Supreme Court orders in the middle of the night are rare these days.

Justices Clarence Thomas and Samuel A. Alito Jr. dissented. The White House did not issue any immediate response.

More than 50 Venezuelans were scheduled to be flown out of the country — presumably to El Salvador — from an immigration detention center in Anson, Texas, according to two people with knowledge of the situation. The American Civil Liberties Union in recent days had already secured court orders barring similar deportations under the law, the Alien Enemies Act, in other places including New York, Denver and Brownsville, Texas.

The situation in Anson was urgent enough that A.C.L.U. lawyers mounted challenges in three different courts within five hours on Friday.

The lawyers started with an emergency filing in Federal District Court in Abilene, Texas, in which they claimed that officers at the Bluebonnet Detention Center in Anson had started distributing notices to Venezuelan immigrants informing them that they could face deportation as soon as Friday night.

They asked Judge James Wesley Hendrix, who is overseeing the case, to issue an immediate order protecting all migrants in the Northern District of Texas who might face deportation under the Alien Enemies Act. When Judge Hendrix did not grant their request quickly — and later rejected it entirely — the lawyers filed a similar request to the U.S. Court of Appeals for the Fifth Circuit in New Orleans.

The lawyers then filed an emergency petition to the Supreme Court, asking the justices to step in and issue an immediate pause on any deportations because many of the Venezuelan men had “already been loaded on to buses, presumably headed to the airport.”

“These men were close to spending their lives in a horrific foreign prison without ever having had any due process,” Lee Gelernt, the lead A.C.L.U. attorney on the case, said on Saturday. “The case has a long way to go. But for now, we are relieved that the court has not allowed the Trump administration to hurry them away in secret.”

Immigration lawyers have been playing a high-stakes game of cat and mouse with the federal government since President Trump issued a proclamation last month invoking the Alien Enemies Act as a way to deport immigrants he claims are members of Tren de Aragua, a violent Venezuelan street gang. The law, which was passed in 1798, has been used only three times before in U.S. history, during periods of declared war.

The efforts by groups like the A.C.L.U. to stop deportations under the act were complicated this month by a Supreme Court ruling that found that anyone subject to the statute needed to be given the opportunity to challenge their removal, but only in the places where they were being detained.

The decision by the justices set off a hunt for anyone who might fall under the authority of Mr. Trump’s proclamation. The A.C.L.U., hoping to come up with a system for determining where those people might be, has asked a federal judge in Washington to issue a nationwide order forcing the government to provide 30 days’ notice to anyone in the country before officials seek to remove them under the Alien Enemies Act.

During a hearing on Friday evening in front of the judge in Washington, James E. Boasberg, Mr. Gelernt said that he was prepared to file what amounted to pre-emptive lawsuits in all of the more than 90 federal judicial districts across the country in an effort to ensure that no Venezuelan migrants were deported without hearings under the act.

Drew C. Ensign, a lawyer for the Justice Department, gave his word that no flights were scheduled to depart from the Bluebonnet center on Friday night or Saturday morning, adding that the migrants there would be given at least 24 hours’ notice before they were deported.

But Judge Boasberg was somewhat skeptical of Mr. Ensign’s assertion, pointing out that the notice forms the government had given to the Venezuelan men did not contain an explicit statement that they were able to challenge their deportations.

There is a history here: In mid-March, during the first hearing to consider the administration’s use of the Alien Enemies Act, Judge Boasberg ordered Trump officials to pause all of the deportation flights it had sent out under the act. But despite his instructions, two planes left Texas and landed in El Salvador. A third plane from Texas holding people whose deportations were not under the act also arrived in El Salvador. In all, more than 200 deportees were stranded in prison there.

Judge Boasberg is now considering opening a contempt investigation into whether the administration violated his order, although an appeals court temporarily put that plan on hold on Friday night. Still, he declined on Friday night to issue a new order stopping deportation flights from northern Texas in part because of jurisdictional concerns that other courts were already mulling the same question.

This latest iteration of the fight over the use of the Alien Enemies Act began on Wednesday when the A.C.L.U. filed suit in Abilene on behalf of two Venezuelan migrants being held at the Bluebonnet facility, asking Judge Hendrix to shield them against deportation. But the judge denied the request, largely because lawyers for the Justice Department told him that the men — known only by their initials, A.A.R.P. and W.M.M. — had not yet been scheduled for removal from the country.

But then on Friday, other Venezuelan migrants at the detention center were informed that they were facing imminent deportation, court papers say. One of them, known as F.G.M., was instructed to sign a removal waiver in English, even though he speaks only Spanish, the papers say.

