nazario and Filomena, the result is utter bewilderment and pain.

Here are some of the recent developments:

• April 6 -- Attorney General Jeff Sessions announced a zero tolerance policy of criminally prosecuting everyone caught unlawfully crossing into the U.S.
• May 7 -- Sessions held a press conference with ICE acting director Thomas Homan at the border fence in San Diego, and said, “If you are smuggling a child, then we will prosecute you and that child will be separated from you as required by law.”
• June 20 -- Last Wednesday, after an outcry over family separation, President Trump signed an executive order stating that the government’s policy is now to keep unauthorized immigrant families together, “where appropriate and consistent with law and available resources.”
• June 21 -- The following day, a senior Customs and Border Protection official told the Washington Post that, in order to promote family unity, the agency would stop referring migrant parents for prosecution if they were traveling with children. The Department of Justice asserted that the zero tolerance prosecution policy still applied to everyone.
• June 23 -- On Saturday, the Department of Homeland Security issued a fact sheet describing steps it was taking to reunite children with their parents. The memo said 522 children had been returned to parents by Customs and Border Protection. And, it said, an additional 2,053 “separated” children were in the custody of the Department of Health and Human Services, whose Office of Refugee Resettlement is responsible for “unaccompanied alien children,” now including those, like Filomena, who were taken from their parents. The memo does not provide a timeline for the reunifications, and what will happen to the children remains uncertain.

A Tough Choice

Back in their mountain village in Guatemala, Filomena used to go just about everywhere with her Papi. When he went to the fields to hoe the potatoes, Filomena went, too. And together they would go home to her mother and 2-year-old brother. She liked to play, and to write and draw in her notebook, said Filomena’s mother, Marcela, who spoke to KQED by phone.

Then a local gang began to menace Nazario. They tried to extort money from him and threatened murder, Marcela said. The Guatemalan government is weak and, after years of civil war and economic hardship, more young men are drawn to gangs and commit violence with impunity. The threat is growing, even in rural areas. Nazario felt he had to escape. He had relatives in California. Maybe he could find refuge there. Worried that Marcela would have difficulty managing the farm with two small children, the couple agreed Nazario would take his daughter with him.

After Nazario had gone, Marcela said the gang members returned, looking for him. They beat her up, she said, but “at least they didn’t kill me.”

A Complicated Legal Maze

In San Diego, Nazario was held by the U.S. Marshals Service while his criminal trial went forward. He spent two weeks locked in a detention facility run by the Geo Group, a private prison company contracted by the government. Because he was a criminal defendant, the government appointed him a public defender. (In immigration matters, however, neither he nor Filomena was entitled to appointed counsel. Many immigrants appear in court without a lawyer.) The authorities never told him where his daughter was.

When federal public defender James Chavez first met with Nazario, he spent a long time trying to explain the complex U.S. system, with its criminal and immigration proceedings. The Guatemalan man found it very confusing.

“Nazario is an individual without any formal education,” said Chavez. “I’m not confident that he fully understood what happened to him. And that’s not uncommon.”

What Nazario did understand was that his daughter was gone from him. He told the lawyer he cried nearly every day.

Chavez began to search, with the help of the ACLU and the Guatemalan Consulate. It took 10 days before he located Filomena. She had been put in the custody of the Office of Refugee Resettlement, known as ORR, and transferred to New York.

“I do not know where New York is. I was told it was very far,” Nazario said in his declaration.

Chavez said he spoke with a kindhearted ORR caseworker who had met with Filomena.

“She just described a little girl who was crying every day, who was missing her father very much,” he said. “Which parallels him crying every day, missing his little girl.”

Officials with ORR did not respond to repeated requests for comment. And Chavez did not want to divulge exactly where Filomena was staying, for fear of jeopardizing her quick release. But most very young children in ORR custody are housed in foster homes, rather than institutional shelters, according to Anthony Enriquez, director of the unaccompanied minors program at Catholic Charities of New York. Foster families are hired by the nonprofit agencies that contract with ORR to care for the children.

