Luis was 13 when he and his mother waded across the Rio Grande in October 2017 and turned themselves over to border patrol near El Paso, Texas.

They were fleeing murderous gang violence in El Salvador in hope of reuniting with Luis’s older brother, William, who was already in the United States. Luis thought their odyssey had ended.

Instead, another began, a journey through a bureaucratic labyrinth which cleaved mother from son in a five-month ordeal of isolation and loneliness, locked rooms and shelters, handcuffs and fingerprints, cross-country flights and crushing, draining uncertainty.

“I remembered God existed when I left the shelter to reunite with my brother,” Luis, now 14, told the Guardian in a phone interview this week.

His experience underscores the fact that many families have been broken up and marooned in legal limbo even before the Trump administration announced a “zero tolerance” policy for illegal border crossings. The fate of some 2,300 separated children remains unclear in the wake of the president’s executive action to end separations.

The family’s decision to leave home and make the trek north came from the moment a gang murdered Luis’s father, an army sergeant, in 2012, another casualty of one of the world’s highest homicide rates.

When gang members threatened William in 2016 he fled, eventually settling in New Orleans. When they started threatening Luis in 2017, on his way to and from school, his mother, Blanca Vásquez, decided to seek safety in the US.

They made it to Ciudad Juarez on the US-Mexican border before being abandoned by their coyote on the Mexican side of the Rio Grande, said Luis. They crossed without him. “The water came up to my waist, about three feet.”

The plan was to seek asylum so they flagged down a border patrol agent, who ordered them to put their hands up. “He kept me outside the patrol car and he put my mother in the patrol car. He handcuffed me. I don’t know why he had to handcuff me. I’m a child and they aren’t meant to do that.”

At the station in Ysleta agents unshackled Luis, fingerprinted his mother and separated them. They would not see each other again until March 2018.

“I was in the hielera (“ice box”) for three days. The first thing I did was ask to call my brother,” said Luis. An agent extracted the phone number from a piece of paper in his mother’s Bible and let him make a five-minute call.

“I wasn’t in contact with my brother again for the three days they had me in that other office. I was there alone. There was a clock. I was locked in. I could not open the door. On the first day they showed me films but for the next two days they didn’t show me anything. They did not ask me anything. I felt alone. I felt bad. I did not know what to do. I did not know anything about my mother.”

Authorities took Luis to the airport in El Paso and gave him fresh clothes but, tall for his age, they did not fit. “I had to wear the clothes I had when they apprehended us at the border because the pants they gave me stopped around my knees.”

He joined 12 other boys who were flown to Houston, then on to a shelter in New York. “I liked how they treated us there. They gave us clothing. They took our details, where we were from, our birth dates, and our documents to help identify us.”

After a week of medical exams the boys started classes in mathematics, English and US history. Luis’s stay ended abruptly in mid-December.

“One night they arrived and told me I was leaving the next day at six in the morning. They gave me a bag and told me to pack it. I didn’t have enough time to get the papers they gave me in school about American history.”

That was when Luis learned he would see William, and remembered God’s existence. “I prayed because I was about to leave that place. I liked the shelter but I thanked God I was about to be with my brother.”

A shelter worker took Luis to the airport and handed him to a Delta employee. He flew to New Orleans to an emotional reunion with William. For the first time in almost two months he also got to speak to his mother by phone.

He learned she had been prosecuted for the misdemeanor offense of unlawful entry. Prosecutors had also threatened to charge her with child trafficking.

After being convicted of the misdemeanor and sentenced to time served Luis’s mother was placed in immigration detention in El Paso and Sierra Blanca, Texas.

She remained in custody until an immigration judge accepted her credible fear claim that she would be murdered if deported to El Salvador.

She was released in March and joined her sons in New Orleans.

“If I could tell you more things I would but I have decided to forget them,” said Luis. “I have decided to forget this moment of my life. I like living here in the United States because I can go out in the streets without being threatened, just like everybody else.”