When he refused to sign, immigration officers told him the waiver was “coming from the president,” according to court papers, “and that he will be deported even if he did not sign it.”

Among those at the Bluebonnet detention center that the A.C.L.U. is seeking to protect from deportation is a 19-year-old known as Y.S.M.

Y.S.M., court papers say, was arrested by immigration agents on March 14 and was sent to the Bluebonnet facility this week. When the agents initially questioned him, court papers say, they told him that a photograph on Facebook showing him in the presence of another person holding a gun proved he was a member of Tren de Aragua.

But according to his lawyer, Y.S.M. informed the agents that what they believed to be a gun was actually a water pistol.

A spokeswoman for the president of El Salvador, Wendy Ramos, did not respond to a request for confirmation of an upcoming flight.

Since March 15, the Trump administration has sent five flights carrying deportees to El Salvador under a deal with its president, Nayib Bukele, to hold detainees deemed by U.S. authorities to be part of criminal gangs in his country’s prison system, for a fee.

Annie Correal, Maggie Haberman and Zolan Kanno-Youngs contributed reporting.

Although many of the events were traditional protests, many also were intended to unite local communities through activities such as food drives. Mass protests during President Trump’s first term, like the Women’s March, often focused on a single topic, but demonstrators on Saturday expressed outrage on a wide range of issues.

In Washington, just a few feet north of the White House, hundreds gathered to berate the administration for not bringing Kilmar Abrego Garcia, the Maryland man who was wrongfully deported to El Salvador, back to the United States.

Aaron Burk, whose girlfriend took a federal buyout from the Department of Energy, said he was worried that the administration would not stop at deporting undocumented immigrants without due process and would imprison and deport U.S. citizens.

“Where does it stop?” he said. Mr. Burk added that his daughter is transgender and that he was most concerned about the dehumanization of minorities.

In Jacksonville, Fla., hundreds took to the streets to protest a number of causes, including the president’s attacks on the L.B.G.T.Q. community and the government’s desire to alter the Endangered Species Act.

“We are losing our country,” said one demonstrator, Sara Harvey. In the last few months, she said she had protested the federal job cuts led by Elon Musk and joined the nationwide protests on April 5.

“I’m worried for my grandchildren,” she said. “I do it for them.”

A celebration in Concord, Mass., to commemorate the 250th anniversary of the beginning of the American Revolution was not part of the organized network of protests, but some people took the occasion to draw parallels between then and now.

Conan Walter, 65, stood on the Old North Bridge holding a large poster with the words “Stop fascism now” scrawled across.

“This celebration is about us getting out from under the King of England’s authoritarian rule,” Mr. Walter said. “That rule is trying to make a comeback today, and it’s important that people step up against that and meet the challenge.”

Nichole Manna contributed reporting from Jacksonville, Fla., and Lila Hempel-Edgers from Concord, Mass.

A third was issued around midnight in 2021, a day after the court allowed a restrictive Texas abortion law to go into effect, signaling that Roe v. Wade was in peril.

Those late-night rulings, on what critics call the court’s “shadow docket,” could convey the sense that the justices were hiding something, engaged in palace intrigue or simply not able to manage their work. In apparent response to such criticism, the justices have in recent years tried to issue orders on emergency matters during business hours.

Indeed, when the court last month rejected President Trump’s emergency request to freeze nearly $2 billion in foreign aid, it released its order first thing in the morning, which is also unusual.

The court’s latest order, blocking the administration from deporting a group of Venezuelan migrants accused of being gang members under a rarely invoked wartime law, was issued at 12:55 a.m. on Saturday morning. Whatever calculations the justices had made in earlier cases, it seemed plain that they viewed this one as a true emergency.

No meeting was announced with Pope Francis, who recently left the hospital after spending five weeks there in serious condition and has since made few public appearances.

Mr. Vance’s Catholic faith permeates his socially conservative politics. But since he took office, some of the Trump administration’s policies have drawn condemnation from the pope.

Francis has strongly criticized the Trump administration’s policy of mass deportations and has urged Roman Catholics to reject anti-immigrant sentiments. Mr. Vance has strongly defended that policy, pointing to the medieval Catholic theological concept of “ordo amoris,” the idea of a hierarchy of duties that prioritizes immediate obligations to one’s family or community over more distant needs.

“You love your family, then you love your neighbor, and then you love your community, and then you love your fellow citizens in your own country, and then after that you can focus and prioritize the rest of the world,” Mr. Vance said in an interview with Fox News in January. “A lot of the far left has completely inverted that.”

