Updated at 3:55 p.m. June 15: This story has been updated to reflect new figures on the number of children taken into federal custody and to reflect plans to construct a tent city for children in Tornillo, Texas.

RIO GRANDE VALLEY — Rudy Ramirez-Mendez stood up from the courtroom bench, the chain shackles at his waist and ankles clanking as the mass hearing where he was being accused of entering the country illegally was nearing an end.

"They will be sending us back to our countries, but what will happen to our children?" Ramirez-Mendez, who came north from Guatemala with a child, asked Judge Juan Alanis.

"Unfortunately, I don't have the answers here," the magistrate judge replied. "As for being separated from your children, that is current policy of the U.S. government."

Ramirez-Mendez was caught in the new "zero-tolerance" crackdown of the Trump administration, where immigrants face criminal prosecution for unlawful border entry. Charging immigrants who improperly enter the U.S. with a crime

for many resulted in the worst of punishments: Children taken away by the federal government and sent to government shelters.

1 / 5Detained immigrants load into buses at the federal courthouse in McAllen, Texas, on June 11, 2018. After immigrants plead guilty for improper entry into the U.S., many are released on time served and may end up back in the civil immigration system. (Nathan Hunsinger / Staff Photographer) 2 / 5Detained immigrants are loaded into buses at the federal courthouse in McAllen, Texas on June 11, 2018. (Nathan Hunsinger / Staff Photographer) 3 / 5A U.S. Border patrol officer loads up chains and shackles at the federal courthouse in McAllen, Texas on June 11, 2018. (Nathan Hunsinger / Staff Photographer) 4 / 5Detained immigrants unload from buses at the federal courthouse in McAllen, Texas, on June 11, 2018. Many more immigrants who cross the border without authorization are now being charged with a crime. They face mass court appearances where most plead guilty.(Nathan Hunsinger / Staff Photographer) 5 / 5A bus of detained immigrants leaves the federal courthouse in McAllen, Texas on June 11, 2018. (Nathan Hunsinger/The Dallas Morning News)(Nathan Hunsinger / Staff Photographer)

Ramirez-Mendez had just pleaded guilty to a criminal misdemeanor, along with 84 other immigrants in chains, in a mass hearing where charges and responses of culpable, guilty, were taken, many in less than a minute.

Outrage is building here along the U.S.-Mexico border and elsewhere as social workers and lawyers scramble to assist desperate families, most of whom are from El Salvador, Guatemala

Honduras, who arrive to be quickly caught up in the criminal courts. They argue many of the families are refugees fleeing violence who therefore merit immigration hearings in the civil system where their asylum cases can be heard.

"Are we reflecting who we are as a country of principles with respect for human life?" asked Sister Norma Pimentel, a Catholic nun who started a McAllen shelter four years ago when families and minors

alone came across the border in swelling numbers.

"If you are a mother and your child is in danger,

you will flee" a place like El Salvador, which has one of the highest murder rates in the world, Pimentel said. "Zero tolerance is inhumane. You are using human beings to make your point. It is wrong."

Federal workers and relief agencies say new, tougher immigration policies are straining their ability to cope with the latest influx of immigrants. Away from the border, in Washington, D.C., others defend the policy, calling it a deterrent for illegal immigration.

"Zero tolerance is an essential part of asserting control," said Mark Krikorian, the executive director of the Center for Immigration Studies, a conservative think tank that wants to limit both legal and illegal immigration.

"Most are not rapists and dope dealers. They are average schmoes," he said. But once they face prison time with those with dangerous criminals, crossing the border will be unattractive, Krikorian said.

The road to 'zero tolerance'

This day, in the stuffy courtroom where every seat was filled, everyone

guilty. Many were sentenced to time served.

Prosecutor Colin

asked the judge to sentence others to only 10 to 30 days behind bars.

Most of those had crossed the border before but had not been found guilty of a crime before. They'd faced only civil action in the immigration courts.

The judge agreed to the light sentences. That might allow defendants to reunited sooner with their families. But the immigrants, and the

weren't sure.

