A Cornell graduate student fearing deportation files a pre-emptive lawsuit.

“This is the first arrest of many to come,” Mr. Trump wrote on the social media platform Truth Social after federal agents picked up Mr. Khalil at his Manhattan apartment on March 8. Mr. Trump called pro-Palestinian activists like Mr. Khalil “terrorist sympathizers” and said “we will find, apprehend and deport” them, “never to return again.”

Another Columbia student, Leqaa Kordia was later detained for overstaying her visa, and yet another, Ranjani Srinivasan, left the country voluntarily after her visa was revoked.

The lawsuit, filed in federal court in the Northern District of New York, asks for national injunctions to block two executive orders issued in February. Both are aimed at the removal or arrest of pro-Palestinian activists or anyone else whom the administration deems guilty of antisemitic speech. A hearing is scheduled for Monday, according to Mr. Taal’s lawyer, Eric Lee.

Two other plaintiffs — a professor and another student at Cornell who are both American citizens — joined Mr. Taal in the suit, arguing that the executive orders chill their rights to free speech.

Mr. Taal, 31, is a citizen of both Gambia and the United Kingdom. He has become known on the Cornell campus in Ithaca, N.Y., as a leading pro-Palestinian voice.

He faced disciplinary action from the university stemming from a protest at a job recruitment event at Cornell last year where weapons manufacturers were among the featured prospective employers. His involvement in that protest led Cornell to require that he study remotely this semester, but he retained his status as a student.

In the lawsuit, Mr. Taal argues that his activism has made him a target of the Trump administration’s plans, based partly on a list that was circulated by a pro-Zionist organization, Betar. According to the lawsuit, Betar submitted Mr. Taal’s name to lawmakers, including Senator John Fetterman, Democrat of Pennsylvania.

The lawsuit also cites an article in The Washington Free Beacon, a right-leaning publication, that named Mr. Taal as the most important student who could face possible deportation under Mr. Trump’s orders.

The statement compared the transfer of Venezuelans to “the darkest episodes of human history,” including slavery and Nazi concentration camps. In particular, the government denounced what it called a threat to kidnap minors as young as 14 by labeling them as terrorists, claiming that the minors were “considered criminals simply for being Venezuelan.”

The government’s statement blamed the United States for the mass migration of Venezuelans, saying years of sanctions — which have been imposed by the U.S. over Maduro’s autocratic rule — had driven its people to flee. It also blamed members of the opposition in Venezuela for working with the United States on what he called “unilateral coercive measures” against the Maduro regime.

“Today, the first 238 members of the Venezuelan criminal organization, Tren de Aragua, arrived in our country,” Mr. Bukele wrote, adding that “the United States will pay a very low fee for them, but a high one for us.”

The Trump administration hopes that the unusual prisoner transfer deal — not a swap but an agreement for El Salvador to take suspected gang members — will be the beginning of a larger effort to use the Alien Enemies Act of 1798 to rapidly arrest and deport those it identifies as members of Tren de Aragua without many of the legal processes common in immigration cases.

The Alien Enemies Act allows for summary deportations of people from countries at war with the United States. The law, best known for its role in the internment of Japanese Americans during World War II, has been invoked three times in U.S. history — during the War of 1812, World War I and World War II — according to the Brennan Center for Justice, a law and policy organization.

On Saturday, Judge James E. Boasberg of Federal District Court in Washington issued a temporary restraining order blocking the government from deporting any immigrants under the law after President Trump issued an executive order invoking it.

In a hastily scheduled hearing sought by the American Civil Liberties Union, the judge said he did not believe federal law allowed the president’s action, and ordered that any flights that had departed with Venezuelan immigrants under Trump’s executive order return to the United States “however that’s accomplished — whether turning around the plane or not.”

“This is something you need to make sure is complied with immediately,” he said.

A lawyer representing the government, Drew Ensign, told the judge that he did not have many details to share and that describing operational details would raise “national security issues.”

The precise timing of the flights to El Salvador is important because Judge Boasberg issued his order shortly before 7 p.m. in Washington, but video posted from El Salvador shows them disembarking the plane at night. El Salvador is two time zones behind Washington, raising questions about whether the Trump administration ignored an explicit court order.

