The federal judge who oversees long-running litigation about the treatment of migrant children in U.S. custody ordered the government Friday to finalize its procedures for providing parents a fateful choice: allow their children to be released to a designated guardian, or remain together in immigration jail.

Such a decision, known informally as binary choice, potentially could transform the family migration dynamics that have confounded the Trump administration and the Obama administration before it, as successive waves of Central American families crossed the border and overwhelmed U.S. capacity to process their humanitarian claims.

Most important, it would dramatically shift the nature of the decision about whether to separate children from their families at the border. Instead of it being up to the government, as it is now, it would be up to the migrant parents themselves.

Judge Dolly Gee, who oversees the legal case dating back to 1997 known as the Flores Settlement Agreement, told the government and the attorneys who represent migrant children to hammer out the framework for advising parents of their rights, as well as the procedures for implementing the binary choice model.

“It’s incumbent on both sides to come up with procedures that are appropriate and thoughtful and effectuate the rights contained in the agreement that doesn’t cause children to be lost,” Gee said.

Gee cited reports this week that attorneys and rights groups have been unable to contact 545 parents who the Trump administration separated from their children. Attorneys for the Justice Department disputed claims that the children were “lost” — they said the children were placed with legal guardians in the United States and in many cases parents have not wanted to claim the children for fear that they would be removed from the country. The government also said the coronavirus pandemic has hampered efforts to locate the families.

Gee said her concern about the binary choice model is that the government might fail to properly vet sponsors and could lose track of children who go to designated caregivers.

“I don’t want some bureaucratic snafu requiring another large effort to put children back in touch with their parents,” Gee said during a virtual hearing Friday in the case, which is in the U.S. District Court for the Central District of California. “I don’t want to be party to a system that will engender that type of disorganization.”

The idea of a binary choice model circulated widely in the aftermath of the “Zero Tolerance” prosecution model that the Trump administration used to separate thousands of children from their parents. Democratic lawmakers have opposed such a model, but attorneys say the Flores Settlement grants minors the right to a quick release from immigration detention, but does not afford their parents the same right.

The Trump administration has been trying to terminate the Flores Settlement in favor of keeping families detained together until courts decide whether they have a valid legal claim or should be deported. That process currently takes several months, or longer, but the government also has proposed fast-tracking the process to reduce the amount of time families are in detention.

In a statement Friday, the Department of Justice said that it opposes what it called “the family separation requirements” in the binary choice model Gee has ordered. The government “intends to maintain family unity to the greatest extent practicable.”

Gee said that claim was “ironic, to say least,” noting that the Trump administration previously “had a policy to involuntarily separate families,” referring to the government breaking up nearly 3,000 families during a six-week span in 2018.

Carlos Holguin, one of the attorneys for the plaintiffs, said the government “should consider releasing families as a whole, but what the government has wanted to do is decide for families.”

“What we’re trying to do is figure out how parents and families can have the ability to make these decisions rather than have ICE decide it for them,” he said, referring to U.S. Immigration and Customs Enforcement.

The Obama administration dealt with this challenge by creating “family residential centers” at three locations where parents could remain in custody with their children. But the limitation on the amount of time children could be held in ICE custody — 20 days — meant that parents typically were released from detention along with their children to await a court hearing.

Trump administration officials blamed this “loophole” for the family migration surge that began in 2017, and led to the White House trying to thwart it through Zero Tolerance. Under that initiative, the government separated parents to prosecute and jail them, while placing their children in shelters. Trump ordered a halt to the practice in June 2018 amid a public outcry, ordering families to remain together. An even larger family migration wave followed.

More recently, the administration has cited the coronavirus pandemic to implement a system of rapid “expulsions” that have largely shut the door to asylum-seekers at the border.

The binary choice model Gee is expected to impose would give migrant parents the option of allowing their children to be released to another designated sponsor — such as a family member — or waive their children’s right to release. ICE could also choose to grant provisional release to a family or utilize electronic monitoring equipment, such as ankle bracelets with GPS trackers, so they would not have to remain in custody.

If the family’s claim is rejected and they are ordered to be deported, the family would leave the United States together.

“It is a tough decision for parents,” Schey said.

Such a move would partly aid the government’s enforcement goals, because parents who opt for the release of their children would be taken out of the family immigration jails, where space is limited, and instead would go to ICE adult detention facilities.

Schey said the government and the plaintiffs are in agreement on most aspects of the binary choice framework. Gee told the parties to iron out their differences and scheduled a new hearing for Dec. 4.