Monday morning, Judge Alanis politely deflected questions about defendants being reunited, telling the immigrants it was the job of another agency. That would be the Office of Refugee Resettlement within the U.S. Department of Health and Human Services. And immigrants could face civil hearings in the clogged immigration system, or simply be deported while their child is in a federally supervised shelter.

In the immigration courts, they would have a chance to request asylum. But U.S. Attorney General Jeff Sessions announced Monday that he would be limiting the application of key asylum claims often used by Central Americans: He said gang violence and domestic violence are not valid reasons for granting asylum.

"That's 90 percent of the asylum claims for Central Americans," said Dallas immigration attorney and asylum expert Paul Zoltan.

Session's decision adds one more layer to the deepening immigration crisis. His April announcement of "zero tolerance" is not the first, and immigrants have been charged criminally for crossing the border in the past. But the directive to charge everyone suspected of crossing illegally with a crime has thrown a wrench into an already overloaded system.

Criminal charges generally result in children being separated from their parents. Now that this is happening more often and to more immigrant families, a wave of revulsion has followed.

Federal public defender Margie Meyers described separations as "horrific." Meyers, who supervises a huge swath of southern Texas, said, "It is a nightmare for parents, but especially for the children."

For Sessions, deterrence is the point. As he said May 7, "if you don't want your child to be separated, then don't bring him across the border illegally."

An overloaded system

The U.S. has a dual-track system of justice for handling immigrants who cross the border without proper authorization.

The vast majority of people who cross the border without authorization end up in the civil immigration courts, where there's a backlog of about 714,000 cases. When an immigrant arrives at the border, if he or she crosses without authorization or makes it to a port of entry to ask for asylum, it can take two to three years for a case to work its way through the court. That means immigrants can buy time while their cases wind through the courts — a fact that immigration hard-liners have emphasized as a fault in the system.

Enter the criminal courts: Prosecutors have had the power to slap immigrants with unlawful entry misdemeanor charges or re-entry felony charges for decades. But its use grew in 2005 with the launch of Operation Streamline at the Texas border. Now, Sessions wants all people making even first-time unauthorized crossings to face a criminal charge.

1 / 10Immigrants wait to be picked up by volunteers from Catholic Charities of the Rio Grande Valley after being dropped off by federal immigration staff at the bus station in McAllen, Texas, on June 10, 2018. These immigrants now face deportation hearings in the civil immigration courts later. (Nathan Hunsinger / Staff Photographer) 2 / 10Immigrants cross in front of the federal courthouse with the assistance of volunteers of Catholic Charities of the Rio Grande Valley after being dropped off by ICE at the bus station in McAllen, Texas, on June 10, 2018. (Nathan Hunsinger / Staff Photographer) 3 / 10Immigrants wait to be picked up by volunteers of Catholic Charities of the Rio Grande Valley after being dropped off by ICE at the bus station in McAllen, Texas, on June 10, 2018. (Nathan Hunsinger / Staff Photographer) 4 / 10An immigrant's personal items at the Humanitarian Respite Center in McAllen, Texas on June 10, 2018. His laces and property were put in a bag while being detained by ICE. (Nathan Hunsinger / Staff Photographer) 5 / 10A immigrant puts shoelaces back on his child's shoes at the Humanitarian Respite Center in McAllen, Texas on June 10, 2018. Their laces and property were put in a bag while being detained by ICE. (Nathan Hunsinger / Staff Photographer) 6 / 10Jonathan Pineda, 23, from El Salvador, holds his son Jonathan Pineda, 2, at the Humanitarian Respite Center in McAllen, Texas on June 10, 2018.(Nathan Hunsinger / Staff Photographer) 7 / 10Batteries for ankle monitors charge at the Humanitarian Respite Center in McAllen, Texas on June 10, 2018. (Nathan Hunsinger / Staff Photographer) 8 / 10After phoning their families, immigrants walk back to the bus station for a ride in McAllen, Texas, on June 10, 2018. (Nathan Hunsinger / Staff Photographer) 9 / 10Immigrants wait to get their bus tickets after at the bus station at McAllen, Texas on June 10, 2018. (Nathan Hunsinger / Staff Photographer) 10 / 10Immigrants wait to get their bus tickets after at the bus station at McAllen, Texas on June 10, 2018. (Nathan Hunsinger / Staff Photographer)

Criminal courtroom staff along the 2,000-mile border from San Diego to Brownsville moved quickly to follow orders from the attorney general. They've picked up the pace: Prosecutions jumped 30 percent in April over May, according to the Syracuse University nonprofit known as the Transactional Records Access Clearinghouse or TRAC.