On Sunday, Mr. Bukele posted a screenshot on social media about Judge Boasberg’s order and wrote, “Oopsie… Too late.”

Attorney General Pam Bondi criticized the judge on Saturday night in a written statement that said that he had sided with “terrorists over the safety of Americans,” and that his order “disregards well-established authority regarding President Trump’s power, and it puts the public and law enforcement at risk.”

Officials from both countries revealed that the deal with the Trump administration also included the transfer of suspected members of the Salvadoran gang MS-13 who were being held in the United States awaiting charges.

“We have sent 2 dangerous top MS-13 leaders plus 21 of its most wanted back to face justice in El Salvador,” Secretary of State Marco Rubio posted on social media on Sunday. Mr. Rubio added that “over 250 alien enemy members of Tren de Aragua” were also sent to El Salvador, which “has agreed to hold in their very good jails at a fair price.”

Two of those MS-13 defendants are charged as senior members of the international criminal organization. Their transfers have raised concerns among some U.S. law enforcement officials, who fear that those individuals, once out of U.S. custody, could escape or issue orders that may endanger witnesses in both countries, according to people familiar with the matter who spoke on the condition of anonymity to describe internal discussions.

The Trump administration has faced problems deporting Venezuelans, hundreds of thousands of whom entered the United States during a surge in migration in recent years.

Venezuela’s leader, Nicolás Maduro, is among a handful of leaders in the region whose governments have not regularly received deportation flights from the United States because of a breakdown in diplomatic relations. Since Mr. Trump took office, Mr. Maduro has gone back and forth on whether his government will receive its deported citizens.

Last month, the United States sent groups of Venezuelans to the naval base at Guantánamo Bay, Cuba, and described at least some of them as gang members. Then on Feb. 20 the Trump administration abruptly repatriated all of the Venezuelan migrants from the base in a transfer through Honduras, with one being brought back to an immigration facility in the United States.

El Salvador had also presented itself as an option for deported Venezuelans. In early February, during a visit by Mr. Rubio, Mr. Bukele offered to take in deportees of any nationality, including convicted criminals, saying he would hold them in the country’s jail system.

Mr. Rubio, who announced Mr. Bukele’s offer at the time, said that the Salvadoran president had agreed to jail “any illegal alien in the United States who is a criminal of any nationality, whether from MS-13 or the Tren de Aragua.”

Tim Balk contributed reporting.

“I’ve been in the investment business for 35 years, and I can tell you that corrections are healthy,” Bessent said.

“All options are on the table,” Waltz said in response to a question on “Fox News Sunday” about whether President Trump would move ahead with new sanctions on Russia this week, as the administraton tries to pressure President Vladimir V. Putin of Russia to agree to a cease-fire in Ukraine. “He has put that out there on the table. And he has also put out a broader and different bilateral relationship with Russia on the table.”

Rubio said that El Salvador had agreed to hold the gang members “in their very good jails at a fair price that will also save our taxpayer dollars.” He thanked and praised President Nayib Bukele of El Salvador, calling him “a great friend of the U.S.”

Here is what we know about the gang:

A rising force out of Venezuela

Tren de Aragua (Train of Aragua, or Aragua Train) has roots in Tocorón prison in Venezuela’s northern Aragua state, which the group’s leaders had transformed into a mini-city with a pool, restaurants and a zoo. They reportedly recorded executions and torture there to maintain control over other prisoners.

As Venezuela’s economy collapsed and its government under President Nicolás Maduro became more repressive, the group began exploiting vulnerable migrants. Tren de Aragua’s influence soon stretched into other parts of Latin America, and it developed into one of the region’s most violent and notorious criminal organizations, focusing on sex trafficking, human smuggling and drugs.

Colombian officials in 2022 accused the gang of at least 23 murders after the police began to find body parts in bags. Alleged members have also been apprehended in Chile and in Brazil, where the gang aligned itself with Primeiro Comando da Capital, one of that country’s biggest organized crime rings.

A recent entry to the United States

Despite the many unknowns about its true size or sophistication in the United States, Tren de Aragua has emerged as a real source of concern for law enforcement in the last couple of years.

In New York City, according to the police the gang has focused on stealing cellphones; retail thefts, especially high-end merchandise in department stores and thefts while riding scooters; and dealing a pink, powdery synthetic drug, known as Tusi, that is often laced with ketamine, MDMA or fentanyl.