The pope seemed to be alluding to Mr. Vance’s argument in a letter he wrote in February to American bishops in which he spoke out against Trump’s policy on migrants.

In the letter, Francis said, “Christian love is not a concentric expansion of interests that little by little extend to other persons and groups.”

“The true ordo amoris that must be promoted,” Francis wrote, is “love that builds a fraternity open to all, without exception.”

Mr. Vance acknowledged the pope’s critical comments, but said he would continue to express his views.

“I was certainly surprised when he criticized our immigration policy in the way that he has,” Mr. Vance said at the National Catholic Prayer Breakfast in February. He added that the news media, along with social media influencers and even some Catholics, “try to bring the Holy Father into every culture war battle in American politics.”

Still, Mr. Vance said that the pope “cares about the flock of Christians” and that he was praying for him.

During Mr. Vance’s meeting on Saturday with Cardinal Parolin and with Archbishop Paul Gallagher, the Vatican’s foreign minister, the officials exchanged opinions on “difficult humanitarian situations, with particular attention to migrants, refugees, and prisoners,” along with other issues, according to a statement from the Vatican.

On Friday, Mr. Vance stood, sat and knelt for two hours in St. Peter’s Basilica, his young daughter sleeping in his arms at one point, as he followed the Liturgy of the Lord’s Passion, during which the faithful are invited to fix their eyes on a statue of the crucified Jesus. Cardinals and bishops proceeded in a line, bent and kissed the statue’s feet.

Kimberlee Woo-leng, 24, a student from Trinidad and Tobago who also attended the service, said she hoped spending Holy Week in Rome would help Mr. Vance “have mercy.”

“I hope it strikes his heart,” she said.

Elizabeth Dias contributed reporting.

Earlier this month, Mr. Trump issued two executive orders revoking the security clearances of Chris Krebs, who led the Cybersecurity and Infrastructure Security Agency under during Mr. Trump’s first term and rebutted his claims that the 2020 election had been rigged and stolen, and Miles Taylor, who once served as chief of staff at the Department of Homeland Security. Mr. Taylor anonymously wrote a New York Times opinion essay in 2018 accusing Mr. Trump of rampant “amorality” and telling of an internal government “resistance.”

Mr. Trump’s executive orders also revoked the security clearances of people and institutions affiliated with Mr. Krebs and Mr. Taylor, and called for investigations into their government tenures. The letter, signed by more than 200 people, criticized those actions as part of a “profoundly unconstitutional break” with precedent.

“Behavior of this kind is more to be expected from a royal despot than the elected leader of a constitutional republic,” the signers wrote. “This is the path of autocracy, not democracy.”

The letter’s signatories include Ty Cobb, a lawyer who led Mr. Trump’s response to a special counsel’s investigation of his ties to Russia during its early phases, and John Mitnick, who served as general counsel for the Department of Homeland Security until he was fired in 2019 after clashing with the White House.

Mr. Cobb and Mr. Mitnick, like many of the other Republicans on the list of signatories, have been openly critical of Mr. Trump since parting ways with his administration.

The letter was spearheaded by the State Democracy Defenders Fund, a group run by Norm Eisen, a senior fellow at the Brookings Institution who served on the staff of the first team of House Democrats that worked to impeach Mr. Trump in 2019.

The Brookings Institution is not involved in the fund, nor was it involved in the letter.

Cases of international students being detained by masked immigration agents over violations cited by the Trump administration that many individual rights groups have described as protected speech have sparked widespread outrage. But most have been challenged in individual lawsuits.

The lawsuit filed in New Hampshire casts a wider net, intending to to stop similar detentions and deportation efforts for students in New Hampshire, Maine, Massachusetts, Rhode Island and Puerto Rico. It also asks the court to reinstate the student visas that have been terminated.

In recent weeks, immigration agencies have rapidly stepped up efforts to punish international students studying in the United States, in many cases because of their involvement in pro-Palestinian protests related to the war in Gaza. In some instances, the lawyers of detained students have described the use of aggressive tactics and students being moved hundreds of miles to detention facilities in Louisiana.

Hundreds of students have been swept up in the deportation campaign. Among those whose cases have drawn national attention are Rumeysa Ozturk, a Turkish graduate student at Tufts University; Mahmoud Khalil, a permanent resident of the United States who studied at Columbia University; and Momodou Taal, a British-Gambian Ph.D. student at Cornell University. Their cases have also prompted pushback from legal groups over what they say is a threat to campus speech.