With such an onslaught of cases coming from federal prosecutors, some immigrant defendants are receiving only 10 to 15 minutes of prep time from public defenders, Meyers said.

The result has been the sharp increase in families separated from children. "Twelve to 20 to 30 clients a day have had their children taken away" in McAllen, said Meyers.

In fact, U.S. Deputy Border Chief Richard Hudson testified at a Senate Judiciary Committee hearing that 658 children were separated from 638 parents during one two-week period in May. The Associated Press reported Friday that nearly 2,000 children who crossed the border between official border crossings had been separated from their parents between April 19 and May 31.

Tents were being prepared in Tornillo, Texas, southeast of El Paso, for children as shelters continue to fill up. Health and Human Services has 100 shelters for about 11,000 and is near capacity. Children spend on average about six weeks in the HHS shelters before being united with their parents or guardians, according to HHS.

Tuesday, the American Bar Association weighed in, calling for zero tolerance to be rescinded by Sessions and Kirstjen Nielsen, the head of Department of Homeland Security, where immigration agencies are housed.

A federal lawsuit filed in California is challenging the family separations. Its two plaintiffs are women, one from the Democratic Republic of the Congo who was separated from her screaming 6-year-old daughter in San Diego and another from Brazil, who was separated from her 14-year-old son in El Paso, according to the pleadings.

Overflowing shelters

As the legal fight warms up, immigrant services and the processing system are overheating. A block away from the dark-glassed federal building in McAllen where the criminal courts are located, Pimentel, the Catholic nun, runs the Humanitarian Respite Center. A sign outside reads "restoring human dignity."

The center was overflowing last Sunday and again Monday with immigrants who had been apprehended by the Border Patrol and released to face deportation cases in the civil system. Nearly all were from Central America.

Filoberto Xol looked gaunt and exhausted as he kept his 16-year-old daughter Claudia close to him. The 40-year-old father had journeyed from Guatemala with his oldest child, fearful that she would be harmed by marauding gangs.

"There is so much violence in Guatemala. The Maras," said Xol, shaking his head as he used the name of an infamous gang. He lowered his head without finishing his sentence.

Xol said he also left Guatemala because the economy was so weak and jobs are scarce. With five children and a wife, he decided he had to luchar, to fight on as a higher-paid worker in the immigrant economies of the U.S.

Claudia Xol, 16, waits at the bus stop after being dropped off by federal immigration staff in McAllen, Texas, on June 10, 2018. (Nathan Hunsinger / Staff Photographer)

His daughter Claudia said she was relieved she hadn't been separated from her father. "Thank God," she said in a whisper.

All around the Xols were dozens of migrant families. Their presence at the shelter underscored the uneven enforcement of the zero tolerance policy. Fathers held daughters. Mothers caressed sons. Families were united, bonded in their hope and misery.

That weekend, it didn't appear anyone at the Catholic shelter had been charged with the criminal misdemeanor of improper entry. They faced other hurdles. Many huddled near electrical outlets because they had to charge the batteries on their ankle monitors, issued by federal immigration authorities.

Jonathan Pineda, a 23-year-old Salvadoran, held his little namesake boy whose curly hair was matted by sweat. He wanted to find a job in Los Angeles and unite with family and friends there.

Why did he migrate to Texas?

"The gangs threatened me with death," he said bluntly, hugging his son a bit tighter.

He headed toward the shelter's kitchen area for a meal. The dining room was dominated with religious icons of the Catholic faith. Among them was an image of the blue-eyed Mexican priest Toribio Romo, a saint whom some migrants look to for protection.

