EL PASO — On a 99-degree day in May, a 24-year-old mother from Guatemala and her nine-year-old son scrambled onto a road near the Border Patrol station in Presidio County, Texas. She carried little with her except the $28 she had left after their long trip north.

Amilia and her son were among the more than 59,100 families apprehended by the Border Patrol after crossing into the U.S. illegally between October and the end of May, according to federal immigration data. Like thousands of others, she was detained at the border while her child was sent away — in her son's case, almost 2,000 miles to a facility in New York state.

But unlike nearly all the rest, Amilia, decided to fight. When the court asked how she would plead, she said, "No culpable" — not guilty — and went to trial.

NBC News Investigations and Noticias Telemundo Investiga obtained audio of Amilia's trial, a rare event in which a migrant charged with illegal entry challenges the criminal case against her. The details of her story, told in her own voice, lay bare the confusion of "zero tolerance," and the grief borne by the parents separated from the nearly 3,000 children now in the government's care.

Like so many others, Amilia, whose name has been changed because she is seeking asylum, said she came to the U.S. because she feared for her safety of that of her child. "Supposedly this is a place where you're not going to have any violence like we have in our country," she testified at her trial in early June. By that time, she had not seen or heard from her child in 22 days.

Listen to a migrant mother describe being separated from her son.

"I have no information about him," she said through tears. "I haven't been able to talk to him."

Under Attorney General Jeff Sessions' "zero tolerance" policy, launched in early May, an increasing number of parents arriving with children were subject to prosecution for crossing the border unlawfully. They were criminally charged, separated from their children and sent to jail to await court proceedings. Amilia was one.

"The government separated the families ... to punish them"

In federal courtrooms along the border, interviews with attorneys, court observation, and public records indicate most parents simply pleaded guilty — the norm in mass criminal immigration proceedings where migrants have little in the way of a winning defense and hope to get out of jail quickly. The details of why they left home, who they were apprehended with and what happened once they were in custody rarely make it into the court record.

In addition to taking the stand in her own defense, Amilia is now one of three Central American asylum seekers who are challenging the prolonged separation from their children in a civil lawsuit. Their complaint claims that the Trump administration's "family separation policy" is "designed, intended, and administered" to deter immigration — even by those seeking asylum — and that it violates their constitutional rights.

"You've got to have a darn good reason if you're going to interfere with parents' rights to care, custody and control of their child," said Jerome Wesevich, an attorney with Texas Rio Grande Legal Aid in El Paso, who represents Amilia in her civil suit.

The Department of Homeland Security declined to comment on Amilia's case, citing pending litigation. It has previously told NBC News that its policy toward family separation is a continuation of "a long-standing policy of the previous administration." The official said DHS only separates families when it cannot prove the family relationship, when they think a child might be at risk, or a parent is taken to jail on criminal charges. "That has not changed," the official said.

Wesevich disputes that, accusing the Trump administration of deliberately dividing families as a deterrent. "The reason the government separated the families was to punish them, to deter other people from coming into the United States because they would see the suffering that they inflicted on these families," he said. "But the Constitution prohibits punishing people who are civil detainees."

Fear is what made Amilia flee Guatemala, she testified. In early June, the tiny Mayan woman with a girlish voice took the stand in a federal courtroom in El Paso and told her story.

She gave birth as a teen, she said, and spent most of her adult years in a village in the western highlands, caring for her son and her siblings while her mother worked.

This spring, she began to get threatening phone calls. The voice on the line didn't identify itself, but she knew it belonged to a gang member. In Guatemala, she explained, gangs regularly extort people, demanding money in exchange for one's life, or the lives of family members.

Amilia testified in Spanish, and an interpreter translated her words for the courtroom. "They told me if I didn't give them any money that they would either harm me, or harm my child," she said.

To stop the calls, she cut off her phone. Within two days, she had borrowed $4,000 from neighbors and taken her son north to Mexico, bound for the U.S. On one bus then another, she followed a winding path blazed by thousands of other migrants.

