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SAN DIEGO — Outside one of the nation’s busiest immigration courts, dozens of migrant families streamed out of a pair of buses that had just pulled in from the Mexican border, all of them hoping to fight deportation and ask for refuge in the United States.

They filed into two packed waiting rooms at the busy federal compound southeast of San Diego. Mothers tried to soothe crying babies. Security guards escorted people to bathroom breaks. Inside the courtrooms, people waiting their turns before the judges slouched on wooden benches as the long hours wore on.

The hearings unfolding several days a week in Southern California are unlike most of the asylum proceedings that have dominated immigration court dockets since Central American families began arriving in large numbers at the southern border in 2014. For the 158 migrants brought in through the San Ysidro port of entry that day in July, their stay in the United States would be brief: Nearly all of them would be returned to Mexico at the end of the day to await, at a distance, what for some of them could be a life-or-death decision.

“I am afraid the Barrio 18 gang will beat me, rape my daughter to hurt me, cut us in pieces and kill us,” a Baptist preacher from El Salvador, who identified himself only as Carlos, wrote in his petition to the court. “I am a pastor of a church who preaches that youth should follow God instead of gangs.”

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For decades, those who could reasonably argue they were fleeing persecution in their homelands could enter the United States and obtain temporary residence and often a work permit while they consulted with a lawyer and prepared to present a full asylum petition to the immigration court.

That all changed under a Trump administration program that began in January. The program requires many migrants seeking admission to the United States to be sent back to Mexico for the duration of their court proceedings, allowing them to cross the border only for their hearings.

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The program is proving to be disastrously difficult for many asylum seekers, who show up for critical court hearings like the ones in San Diego with no legal representation and little understanding of what is needed to successfully present a case. Some have not even been informed of when their cases would be heard or were given the wrong date or the wrong courthouse.

According to an analysis of immigration court data by the Transactional Records Access Clearinghouse at Syracuse University, 1,155 cases under the migrant protection protocols, known as the “Remain in Mexico” program, had been decided by the end of June. Only 14 of these petitioners — 1.2 percent — had legal representation. Out of 12,997 cases still pending, 163 were filed with the aid of a lawyer, or 1.3 percent.

Access to counsel is a challenge even for those pursuing their cases from within the United States: Only 37 percent of them have representation. But for those waiting in Mexico, the border can pose an insurmountable barrier. Even if a migrant can afford to pay, finding a lawyer willing to take the case of a client living in Mexico is a challenge. In San Diego, the two legal aid organizations accepting clients in Tijuana are overwhelmed.