The new lawsuit challenges those arrests as an arbitrary overreach by immigration officials and a violation of students’ due process rights.

In moving to deport the students, the Trump administration has used charged rhetoric. In several cases it has argued that by expressing support for pro-Palestinian demonstrations — sometimes only indirectly — the students’ presence in the United States amounted to a national security threat. Officials have routinely referred to student visas as a privilege that can be revoked at any time and have characterized the students as supporters of “pro-jihadist protests” and terrorism.

The lawsuit was filed on behalf of five students from China and India. It did not specify what rationale was given for their visas being terminated.

“These terminations — across the board — flout the applicable regulations governing student status termination and the regulations governing failure to maintain student status,” it said.

The lawsuit lists an array of harms facing students studying on a visa, including imminent detention and deportation, and loss of their progress toward a degree or graduate research. It noted that as of a week ago, the four states involved and Puerto Rico have collectively seen at least 112 people whose student statuses were terminated.

It asked a federal judge to issue a ruling to block the Trump administration from carrying out future detentions and deportations of any student across the nearly 200 accredited colleges and universities in the states involved.

The April 11 letter from the White House’s task force on antisemitism, this official told Harvard, should not have been sent and was “unauthorized,” two people familiar with the matter said.

The letter was sent by the acting general counsel of the Department of Health and Human Services, Sean Keveney, according to three other people, who were briefed on the matter. Mr. Keveney is a member of the antisemitism task force.

It is unclear what prompted the letter to be sent last Friday. Its content was authentic, the three people said, but there were differing accounts inside the administration of how it had been mishandled. Some people at the White House believed it had been sent prematurely, according to the three people, who requested anonymity because they were not authorized to speak publicly about internal discussions. Others in the administration thought it had been meant to be circulated among the task force members rather than sent to Harvard.

But its timing was consequential. The letter arrived when Harvard officials believed they could still avert a confrontation with President Trump. Over the previous two weeks, Harvard and the task force had engaged in a dialogue. But the letter’s demands were so extreme that Harvard concluded that a deal would ultimately be impossible.

After Harvard publicly repudiated the demands, the Trump administration raised the pressure, freezing billions in federal funding to the school and warning that its tax-exempt status was in jeopardy.

A senior White House official said the administration stood by the letter, calling the university’s decision to publicly rebuff the administration overblown and blaming Harvard for not continuing discussions.

“It was malpractice on the side of Harvard’s lawyers not to pick up the phone and call the members of the antisemitism task force who they had been talking to for weeks,” said May Mailman, the White House senior policy strategist. “Instead, Harvard went on a victimhood campaign.”

Still, Ms. Mailman said, there is a potential pathway to resume discussions if the university, among other measures, follows through on what Mr. Trump wants and apologizes to its students for fostering a campus where there was antisemitism.

Mr. Keveney could not be reached for comment. In a statement, a spokesman for the antisemitism task force said, “The task force, and the entire Trump administration, is in lock step on ensuring that entities who receive taxpayer dollars are following all civil rights laws.”

Harvard pushed back on the White House’s claim that it should have checked with the administration lawyers after receiving the letter.

The letter “was signed by three federal officials, placed on official letterhead, was sent from the email inbox of a senior federal official and was sent on April 11 as promised,” Harvard said in a statement on Friday. “Recipients of such correspondence from the U.S. government — even when it contains sweeping demands that are astonishing in their overreach — do not question its authenticity or seriousness.”

The statement added: “It remains unclear to us exactly what, among the government’s recent words and deeds, were mistakes or what the government actually meant to do and say. But even if the letter was a mistake, the actions the government took this week have real-life consequences” on students and employees and “the standing of American higher education in the world.”

The letter shocked Harvard not only because of the nature of the demands but because it was sent when the university’s leadership and the lawyers it hired to deal with the administration thought they could head off a full-bore conflict with Mr. Trump.

For two weeks, Harvard’s lawyers, William Burck and Robert Hur, listened as Trump officials, in fairly broad strokes, laid out the administration’s concerns about how the school dealt with antisemitism and other issues.

On the administration’s side of this dialogue were three lawyers: Josh Gruenbaum, a top official at the General Services Administration; Thomas Wheeler, the acting general counsel for the Department of Education; and Mr. Keveney.

The back and forth lacked specifics on what the administration wanted Harvard to do. The Trump administration lawyers said they would send Harvard a letter last Friday that laid out more specifics.

By the end of the workday on Friday, the letter had not arrived. Instead, overnight, the lawyers from Harvard received a letter, sent from Mr. Keveney in an email, that was far different from the one the school had expected.

