As the Obama administration prepares for a new surge of illegal immigrant children this year, some of those from previous waves are turning up on court dockets across the country, charged with serious crimes such as capital murder and aggravated rape.

The cases are exposing many of the holes in the immigration system and the way the U.S. has tried to grapple with children fleeing economic troubles, domestic abuse or gang violence in Central America — and sometimes bringing those very troubles to the U.S. with them.

From the law, which requires most of the children to be turned over to social workers, to immigration authorities and the court system, which allow most of them to abscond, never showing up to be deported, to the lack of a safety net to help the children once they’re free in the country, the cases suggest a broken process nearly from start to finish, with some children getting lost in the system and others being released because of overcrowding, only to reappear when they’re called before a judge to answer for a bigger crime.

“The eagerness of the administration to open our borders is not without consequence,” said Rep. Duncan Hunter, a California Republican who has tracked the issue. “Now we’re seeing some of these same minors in the criminal justice system, and the crimes some are being brought in for are very serious, even heinous. The administration, with their approach, wants to assume everyone that shows up on America’s doorstep has good intentions, but that’s a dangerous assumption, and we’re seeing evidence of the fact.”

The administration admits it was overwhelmed by last summer’s surge, which officials said caught them by surprise, with more than 60,000 so-called “unaccompanied minors” — children traveling without a parent — streaming across the border in fiscal year 2014. The pace is picking up once again heading into the warmer months of 2015, according to the latest government statistics, and though it’s down from 2014’s frenetic rate, it’s still shaping up as the second-worst year on record.

Oftentimes the children don’t even sneak into the country but instead boldly seek out a Border Patrol agent to turn themselves in to, trusting that generous laws, crowded courts and bureaucratic confusion will give them a chance to disappear into the shadows.

That was the situation with Jonny Alberto Enamorado-Vasquez, whose journey from Honduras to a Houston jail, where he awaits trial on capital murder, is one of the more extreme cases.

According to government documents, Mr. Enamorado fled Honduras on Sept. 22, 2012, hoping to connect with his father, who was supposed to be living in New Orleans, presumably without authorization. He took buses across Guatemala and Mexico, ending up in Reynosa, a town directly across the border from McAllen, Texas, where he holed up at a safe house for a couple of days before jumping the border on Oct. 7.

He was immediately caught by agents doing line watch, who said they were unable to track down his father. From that point on, Mr. Enamorado was in and out of authorities’ custody, passed between the Border Patrol, detention officers at Immigration and Customs Enforcement and the social workers at the Department of Health and Human Services, and eventually released from detention in late October because of what the government described as “lack of space.”

Little more than two years later he was back in the criminal justice system, with Houston police accusing him of being part of a January homicide that saw three armed men burst into a smoke shop, find and confront owner Michael Phelan, which sparked a gunbattle that killed Phelan.

Mr. Enamorado initially fought extradition from Louisiana but caved and is now in Houston. The lawyer listed as defending him in his murder case didn’t return a message seeking comment.

Part of the difficulty appears to be Mr. Enamorado’s age. He initially was booked as a 17-year-old and processed as a juvenile and placed in an HHS home for illegal immigrant children. But it appears authorities realized he was actually a year older, making him an adult and thus not eligible for the special treatment afforded children.

HHS said it couldn’t comment on specific cases under its purview. Customs and Border Protection, which oversees the Border Patrol, said it was barred from commenting publicly because of privacy laws.

But Jessica Vaughan, policy studies director at the Center for Immigration Studies, said it’s not surprising some of the children end up in trouble.

“Considering the countries they’re coming from and the prevalence of gang activity and recruitment of youth into gangs, and the fact that many of these children have grown up without at least one of their parents in difficult circumstances, you can’t discount the threat they pose,” she said.

Analysts said it’s not clear what the overall crime rate is among unaccompanied children released into society, but fears over the issue helped derail a number of efforts last summer to place children in detention homes in communities across the country.

The Obama administration characterizes the children as victims of a chaotic situation in Central America, and it has asked Congress to provide more money for El Salvador, Guatemala and Honduras to try to help those countries try to recover from slumping economies and spiking levels of violence.

“Many families and young people are faced with dire choices, a ‘Sophie’s Choice,’ if you will, which they must either reach an accommodation with criminal groups, watch their children join up, watch their children die or flee. It’s not surprising that many decide to flee,” Eric L. Olson, who studies Latin America at the Woodrow Wilson International Center for Scholars, told the Senate at a hearing on the issue last month.

Administration critics, though, disagree, saying dangerous conditions and poverty have existed in the region for decades, but what’s changed in recent years are the enticements to come to the U.S. — including the belief that U.S. enforcement is weak.

Indeed, the very punishment the Obama administration was touting last year — detailing an eventual deportation court date with unofficial permission to be in the country until then — was the same document smugglers were citing, saying it gave illegal immigrants a chance to be released into the country, where they could dissolve into the shadows with the rest of the 11 million illegal immigrants.

“After day one they don’t look back over their shoulders, saying, gosh, I’ve got to report for that hearing. They are home free. And their expectation is that by the time they need to appear, there is going to be an amnesty or a legalization,” Roger F. Noriega, former assistant secretary of state for the Western Hemisphere, told the Senate Committee on Homeland Security and Government Affairs last month.

Indeed, of the illegal immigrant kids who had deportation court dates between July 2014 and February 2015, less than 40 percent even bothered to show up. The rest were ordered deported in absentia — but they had already absconded.

That was the case with Jalmar Mejia-Lopez, whom Louisiana authorities arrested and charged with aggravated rape last month after receiving an anonymous tip that the now-21-year-old illegal immigrant had impregnated his 12-year-old girlfriend, who was living with him.

Mr. Mejia first drew the attention of authorities in July 2011, when two Border Patrol agents saw him wandering near the Rio Grande in Texas, his tattered and muddy clothes tipping them off that he had probably just jumped the border. His story was much the same as Mr. Enamorado‘s: He’d fled his home in Honduras and traveled by bus and train to reach the U.S. border, where he waded across the Rio Grande at night with the hope of eventually reaching his brother living in Virginia.

He didn’t know his brother’s phone number, his father was dead, and his mother still lived at home in Honduras, so authorities processed him and turned him over to social workers at HHS, who quickly placed him with a social worker at a Catholic church in Philadelphia, who identified herself as a “family friend” and promised to look after him. A year later, he missed his deportation hearing, was ordered kicked out in absentia and disappeared into the shadows along with more than 11 million other illegal immigrants.

He surfaced again when the East Baton Rouge Sheriff’s Office got the tip earlier this year and tracked it down, discovering Mr. Mejia with his 12-year-old victim, who’d lived with Mr. Mejia at his apartment for several months.

“The 12-year-old victim stated that she is approximately four months along in the pregnancy and that she is in love with the defendant,” the sheriff’s office said in a statement of probable cause filed in the case. They discovered he’d had several outstanding local warrants for traffic violations, including driving without a license and failure to maintain control of his vehicle.

Efforts to reach the social worker who initially took Mr. Mejia were unsuccessful. A person answering the phone at her given number said he didn’t know her, and the Catholic church where she was employed said she no longer worked there and did not have forwarding contact information.

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