The police have also said that the gang is believed to recruit members from inside the city’s migrant shelters, and has variously had conflicts or made alliances with other gangs.

In other parts of the country, people accused of affiliations with Tren de Aragua have been charged with crimes such as shootings and human trafficking, mostly targeting members of the Venezuelan community.

In May 2024, federal officials uncovered a sex-trafficking ring in which they said the gang was forcing Venezuelan women into sex to repay debts to smugglers who assisted with border crossings. The ring stretched across Louisiana, Texas, Virginia, Florida and New Jersey, according to a complaint filed in federal court.

The group’s presence in the United States was a flashpoint of the 2024 election, as Mr. Trump accused the Biden administration of letting criminals into the country. During a presidential debate, he falsely suggested that the gang had taken over Aurora, Colo.

A source of stigma for migrants

The Trump administration has repeatedly described Tren de Aragua as a focus of its deportation efforts. Venezuelan migrants seeking asylum say the gang’s presence and the discourse around it in the United States have created hurtful stigma and discrimination against them.

“Any of us who have tattoos, they think that we are Tren de Aragua,” said Evelyn Velasquez, 33-year-old Venezuelan woman, told The New York Times in September. “I’ll go apply for a job and when they hear that we are Venezuelan, they turn us down.”

In February, the White House press secretary said that 10 men detained and housed in Guantánamo Bay, Cuba were members of Tren de Aragua. The sister of one of the men detained said that he was not a gang member.

In late February, the Trump administration abruptly emptied two detention sites the government had used to hold 177 Venezuelans flown in from the United States, including a military prison building formerly used to hold terrorism detainees. Federal officials moved out a second group of migrants this month.

But shortly after the announcement, James E. Boasberg, a federal judge in Washington, D.C., said he would issue a temporary order blocking the government from deporting any immigrants under the law.

In a hastily scheduled hearing, he said he did not believe the law offered grounds for the president’s action, and he ordered any flights that had departed with Venezuelan immigrants under the executive order to return to the United States “however that’s accomplished — whether turning around the plane or not.”

“This is something you need to make sure is complied with immediately,” he directed the government.

Lee Gelernt, a lawyer for the American Civil Liberties Union, which sued over the executive order, said in an interview after the hearing that he believed two flights were “in the air” on Saturday evening.

During the hearing, Judge Boasberg said he was ordering the government to turn flights around given “information, unrebutted by the government, that flights are actively departing.”

A lawyer representing the government, Drew Ensign, told the judge that he did not have many details to share and that describing operational details would raise “national security issues.”

After the hearing, the government filed an appeal. In a statement late Saturday, Attorney General Pam Bondi said the judge had put “terrorists over the safety of Americans” and placed “the public and law enforcement at risk.”

“The Department of Justice is undeterred in its efforts to work with the White House, the Department of Homeland Security, and all of our partners to stop this invasion and Make America Safe Again,” she added.

The president’s order, dated Friday, declared that Venezuelans who are at least 14 years old, in the United States without authorization and part of the Tren de Aragua gang are “liable to be apprehended, restrained, secured and removed.”

The Alien Enemies Act allows for summary deportations of people from countries at war with the United States. The law, best known for its role in the internment of Japanese Americans during World War II, has been invoked three times in U.S. history — during the War of 1812, World War I and World War II — according to the Brennan Center for Justice, a law and policy organization.

Hours before the White House published its proclamation, the American Civil Liberties Union filed a lawsuit on behalf of five Venezuelan men seeking to block the president from invoking the law. All five men were accused of having links to Tren de Aragua but deny that they are in the gang, Mr. Gelernt said. One of the men was arrested, the lawsuit said, because an immigration officer “erroneously” believed he was a member of Tren de Aragua because of his tattoos.

Judge Boasberg initially issued a limited order on Saturday blocking the government from deporting the five men.

The Trump administration promptly filed an appeal of the order, and the A.C.L.U. asked the judge to broaden his order to apply to all immigrants at risk of deportation under the Alien Enemies Act. At the hearing Saturday evening, Judge Boasberg said he would issue a broader order applying to all “noncitizens in U.S. custody.”

