The Justice Department and attorneys agreed to delay the court proceedings for the mother-daughter pair until later that night, but despite the decision, an attorney on the case received word that Carmen and her daughter were already at an airport ready to be deported.
The ACLU said the government had on Wednesday assured the court that no plaintiff in the case would be deported before midnight on Thursday.
"This is pretty outrageous", the judge told the Washington Post.
The case is Grace v. Sessions, 1:18-cv-01853, in U.S. District Court for the District of Columbia.
"I'm not happy about this at all", he said. "This is not acceptable".
He ruled in favor of the ACLU's request to put the deportation on hold, and ordered the Trump administration to "turn the plane around".
The order issued Thursday stated that the defendants, including Sessions, Nielsen, U.S. Citizenship and Immigration Service Director Lee Francis Cissna and Executive Office of Immigration Review Director James McHenry, "shall return "Carmen" and her daughter to the United States FORTHWITH".
The ACLU's lawsuit, where they represent Carmen and 11 other people from Central American countries, is based on a claim that the administration is unfairly preventing people from seeking asylum and not allowing them to have fair hearings.
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The two did land in El Salvador after their forced removal from the US, but per the ACLU's efforts, did not disembark from the plane and were flown back to the USA immediately.
A Department of Homeland Security official said the agency is "complying with the court's order, and upon arrival in El Salvador, the plaintiffs will not disembark and will be promptly returned to the United States". Several co-workers at the factory where Carmen worked had been murdered, and her husband is also abusive, the paper added, citing records.
But at the border, the government determined after interviewing her that she did not meet the "credible fear" threshold required to pursue an asylum claim in the USA, and an immigration judge upheld that decision.
There are about 700,000 backlogged asylum cases crawling through federal courts, according to the DOJ.
In changing the standards for seeking asylum, Sessions said in June that 'the mere fact that a country may have problems effectively policing certain crimes, such as domestic violence or gang violence, or that certain populations are more likely to be victims of crime, can not itself establish an asylum claim'.
During the hearing, the judge ordered a temporary stay on deporting the nine women and three children who filed the lawsuit, according to a court filing.
The Justice Department has yet to comment on the incident, but an infuriated Judge Sullivan has since threatened to hold Attorney General Jeff Sessions in contempt for the attempted deportation, which he says is "unacceptable". "Despite asylum officers finding that their accounts were truthful, they. ultimately denied them asylum protection because they did not have a 'credible fear of persecution'".