It can take as much as 10 days before Catholic Charities staff can communicate with kids in ORR custody, said Enriquez. Once they do, he and his staff work with ORR case managers to establish contact between children and their parents. Filomena was able to speak to her mother about three weeks ago.

Marcela said her little girl told her she did not want to be where she was. She wanted to be back home with her family.

“I’m desperate,” said Marcela in Spanish. “I don’t know where she is. I don’t know what that place is like. I still don’t know how she is. So I feel desperate. I feel sad every day.”

In New York, the Catholic Charities lawyers are scrambling to get the children’s cases before a judge in the notoriously overburdened immigration courts. If they succeed in getting a case onto an expedited docket, it can be heard in one to two weeks, said Enriquez.

“As dedicated lawyers, we’re trying to move this as fast as possible,” he said. “The longer children are separated, the greater the risk of psychological damage.”

But because the immigration court process for children has more protections, it can take longer. All unaccompanied children, including those like Filomena who were rendered unaccompanied, are entitled to a hearing before an immigration judge. By contrast, adults like Nazario are subject to a summary deportation, called expedited removal. Recent border crossers are entitled to see an immigration judge only if an asylum officer from U.S. Citizenship and Immigration Services finds they have a credible fear of persecution in their home country.

In order to get separated children back to their parents more quickly, Enriquez said, Catholic Charities lawyers are now requesting that judges ask ICE prosecutors to withdraw their cases.  This allows the court to release the child to be returned home. Enriquez said he and other lawyers are also using the court proceeding to hold the government accountable: “We can always say, ‘Your Honor, you should ask the government lawyer: Where is the parent? Why has this child been separated? Why is there not a system to reunify the family before deportation? Why can’t the government facilitate more communication?’”

Giving Up on Protection in the U.S.

Back in San Diego, Nazario remained distraught. In spite of the danger that propelled him north, he decided to abandon his asylum claim. If he had pursued asylum he would likely have been locked up for months or even years -- without Filomena.

In his declaration he said: “After being in jail for two weeks and having my daughter taken away from me, I decided that the United States is not a place that would protect me.”

On May 30, he pleaded guilty to illegal entry in criminal court and was sentenced to time served. His hope was that if he accepted deportation by immigration authorities, he would be reunited with his child.

Then federal marshals handed Nazario over to ICE, which took him to a different private prison in San Diego just for people in immigration proceedings -- the Otay Mesa Detention Center, run by a company called CoreCivic. His lawyer said it took a couple more weeks before an ICE agent came to talk to Nazario about his asylum claim and his decision to give it up.

“My impression of Nazario is that he was deeply depressed, maybe even broken,” said public defender Chavez, who met with Nazario five or six times while he was jailed in San Diego, visiting even after the criminal case had been resolved.

Finally, on June 19, ICE transferred Nazario to Arizona. And on June 20, the very same day that President Trump reversed his stance on separating families, Nazario was flown back to Guatemala City. Filomena was not with him.

In the five weeks Nazario spent in U.S. government custody, he was never once able to speak to Filomena. He didn’t have money for a jail phone call. And James Chavez, juggling the legal demands of many other cases, couldn’t make it happen.

But Chavez said that Nazario’s case was the most disturbing he’d had in a decade as a federal defender. And he wasn’t willing to let it go.

“This case has touched me personally, being a father of two small children myself and having gotten to know a good man who’s going through a real nightmare,” he said. “Just as a fellow human being, I want to make sure I do everything I can to help him be reunited with his young daughter.”

So he said he’ll keep working with the Guatemalan Consulate and the immigration lawyers in New York, to get Filomena sent safely back to Guatemala. It could take weeks.

NOTE: KQED spelled the name of the girl in this story "Filemona," as it appeared on a U.S. court document filed by her father. In fact, her name is spelled "Filomena" and appears that way on her Guatemalan birth certificate.