In the lawsuit, lawyers for the American Civil Liberties Union wrote that the Venezuelans believed that they faced an immediate risk of deportation. “The government’s proclamation would allow agents to immediately put noncitizens on planes,” the lawsuit said, adding that the law “plainly only applies to warlike actions” and “cannot be used here against nationals of a country — Venezuela — with whom the United States is not at war.”

The judge agreed, saying that he believed the terms “invasion” and “predatory incursion” in the law “really relate to hostile acts perpetrated by enemy nations.”

The White House and the Homeland Security Department, which runs the nation’s immigration system and was named in the lawsuit, did not immediately respond to requests for comment.

Noah Feldman, a constitutional law professor at Harvard, said the fate of the case, which could ultimately wind up at the Supreme Court, would hinge on “how much deference the courts pay to the president’s determination that there’s a threatened incursion.” Judges would have to make that determination “without a lot of precedent,” Professor Feldman added.

President Trump, who campaigned last year on a promise to initiate the largest deportation operation in U.S. history, has often referred to the arrivals of unauthorized immigrants as an “invasion.” One of the first executive orders he issued after returning to the White House was titled, “Protecting the American People Against Invasion.”

His proclamation invoking the Alien Enemies Act appeared to be narrowly focused on Tren de Aragua, a gang that emerged from a Venezuelan prison and grew into a criminal organization focused on sex trafficking, drug dealing and human smuggling.

But if the Trump administration’s interpretation of the law is ultimately upheld, it could empower the administration to remove other immigrants age 14 or older without a court hearing. That would enable the extraordinary move of arresting, detaining and deporting immigrant minors without the due process afforded to immigrants for decades.

Skye Perryman, president of Democracy Forward, a legal group that joined the A.C.L.U. in submitting the challenge to the executive order, said in a statement that Saturday was a “horrific day in the history of the nation, when the president publicized that he was seeking to invoke extraordinary wartime powers in the absence of a war or invasion.”

Zolan Kanno-Youngs and Glenn Thrush contributed reporting.

Ms. Leavitt added that Mr. Boehler had played a “critical role” in the February release of Marc Fogel, a teacher who was arrested on charges of bringing medical marijuana into Russia in August 2021.

Mr. Boehler, a health care entrepreneur and close ally of Jared Kushner, Mr. Trump’s son-in-law, has had a roving presence in the White House during both of Mr. Trump’s terms. In 2020, he worked on the federal government’s response to the Covid-19 pandemic, helping coordinate emergency response efforts and the Trump administration’s coronavirus vaccine development initiative, Operation Warp Speed.

Dustin Stewart, who served in the Biden administration as the deputy special envoy for hostage affairs and has worked closely with Mr. Boehler in recent months, was expected to continue serving as the acting special envoy until the Trump administration decides who should hold the job permanently, a senior administration official said.

Mr. Boehler asked to be withdrawn from consideration for the job, according to two senior administration officials, in part because he did not want to divest from his health care investment firm, which would have been required for the Senate-confirmed position. The officials spoke on the condition of anonymity to discuss personnel matters.

A special government employee is an executive branch appointee named to “perform important, but limited, services to the government, with or without compensation, for a period not to exceed 130 days” during a one-year period. Elon Musk, who is leading the cost-cutting initiative known as the Department of Government Efficiency, is also a special government employee.

Mr. Boehler is expected to still have broad latitude to work on hostage negotiations from his State Department office, one official said.

Mr. Rubio asked Mr. Boehler this month to meet with senior Hamas leaders in Qatar, an attempt to jump-start cease-fire talks and secure the release of Edan Alexander, the last remaining Israeli American captive believed to be alive, and the bodies of four others. The talks did not produce an agreement, and Mr. Rubio referred to them as a “one-off.”

The talks broke with the United States’ practice of refusing to negotiate directly with Hamas, which the State Department has designated as a terrorist group. And they upset Israeli officials, who were surprised by the visit. Ron Dermer, a close adviser to Israel’s prime minister, Benjamin Netanyahu, confronted Mr. Boehler in a phone call over the Hamas talks, according to a senior administration official.

Mr. Boehler was also heavily involved in the release this week of American prisoners held in Kuwait on drug charges.

