In October 2023, three days before Hamas fighters attacked Israel, Columbia University’s new president stood outside Low Library and posed a foundational question.

“What,” she asked, “does the world need from a great university in the 21st century?”

The president, Nemat Shafik, argued that the world required much. Rigorous thinkers who were grounded in the age’s great debates. Researchers whose breakthroughs could transform societies. Universities that extended their missions far beyond their gates.

Seventeen months later, Dr. Shafik is gone and the Trump administration is offering a far different answer. The ideal Dr. Shafik described, much of it historically bankrolled by American taxpayers, is under siege, as President Trump ties public money to his government’s vision for higher education.

That vision is a narrower one. Teach what you must, defend “the American tradition and Western civilization,” prepare people for the work force, and limit protests and research.

“I have not experienced, across 46 years of higher education, a period where there’s been this much distance” between the agendas of university leaders and Washington, said Robert J. Jones, the chancellor of the University of Illinois Urbana-Champaign.

The outcome of this clash over the purpose of higher education stands to shape American culture for a generation or more. If the president realizes his ambitions, many American universities — public and private, in conservative states and liberal ones — could be hollowed out, imperiling the backbone of the nation’s research endeavors.

Two months into Mr. Trump’s term, universities are laying off workers, imposing hiring freezes, shutting down laboratories and facing federal investigations. After the administration sent Columbia a list of demands and canceled $400 million in grants and contracts, university leaders across the country fear how the government might wield its financial might to influence curriculums, staffing and admissions.

“Colleges have gotten hundreds of billions of dollars from hard-working taxpayers,” Mr. Trump said in a campaign video. “And now we are going to get this anti-American insanity out of our institutions once and for all. We are going to have real education in America.” The goal, Mr. Trump declared, is to reclaim “our once-great educational institutions from the radical left.”

Other Republicans have spoken, often in more measured language, about their own frustrations with higher education. Senator Bill Cassidy, the Louisiana Republican who chairs the Senate Committee on Health, Education, Labor and Pensions, bluntly complained during a hearing last month that colleges were “not preparing students to succeed in the modern work force.”

With presidential power magnified by a largely genuflecting Congress, Mr. Trump’s challenges to academic freedom and First Amendment protections have not provoked broad and visible public outrage. The sobering reality for university leaders is that Mr. Trump has the administrative upper hand, and academia has startlingly few vocal allies.

The fusillade against higher education led by Mr. Trump and Vice President JD Vance — men with Ivy League degrees — is more furious than past conservative crusades against the country’s elite academic institutions. The administration, though, is capitalizing on imperfections that have been tearing at the system’s stature for years.

“His genius was in understanding and then exploiting the resentments, the anxieties, and the vulnerabilities of” voters who already had “critical sentiments” toward higher education, Ronald J. Daniels, the president of Johns Hopkins University, wrote of Mr. Trump in his 2021 book, “What Universities Owe Democracy.”

Private polling conducted for universities shows that many people believe that these nonprofit institutions are anything but — one consequence of high tuition costs. Even though a college education almost always provides graduates with higher lifetime incomes, rising debt has made the value of a degree a matter of debate. Politicians have eagerly caricatured colleges as sanctuaries of intolerance and “wokeism” where admissions processes have sometimes considered race or favored the well-connected.

For all of their grand talk — “For Humanity” is the name of Yale University’s $7 billion fund-raising campaign — administrators and professors often acknowledge that they have not mustered easy-to-digest responses against even routine criticisms.

Universities strained to be more accessible, building up more diverse classes and handing out more financial aid. But Chancellor Jones, who will become the University of Washington’s president this summer, nevertheless described higher education’s public relations strategy as “a work in progress.”

Many leaders concede that while the role of the university in American life is clear to them, it has grown muddled to many.

“Higher education has always been able to stand up and invoke its moral authority,” said Roger L. Geiger, a distinguished professor emeritus at Pennsylvania State University and a leading authority on the history of American colleges. “What’s happened is they’ve simply lost that moral authority.”

The Pew Research Center found in 2012 that 26 percent of Americans believed that colleges and universities were negatively affecting the United States. Last year, even before the campus demonstrations that led to thousands of arrests, Pew reported that figure had increased to 45 percent.

Much of Mr. Trump’s higher education agenda during his first term empowered for-profit colleges. Now, though, Mr. Trump is taking clearer aim at the cultures and missions of major nonprofit universities. His tactics, university officials and researchers believe, could throw American higher education toward an earlier time — closer to when, as Dr. Shafik put it, universities “were kept separate from the world around them.”

American higher education predates the republic itself. Harvard, for example, was established in the colonial period to educate clergymen. George Washington’s idea for a national university was never realized, but Abraham Lincoln found more success pursuing the idea that higher education was entwined with American ambition when he signed the measure that led to publicly funded land-grant institutions.

Research became a focus of universities late in the 19th century. The nation’s reliance on universities greatly accelerated during and after World War II, as the United States began to lean on academia more than most other countries.

Essential to the system was Washington’s new willingness to underwrite overhead costs of expensive research projects. By 1995, the National Academy of Sciences concluded that universities were “the core strength” of the American research-and-development apparatus. Universities also assumed part of the United States’ soft-power strategy, working on foreign aid projects that spanned the globe.