Oscar Serrano, a 30-year-old Honduran immigrant, kept his 10-year-old look-alike daughter near him as he charged his ankle monitor. He was picked up by the Border Patrol after he crossed near Rio Grande City, about an hour from McAllen. He had government documents that show he'd been placed into removal proceedings in the immigration court system.

Ashley smiled at her father as he spoke about his fears — and the rumors spreading among immigrants who had been in Border Patrol custody.

"They say the older children get separated from their parents. But not the smaller ones," he said, gazing at his daughter.

Immigrants wait to be processed on the U.S. side of the international bridge in between Hidalgo, Texas, and Reynosa, Mexico, on June 9, 2018. At times, immigrants have camped for days on the bridge because U.S. Customs and Border Protection said they had "housing capacity" issues. (Nathan Hunsinger / Staff Photographer)

Backup at the bridge

On that weekend, others camped on the Hidalgo international bridge, hoping to get into the U.S. with plans to ask for asylum at the official port of entry. Among the Hondurans and Salvadorans were many Cubans. Humanitarian groups brought them a stream of ham sandwiches, roasted chicken, sports drinks, water, foam mattresses and sun umbrellas in hues of orange and yellow and blue.

Irma Avila, 21, had been camped out on the bridge for four days, inside the U.S. boundary line. She rode a Mexican train north called La Bestia, The Beast, she said. Gangs tried to shake down immigrants constantly. "If you can't pay, they throw you off," Avila said. Nearby, her 6-year-old ate a roasted chicken leg down to the bone.

Customs and Border Protection spokesman Phil Barrera said immigrants had been camping on the bridge because of "housing occupancy" problems — a lack of detention space and beyond the control of the CBP. He referred questions to another government agency.

By Tuesday morning, the bridge was clear of the campers. It wasn't clear if Avila and her daughter had finally been allowed to ask for asylum.

Below the bridge, the murky green waters of the Rio Grande rushed through. In Texas, many immigrants from El Salvador, Guatemala and Honduras have been caught rafting across the waters. About a quarter of adult immigrants who are caught by the Border Patrol are actually criminally prosecuted in April, according to TRAC. It's not zero tolerance yet.

That's fine, says Krikorian, the immigration hard-liner, because the message will spread among Central Americans. "The U.S. attorneys need to prosecute as many as they can. It doesn't mean they can prosecute all of them all the time."

1 / 8Michelle, 6, drinks from a Whataburger cup on the U.S. side of the Hidalgo bridge in between Hidalgo, Texas, and Reynosa, Mexico, on June 9, 2018. (Nathan Hunsinger / Staff Photographer) 2 / 8Imelda Avila (left) and her daughter Michelle Avila, 6, from Honduras wait for a fourth day to be processed on the U.S. side of the Hidalgo bridge in between Hidalgo, Texas, and Reynosa, Mexico, on June 9, 2018. (Nathan Hunsinger / Staff Photographer) 3 / 8The approach to the walking bridge across the Rio Grande on the Mexico side of the border in Reynosa on June 9, 2018.(Nathan Hunsinger / Staff Photographer) 4 / 8People pass by U.S. Customs and Border Protection officers on the bridge between Hidalgo, Texas, and Reynosa, Mexico, on June 9, 2018. (Nathan Hunsinger / Staff Photographer) 5 / 8U.S. Customs and Border Protection officers on the U.S. side of the Hidalgo bridge between Hidalgo, Texas, and Reynosa, Mexico, on June 9, 2018. (Nathan Hunsinger / Staff Photographer) 6 / 8People cross from the Mexico side of the walking bridge between Hidalgo, Texas, and Reynosa, Mexico, on June 9, 2018. (Nathan Hunsinger / Staff Photographer) 7 / 8A boy looks at the car bridge over the Rio Grande as he waits on the walking bridge to be processed by U.S. officials on June 9, 2018. (Nathan Hunsinger / Staff Photographer) 8 / 8By June 12, no one was waiting to be processed on the U.S. side of the Hidalgo bridge. (Nathan Hunsinger / Staff Photographer)

Corrected on June 15 at 3:40 p.m.: An earlier version of this story incorrectly spelled the name of prosecutor Colin Maguire.