Mr. Trump, who is now the chairman of the Kennedy Center, is scheduled to speak at a meeting of its board on Monday afternoon, when proposed changes to the honors advisory committee will be on the agenda, according to the individuals and a copy of the agenda that was obtained by The New York Times.

Since 1978, the Kennedy Center has named honorees to be recognized each year at a star-studded televised gala without interference from the White House. The center has honored a broad spectrum of artists and performers, including Lucille Ball, Dolly Parton, Clint Eastwood, Fred Astaire and the Grateful Dead.

But Mr. Trump is seeking a more direct role. He replaced all the Biden appointees on the center’s once-bipartisan board, was elected chairman and installed a loyalist, Richard Grenell, as its president. The board is scheduled to meet Monday to consider a resolution, which has not been previously reported, that would give Mr. Trump more control over the selection of honorees.

The resolution states that members of the committee responsible for selecting honorees “shall be appointed by the chairman of the board, and shall serve at the pleasure of the chairman,” according to a copy obtained by The Times. That would give Mr. Trump broad power to hire and fire those who help decide who will receive the honor, which recognizes people and institutions for lifetime artistic achievement. The committee will recommend a slate of honorees to the Kennedy Center’s president for approval, the resolution says.

In the past, Kennedy Center officials chose the members of the committee responsible for proposing honorees after receiving recommendations from former honorees, the board, the arts community and the general public. Last year, the committee was chaired by the philanthropist David C. Bohnett and included board members, Kennedy Center officials and artists, including Gloria Estefan, Sally Field, Renée Fleming, Herbie Hancock, Judith Jamison, Lionel Richie and John Williams.

It is not clear what Mr. Trump has in mind for the committee, or what kind of artists he would like to see honored at the Kennedy Center. Since the start of his second term, he has turned to stars like Mel Gibson, Sylvester Stallone and Jon Voight to serve as envoys to Hollywood.

The Kennedy Center declined to discuss the upcoming board meeting or the resolution to change the honors process.

Mr. Grenell said in a statement that “the financial situation at the Kennedy Center is a serious problem that has been hidden from the public for too long, and so Donald Trump is committed to putting the Kennedy Center on a solid financial foundation by having programming that appeals to everyone, not just a few.”

Officials at the White House did not immediately respond to a request for comment on Saturday afternoon.

Mr. Trump has a stormy history with the Kennedy Center Honors, the institution’s most important fund-raiser of the year, which is televised on CBS and includes a White House reception ahead of the awards. Several of the artists who were honored in 2017, early in the first Trump administration, criticized Mr. Trump and suggested that they would boycott the White House reception. After that Mr. Trump broke with tradition and stayed away from the honors galas for his entire term.

At the start of his second term, Mr. Trump set his sights once again on the Kennedy Center. He ousted the center’s longtime chairman, the financier David M. Rubenstein, the center’s largest donor, and fired Deborah F. Rutter, the center’s president for more than a decade.

Mr. Trump’s push to expand his influence over the Honors program is part of a broader campaign to reshape the Kennedy Center’s cultural identity. Promising a “Golden Age in Arts and Culture,” Mr. Trump has vowed to rid the center of “woke” influences, drag shows and “anti-American propaganda.” He has appointed close allies to the board, including his chief of staff, Susie Wiles; Laura Ingraham, the Fox News host; and Dan Scavino, a longtime aide.

While Mr. Trump’s plans for the center are still taking shape, Mr. Grenell, a former ambassador to Germany who is serving as the center’s interim president, has said the center intends to host a “a big, huge celebration of the birth of Christ at Christmas.”

Mr. Trump’s actions have prompted an outcry from artists and patrons of the Kennedy Center. Several prominent figures, including the actress Issa Rae and the musician Rhiannon Giddens, have canceled engagements at the center in protest. The musical “Hamilton” recently scrapped a planned tour there next year.

Vice President JD Vance and the second lady, Usha Vance, whom Mr. Trump also appointed to the board, were loudly booed while attending a concert on Thursday by the National Symphony Orchestra, one of the center’s flagship ensembles.

Hawaii is fast-tracking job applications. Virginia started a website advertising its job market. Gov. Josh Shapiro of Pennsylvania signed an executive order aimed at attracting federal employees to the state’s 5,600 “critical vacancies” in the state government. Both New Mexico and Maryland announced expanded resources and agencies to help federal workers shift into new careers in the state, and Gov. Kathy Hochul of New York is encouraging people to “come work in the greatest state in the nation.”