Starting in about 2011, the U.S. began to see a rise in the number of families and unaccompanied children migrating north from Central America's Northern Triangle. Poverty is one driver. But many also seek asylum from violence and political persecution.

The Obama administration reacted by significantly expanding family detention, expediting the deportation of families apprehended crossing the border. But it also instituted a directive that immigration enforcement "not unnecessarily disrupt the parental rights" of those in custody. As a result, parents with minor children were not a priority for criminal prosecution.

In August 2017, the Trump administration re-wrote that policy. The new guidelines removed the definition of parental rights from the directive, as well as the section encouraging prosecutors to use discretion in cases of parents with minor children.

"They just took a delete pen to it," said Wesevich, Amilia's civil attorney. "We are arguing that it means that they decided that they would develop detention standards regardless of the impact on parental rights. It's basically saying that we don't care if we act unconstitutionally."

A spokesperson for Immigration and Customs Enforcement (ICE) told NBC News that the new directive allowed "for the fair execution of immigration enforcement laws while also balancing those equities of detained parents who need to access child welfare proceedings."

"We cannot write the kids out of existence"

That is the changed landscape Amilia entered when she and her son waded across the Rio Grande into Texas in mid-May. Once on the U.S. side, mother and son climbed a dirt slope to the top of a levee.

There, Amilia testified, she found a group of other women and children. They began to walk north, toward the international bridge where the Border Patrol station sits. A few moments later, a Border Patrol agent arrested the group.

Amilia said she did not try to run. She said she believed that if she came with her child, she could stay. "We were told that as soon as you arrive to the border, immigration would take you somewhere," she told the court. "I was waiting for them to do that."

Amilia and two other mothers, who would be tried with her, were processed at the Border Patrol station. Agents asked her to sign a form acknowledging she had been read her Miranda Rights. Testimony at trial revealed Amilia had signed it with an "X" because, the Border Patrol agent testified, "she can't read or write."

That night, Amilia and her son slept together in the custody of the Border Patrol. The following day, agents came to talk to her. "They came in the morning and they told me they were going to take my child, and they were going to prosecute me," she testified, her voice catching as she began to cry.

One day after she arrived in Texas, Amilia's child was gone.

Her public defender Chris Carlin would later discover there was no reference to her child in the paperwork filled out by the Border Patrol. Nor did children appear in the files of the other two women arrested with her.

Carlin told the court that it raised fundamental legal issues in her prosecution.

"There is no mention of a child whatsoever in this file," he argued. "What that means is that in the future if anybody accesses the [immigration file] they would never know that these women came in with a child. And that implicates a fundamental due process concern that is part of this prosecution. We cannot write the kids out of existence."

Carlin asked Amilia, "You wanted to protect your child by coming here, didn't you?

"Yes," she testified.

"Are you afraid you've lost your child now?" he asked.

By this time, she had stopped crying. Quietly, she answered, "Yes."

The magistrate judge who heard Amilia's case found her guilty of illegal entry and sentenced her to time served. She is now appealing her conviction and pursuing an asylum claim from the confines of a detention facility in Texas. She is also among the class of parents covered by a federal court injunction ordering that all separated families be reunited by July 26.

As a result of her civil lawsuit, Amilia learned that her son was in a shelter in New York. They now speak twice a week. But she told the civil court in a declaration that on the phone, her son can do little more than cry.

"My son used to be such a happy child," she wrote. Now in their short conversations, she said, "he only asks when we will see each other and begs to be with me."

Since they've been apart, Amilia wrote, she has had trouble eating and sleeping. "When I go to eat I am reminded of when we used to eat together," she wrote. "When I try to sleep I remember how he always slept with me."

"It breaks my heart not to have him with me," she said. "I don't understand how someone could take their child away from their mother. I think, 'Don't they have children too?'"