It listed a series of demands that would reshape student and academic life in ways Harvard could never agree to. On Monday, Harvard said publicly that it could not accede to them.

Shortly thereafter, Mr. Gruenbaum called one of Harvard’s lawyers, according to two people with knowledge of the calls. At first he said he and Mr. Wheeler had not authorized the sending of the letter. Mr. Gruenbaum then slightly changed his story, saying the letter was supposed to be sent at some point, just not on Friday when the dialogue between the two sides was still constructive, one of the people said.

A lawyer for Columbia University received a similar call from Mr. Gruenbaum around the same time, two people with knowledge of the call said. He, Mr. Wheeler and Mr. Keveney had also been engaged with Columbia about changes the task force wanted that university to adopt, and Mr. Gruenbaum wanted the Columbia lawyer to know that the letter to Harvard was “unauthorized,” the two people with knowledge of the call said.

Mr. Gruenbaum did not respond to a message seeking comment.

Later Monday, Harvard’s corporation and senior leaders were briefed on Mr. Gruenbaum’s assertion that the letter should not have been sent. The briefing left many on Harvard’s side convinced that the letter had been a mistake, three people familiar with the matter said.

Harvard officials, including several who worked in government earlier in their careers, were shocked that such an important letter — bearing the logos of three government agencies, with signatures of three top officials at the bottom — could be sent by a mistake.

But at that point, there was no way for Harvard to undo what had already been set in motion. The university had already declared that it would rebuff the letter’s demands. And despite claiming that the letter should not have been sent, the Trump administration did not withdraw it.

In response to Harvard’s decision to fight, the White House announced that Mr. Trump was freezing $2.2 billion in grants to the school. Within a day, he was threatening to revoke Harvard’s tax-exempt status.

Maureen Farrell contributed reporting.

On Wednesday, Judge Boasberg, concerned that the White House had ignored his order to pause all deportation flights headed to El Salvador under the wartime law, known as the Alien Enemies Act, gave Trump officials a choice. He said they could provide the men who were sent without hearings to El Salvador the due process they had been denied or they could face a searching contempt investigation into who among them was responsible for having not complied with his directives.

In court papers filed on Friday morning, lawyers for the Justice Department told the appeals court that neither option was acceptable. The lawyers accused Judge Boasberg of overstepping his authority by seeking, on the one hand, to tell the Trump administration how to conduct foreign policy and, on the other, to effectively try to assume the role of an investigating prosecutor.

The appeals court made clear that it was not ruling on the merits of the Justice Department’s accusations. The panel simply wanted additional time to consider the complexities of Judge Boasberg’s plan.

That plan, laid out in an order this week, suggested that the judge was trying to pin down who in the administration was behind what he called the “willful disregard” of his oral instructions issued during a hearing on March 15. Speaking from the bench that day, he said any deportation flights headed to El Salvador under the Alien Enemies Act needed to be halted at once and that any planes already in the air should turn around.

But that did not happen, leaving nearly 140 Venezuelan migrants in the custody of jailers at a notorious Salvadoran prison known as the Terrorism Confinement Center, or CECOT.

Jude Boasberg’s proposal for the contempt proceedings explained in detail the increasingly painful measures the administration might face if it did not provide due process to the Venezuelan men.

The judge said it would begin with sworn declarations and then move on, if needed, to courtroom testimony under oath.

If he still could not determine who had given the directions to disobey his order, he said he would refer the case to the Justice Department for criminal prosecution. Aware that the department under Mr. Trump’s control would not be likely to file charges, Judge Boasberg said he would play a final card: a special provision of the criminal contempt law that would, in effect, allow him to appoint an outside prosecutor.

The Justice Department seemed particularly outraged that Judge Boasberg was considering appointing an outside prosecutor to pursue criminal charges against administration officials if, indeed, a case was warranted and the department itself refused to bring it.

The federal rules of criminal procedure say that in instances of criminal contempt, courts must first ask “an attorney for the government” to prosecute. But if the government declines the request, the rules maintain, “the court must appoint another attorney to prosecute the contempt.”

The Justice Department sought to push back on the idea that Judge Boasberg could find his own prosecutor to go after people inside the White House.

“District courts cannot outsource prosecutorial power to private citizens,” department lawyers told the appeals court, “insulate them from executive branch control and then unleash them against the executive branch.”

The appeals court, looking forward, asked the Justice Department and lawyers for the Venezuelan men to file additional papers about the proposed contempt proceedings next week.