There has been interest. The New York governor’s office said roughly 150 people have signed up to attend information sessions hosted by the state’s Department of Labor.

But it’s too soon to say how many federal employees are applying for state-level roles and how exactly demographics could shift as a result, according to William H. Frey, a demographer at the Brookings Institution.

There were about 2.3 million civilians employed by the federal government’s executive branch when President Trump was sworn into office on Jan. 20. Thousands of government jobs have been cut as part of DOGE’s cost-cutting efforts across a range of agencies, including the Centers for Disease Control and Prevention, the Food and Drug Administration and the National Institutes of Health.

Some of those fired employees have since been rehired, and courts have temporarily stopped some of the administration’s efforts. Many federal employees, including those who have highly specific government skills, are suspended in the unknown and looking for new roles pre-emptively.

State governments have begun competing to attract those federal employees to unfilled state roles. The effort also has political overtones, with states run by Democrats leading the charge.

“If the Trump administration turned you away, Minnesota wants you,” Gov. Tim Walz of Minnesota said.

Walz, the Democratic vice-presidential candidate during last year’s election, announced efforts to help federal employees find jobs in Minnesota on March 6, the day after the Trump administration said it planned to cut over 80,000 employees from Veterans Affairs.

Gov. Kathy Hochul of New York launched an ad campaign targeted at federal employees last week. “We won’t denigrate you. We will treat you with dignity and respect that you deserve because, in New York, we know it’s not the demagogues and the technocrats who make America great, it’s public servants,” she said in a statement.

On Feb. 18, Gov. Josh Green of Hawaii signed an executive order designed to attract federal workers and fast-track the state’s hiring process.

“We’ve already had 1,239 applications for technology jobs, investigator positions and corrections officers, to name a few categories,” Mr. Green said in an email. “We’ve needed a lot of these positions to be filled.”

Maryland, which has the second-highest concentration of federal employees outside of Washington, set up a variety of initiatives for former federal workers, including a way to help those interested in starting a second career with Maryland’s public schools. Senator Chris Van Hollen of Maryland, in announcing the state’s efforts, called the federal government cuts an “illegal purge.”

“This is not about efficiency. This is about rigging the government for the already rich and powerful, like Elon Musk,” he said in a statement.

While states are using this as an opportunity to oppose Mr. Trump, workers are unlikely to follow that lead, Dr. Frey said.

“People move because of jobs,” he said. “They don’t move for politics.”

As more states and cities are introducing initiatives to support former federal workers, many public servants are hoping to be able to stay put.

Colin Murphy, a former product manager at 18F, a previous unit at the General Services Administration, was thrilled to see his city of Cleveland, Ohio, announce a Rapid Response Hub for federal employees.

“I would love to see my experience and my knowledge I’ve gathered at the federal level be transferred to any state that is willing to take me,” Mr. Murphy said, adding, “Ultimately, I got in this role to serve the people, and I would do anything to serve the people that I live with.”

Not every state is courting federal workers because of politics. Gov. Glenn Youngkin, Republican of Virginia, debuted a new initiative and website last month titled, “Virginia Has Jobs.” Choosing his words carefully, he expressed support for the efforts of DOGE, calling the federal government inefficient and saying change “needs to happen.”

“We have a lot of federal workers in the commonwealth,” he continued, “And I want to make sure they know we care about them and we value them and we want them to find that next chapter should they experience job dislocation here in Virginia.”

Instead, those field offices will report to three branch directors at headquarters who will be in charge of the East, West and Central regions. The remaining three F.B.I. offices and the largest in the country — New York, Washington and Los Angeles — will answer to the deputy director.

“These changes are meant to empower our S.A.C.s through improved engagement and leadership connections,” said the email, which was sent on Friday, referring to special agents in charge, who typically oversee field offices in a given region.

It represents a shift after a quarter-century of an F.B.I. run under a structure put in place by Robert S. Mueller III after the Sept. 11 attacks. The model was established to address administrative lapses and bolster efforts to deter terrorism. In Mr. Patel’s iteration, he has appointed a total of five branch directors, eliminating the executive assistant directors who previously managed the F.B.I. on a daily basis.

