José was seven years old when they put him on the raft.

The smugglers were sending him across the Rio Grande to reunite with his mother, who had left him back in Honduras two years earlier and moved to Texas.

He boarded the raft with his sole possession: a piece of laminated paper bearing her phone number and address.

His mother had borrowed $3,500 (£2,700) from a cousin and a friend to pay the coyotes.

Her brother handed José over to the men, who tried to scare the boy into staying quiet as the raft pushed off from the Mexican shore.

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“They were telling me that they were going to report me to my country,” José said. “But I didn’t believe him.”

What the boy didn’t know was that reaching his mother would be much harder than finding a Border Patrol agent, spending a few days in custody and then looking for his mother’s house, as he had been told to do.

He found the Border Patrol, all right, but instead of being handed over to his mother, José was sent to a foster care facility in New York, where he was held for nearly eight months as his mother tried to win permission for his release. She didn’t succeed until April.

José was what the federal government calls an “unaccompanied minor” — an abstract clinical description for a dangerously specific human drama that has been playing out in ever-larger numbers along the southwest border.

Although the Trump administration has officially ended its policy of taking children away from their parents if families are caught crossing the border illegally, young children like José continue to be held in US immigration detention facilities, sometimes for months at a time, because of regulations requiring complicated screening procedures that officials say are intended to ensure the children’s safety.

Much of the time, young people take the dangerous journey from Honduras, Guatemala and El Salvador on their own or with a smuggler to rejoin parents in the United States.

In many cases, their parents came to the United States illegally, settled somewhere and then, possibly years later, sent for the children they left behind.

It is a phenomenon that has been going on for decades, but as the number of Central American migrants arriving at the border continues to grow, there has also been a sharp increase in young people travelling alone.

While there were 38,189 apprehensions on the south-western border of Central American children travelling alone in the 2018 fiscal year, there have been 37,669 in the current fiscal year as of April.

José’s mother, Patricia, 23, did not want to disclose her or her son’s last name, because of fears of reprisals from the government because of their immigration status.

Patricia is in the country illegally, and an immigration court judge has ordered her to be deported.

Their story began in 2016, when Patricia left Honduras, leaving her son, whose father had died before he was born, with relatives.

She settled in Bryan, Texas, started a new life as a house painter and gave birth to another child, a daughter, now 2.

Trump compares US-Mexico border to Disneyland and calls end to family separations a disaster

Finally, she said, she told relatives she was ready for them to send José to her.

She had assumed he would spend some time in Border Patrol custody, she said, but had no idea he would be sent to a foster care program in New York while the government decided whom he should be released to.

Weeks went by.

Then months. Finally, the paperwork settled, José was put on a plane bound for Houston on 11 April and joined his mother.

Nearly eight months had elapsed since he left Honduras.

To discourage the large migration flows, the Trump administration has repeatedly called attention to the dangers that parents are subjecting their children to on the journey from Central America.

Children have been abandoned by coyotes, like the 3-year-old boy that Border Patrol agents discovered alone and crying in April in a cornfield; they have survived near-drownings, sexual and physical abuse, and gruelling hikes.

The uncertainty and hardships often continue once the children are in government hands, say many of those who work with newly arrived migrants, even though the government no longer has a policy of separating families.

In the case of José’s family, Patricia said she had difficulty communicating with her son after he arrived in the United States, or even finding out what was happening to him.

“I would send messages, and sometimes I wouldn’t get a response, and sometimes I would,” she said. “I had never seen an extreme case that would take this long.”

After he was apprehended at the Texas border, José was placed with the Cayuga Centres, a New York non-profit group that runs a foster-care program that receives federal money to assist migrant children.

He remained in Cayuga’s custody from early September until he was released in April.

The federal Office of Refugee Resettlement oversees the care and housing of unaccompanied minors, whom the government calls unaccompanied alien children, or UACs.

Baby girl returned to Honduran mother after separated and detained at US-Mexico border

A spokeswoman declined to comment about José, noting in a statement that to protect the privacy and security of children in the country illegally, “their locations are kept confidential and we do not identify or discuss specific UAC cases”.

The average length of care in the federal unaccompanied minor program is 66 days, or about two months.

Jose’s case was an unusually complex one involving an investigation of a possible child-safety issue, according to some of those working on the case.

Patricia said she knew of no circumstance that would have justified keeping her son away from her for so long.

José has had a rough transition after spending two years apart from his mother in Honduras, then enduring the crossing, the months in custody and his enrolment in first grade at a new school in a new city.

He has acted out, his mother said, as he tries to find his footing.

Another mother in the country illegally who lives in Bryan knows how hard that transition can be.

Jesus, an acquaintance of Patricia’s, came to the United States several years ago after leaving her own son behind in El Salvador, then sent for him.

The boy, Ernesto, was 12 years old when he made the crossing with an older teenage cousin a few years ago.

Now 15 and a sophomore at a Bryan high school, Ernesto, whose family also asked that their last names not be used, said many students at his school had made the frightening river crossing over the Rio Grande to join their parents in the United States.

It is a bond among them that often goes unspoken. “I don’t really talk about it,” he said.

Ernesto said he struggled to learn English and to become a son again — he had been only 4 when his mother left El Salvador. “I didn’t have the money to bring him with me,” Jesus said.

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Both Patricia and Jesus defended their decisions to make new lives in the United States before sending for their children.

The escalating gang violence in El Salvador convinced Jesus to pay a smuggler to bring Ernesto, she said.

“He was more in danger there than anything, so that’s why I decided for him to come,” she said. “It’s a risk you have to take, for good or for bad. You can’t explain it, from the time you leave them to the time you see them, there’s just so much. There’s so many emotions, you can’t explain it.”

Patricia, too, said she knew the risks of the journey, but she felt more at ease because her brother would be with José most of the way.

Still, she said, she had trouble sleeping as José and her brother travelled to the border. “I thank God that he crossed safely,” she said, “because I’ve seen lots of news stories where a lot of my people have suffered tragedies and have died.”