Lawyers for Mahmoud Khalil have asked a federal judge to intercede after an immigration court judge ordered last week that he be removed to Syria or Algeria.
Mr. Khalil, who was a Columbia University graduate student when he was abruptly arrested by the Trump administration this year, is not in imminent danger of deportation.
A standing order from the federal judge, Michael E. Farbiarz, prohibits Mr. Khalil’s removal from the country. He has until October to appeal the immigration judge’s decision and further appeals could forestall his deportation.
But several months after he was released from detention in Louisiana, his legal plight is growing more dire.
Mr. Khalil’s case is progressing in two separate courts: A federal court in New Jersey, where Judge Farbiarz is scrutinizing constitutional issues, and an immigration court in Louisiana.
Immigration judges are part of the executive branch, not the judicial, and Judge Jamee E. Comans, who works for the Justice Department, appears eager to speed the matter along.
The tension between the judges has intensified, and the request by Mr. Khalil’s lawyers that Judge Farbiarz intervene, made in a court filing on Wednesday, could escalate the battle between the executive branch and the judiciary.
Mr. Khalil’s lawyers asked Judge Farbiarz for permission to refile their initial complaint with arguments that would encompass Judge Comans’s latest action, which they characterized as part of a pattern of retaliation by the Trump administration.
Mr. Khalil was a prominent presence at pro-Palestinian protests on the Columbia campus. When he returned to the White House, Mr. Trump was quick to crack down on those demonstrations and the schools that hosted them.
Since Mr. Khalil’s March arrest, the Trump administration has sought to deport him, although he is a legal permanent resident whose wife and infant son are American citizens.
The secretary of state, Marco Rubio, cited a rarely used statute as the legal rationale for Mr. Khalil’s deportation, saying that his mere presence in the United States spread antisemitism.
More than a week later, after Mr. Khalil’s lawyers had begun to fight for his freedom, the administration added a separate rationale for deportation, saying that Mr. Khalil had failed to disclose membership in several organizations when he applied for legal residency in March 2024. A lawyer for Mr. Khalil has called those allegations “bogus.”
Mr. Khalil was detained in Louisiana for more than three months. He was behind bars in April when his wife gave birth to their son.
In May, Judge Farbiarz ruled that the law cited by Mr. Rubio was likely unconstitutional. The following month, the judge said that Mr. Khalil could no longer be held on that basis. After the government argued that it was instead holding Mr. Khalil based on the allegations related to his residency application, Judge Farbiarz ordered his release.
But the immigration court process continued.
On June 20 — the day of Mr. Khalil’s release — Judge Comans put in a written order her earlier statement that Mr. Khalil could be deported on the basis of the statute Mr. Rubio cited.
In July, Judge Farbiarz ordered that decision nullified.
Judge Comans heeded his order, but responded furiously in footnotes, accusing Judge Farbiarz of “interfering with the legal process and the authority of the immigration court.”
Last week, she said that Mr. Khalil could be deported in light of the allegations about his residency application.
According to Mr. Khalil’s lawyers, she continued to grant weight to Mr. Rubio’s determination.
She also said that because Judge Farbiarz had refused to allow her to rely on that determination, she was “compelled to make alternative findings.” Therefore, she indicated, she was using the allegations about Mr. Khalil’s residency application as a basis for deportation.
The Trump administration has accused Mr. Khalil of neglecting to disclose that he had worked with a United Nations agency that assists Palestinian refugees, as well as membership in Columbia University Apartheid Divest, a coalition of student groups involved in pro-Palestinian demonstrations.
Mr. Khalil’s lawyers have said that Mr. Khalil participated in an internship at the U.N. agency through Columbia and considered it coursework rather than employment. They say Mr. Khalil was not a member of the coalition but a mediator, and that he took on that role after he applied for permanent residency.
In a statement Wednesday, Mr. Khalil said the administration had “resorted to fabricating baseless and ridiculous allegations in a bid to silence me for speaking out and standing firmly with Palestine, demanding an end to the ongoing genocide.”
A Justice Department spokesman did not immediately respond to a request for comment.
Mr. Khalil has 30 days to appeal Judge Comans’s decision to the Board of Immigration Appeals, which may then consider his case at length. Mr. Khalil’s lawyers are concerned that the process might be swift — the board is also part of the Justice Department.
He could then appeal to a federal appeals court in Louisiana, though, as his lawyers noted, that appeals court often refuses to allow immigrants to stay in the country as they are appealing.
Jonathan Wolfe contributed reporting.
Jonah E. Bromwich covers criminal justice in the New York region for The Times. He is focused on political influence and its effect on the rule of law in the area’s federal and state courts.
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