The announced changes were not unexpected, as Mr. Patel has already moved to reduce the number of F.B.I. employees working at headquarters and push them into the field, making good on a pledge he made before becoming director. His efforts have drawn praise from President Trump.

The swift decision to alter the hierarchy of the F.B.I. comes just weeks after Mr. Patel was confirmed, raising questions among former and current agents about the thoroughness of the plan. In particular, they said, they worried that the changes could result in less coordination between field offices and create intelligence gaps. Still, even former senior executives skeptical of Mr. Patel’s leadership and relative lack of experience believe the new model, while imperfect, could be an improvement and certainly reduce the deputy director’s immense responsibilities.

In theory, the move could help the new deputy director, Dan Bongino, who has never worked for the F.B.I. and has a limited understanding of its complex and global operations, transition into an important role that has traditionally been filled by a senior agent. The changes could free him up more to handle domestic and international investigative and intelligence activities, among other things. The previous deputy director had dozens of direct reports, including all the top agents in the field.

How Mr. Patel came up with his plan so quickly is not exactly clear, but he has been relying on a newly established group of former agents, known as the director advisory team, for guidance. But those agents are long retired and only one had reached the senior ranks.

One former F.B.I. official familiar with the advisory team’s work said that members had been considering a regional model, but it differed from the one that was announced. A former senior agent on the advisory team who had worked with F.B.I. leadership before Mr. Patel arrived had even written a white paper that included a similar model.

The former official said that Mr. Patel’s plan was better than previous proposals, but that its success hinged on having strong leaders in those roles.

Changes to the top ranks of the F.B.I.’s structure had been discussed long before Mr. Patel’s arrival, former senior F.B.I. officials said, along with reducing the number of employees located in the Capitol region. One former executive who left several years ago but was deeply involved in the bureau’s management applauded Mr. Patel’s effort.

As part of his plan, Mr. Patel named five acting branch directors to essentially run the F.B.I. after the former executives in charge of those areas were abruptly pushed out.

Among the new acting branch directors is Michael Glasheen, who ran counterterrorism at the Washington field office when he took the job in August 2021, after the attack on the Capitol on Jan. 6 of that year. Mr. Glasheen will be in charge of “field services,” but what responsibilities fall under his purview were not exactly clear. Previously, the bureau had executive assistant directors for science and technology and intelligence. Former F.B.I. officials said Mr. Patel decided to put intelligence under the operational control of the national security branch.

Mr. Patel has said: “The biggest problem the F.B.I. has had has come out of its intel shops. I’d break that component out of it.”

Also promoted was Steven Jensen, who was tapped to oversee the bureau’s national security programs. Mr. Jensen most recently ran the F.B.I.’s field office in Columbia, S.C. Former agents said the selection of Mr. Jensen stood out because he ran a major section at the bureau that helps manage the threat of domestic terrorism. In that role, he helped coordinate the F.B.I.’s nationwide investigative efforts in connection with the Jan. 6 attack.

President Trump and his allies, including Mr. Patel, have attacked the bureau for arresting those involved in the Jan. 6 riot. It was not known if Mr. Patel had questioned the men about their views on the F.B.I.’s response to Jan. 6.

In a speech at the Justice Department on Friday, Mr. Trump said he had “pardoned hundreds of political prisoners who had been grossly mistreated. We removed the senior F.B.I. officials who misdirected resources to send SWAT teams after grandmothers and J6 hostages.”

Now the president’s director, Mr. Patel, is promoting the men Mr. Trump has falsely accused of wrongdoing.

The Jan. 6 investigation was the largest in the bureau’s history, with more than 5,000 F.B.I. employees taking part in about 2,400 investigations. Before Mr. Patel arrived, the agency’s acting leaders clashed with the Justice Department, which had demanded the names of bureau personnel who worked on the investigations.

The demand elicited fears at the time that the administration would conduct a purge or make their names public, possibly putting their lives at risk. So far, the Justice Department has not done so.

Critics of the agency have said that if the bureau had taken a more aggressive stance in the run-up to Jan. 6, the rioting at the Capitol might have been prevented. But the bureau lacked imagination and failed to connect to the dots, ultimately missing a chance to thwart the domestic terrorism attack that further polarized the country.