That symbiotic arrangement is now in jeopardy. The administration has framed its proposed cuts to overhead expenses, for instance, as a way “to ensure that as many funds as possible go toward direct scientific research costs.” But administration officials have also depicted the longstanding framework in harsh terms, including the assertion that it created a “slush fund” for liberal university administrators.

As Dr. Geiger put it, the Trump administration’s approach represented “a new era.” Besides upending individual studies, cuts to federal money could unleash dramatic consequences for the structures and objectives of universities.

“No one can assume, for example, that biochemistry is going to have a sustained future of generous funding,” said John Thelin, a professor emeritus at the University of Kentucky and a former president of the Association for the Study of Higher Education.

He could think of no president, provost or medical school dean who had, in recent years, appeared particularly nervous about an evaporation of funding. These days, it is hard to find a president, provost or medical school dean who is not anxious about something.

At Illinois, the federally funded Soybean Innovation Lab will close next month. Dr. Jones fears that research on everything from insulin production to artificial intelligence could ultimately wither, undermining the university’s ability to advance what he called “the public good.”

“Before, we were just trying to tell our story to improve the value proposition in the eyes of the public, but now it becomes a bigger, much larger issue than that,” said Dr. Jones, one of the few top university chiefs who have been willing to be interviewed on the record since Mr. Trump’s inauguration.

The threat is also acute at private institutions, even those with the biggest war chests. Johns Hopkins said last week that it would eliminate more than 2,000 jobs in the United States and overseas, the largest round of layoffs in its history. The University of Pennsylvania, Mr. Trump’s alma mater, is among the universities with new hiring freezes. (It announced that step before the Trump administration said on Wednesday that it would pause about $175 million in funding for Penn because it had allowed a transgender woman to compete on its women’s swim team.)

In recent weeks, presidents at public and private universities alike have weighed how long any institutional lifelines could last. But professors doubt that a major university can meet its modern ambitions without a relatively open spigot of federal support.

“Ultimately, the university cannot exist without research,” said Brent R. Stockwell, the chair of biological sciences at Columbia. “It would be really, really more akin to a high school or a local community college where you’re just teaching some classes without world-class researchers bringing the frontier of knowledge into the classroom.”

So far, Mr. Trump has not signaled any interest in retreat. That has left academic leaders searching urgently for how to save an ideal they insist is imperative.

Asked whether he feared a wholesale remaking of the American university, Dr. Jones replied that he did not like to use the word “fear.” But, he added, “it is a concern — I can’t say that it is not one of those things that a lot of us are concerned about.”

Sharon Otterman contributed reporting.

As conservatives fought against cancel culture on college campuses, they developed a particular fondness for the First Amendment. It was un-American, they argued, to punish someone for exercising their right to speak freely.

Today, however, many of those same conservatives, now in power in state and federal government, are behind a growing crackdown on political expression at universities, in ways that try to sidestep the Constitution’s free-speech guarantees.

President Trump and Republican lawmakers say that new laws and policies are necessary to protect students from harmful and objectionable content, to prevent harassment and to discourage conformity.

To that end, Mr. Trump has threatened to withhold hundreds of millions of federal dollars from universities because they moved too slowly to quell protests that left many Jewish students feeling threatened. And Republicans in state legislatures have drafted sweeping prohibitions against classroom “indoctrination” and the display of certain L.G.B.T.Q. symbols. They have also demanded the removal of art they consider inappropriate.

In some cases, the Trump administration has said existing federal law already gives the president all the power he needs to act. When Mr. Trump said he would deport student activists, for example, he claimed to be acting in the interest of American foreign policy.

Tellingly, administration officials have said they are not bound by the First Amendment when it comes to noncitizens.

“This is not about free speech,” said Secretary of State Marco Rubio. “This is about people that don’t have a right to be in the United States to begin with. No one has a right to a student visa. No one has a right to a green card.”

Critics of this broad approach, including some on the right, say Republicans are being just as heavy-handed and censorious as they claimed the left was toward them.

“That makes the situation so much worse,” said Greg Lukianoff, chief executive of the Foundation for Individual Rights and Expression, a free-speech group that often represents moderates and conservatives who claim they’ve been retaliated against for their political views.

“Now we have all this federal pressure and pressure from state governments — sometimes really direct and clear, and sometimes hazy and confusing,” he said, adding, “There’s a lot fewer people who care about the nonpartisan defense of free speech now.”

For many First Amendment experts and academics, the new laws and orders reveal an especially insidious threat: Public officials who are willing to marshal the power of the state against people whose views they dislike.

“A number of people in elected office have gotten extraordinarily comfortable with the idea that they should use that office to control the spread of ideas and information,” said Jonathan Friedman, a managing director at PEN America, a free speech advocacy group.

“And at a fundamental level, that’s what makes all of this so dangerous,” Mr. Friedman added.

While the federal government’s role in some aspects of education is fairly limited, it does hold powerful tools that the Trump administration has been eager to use. It can launch civil rights investigations, for instance, or withhold research grants.

States, which provide more funding for public schools and universities than the federal government does, have greater leverage and control.

Legislation approved last month by the Ohio State Senate sets parameters for the discussion of any “controversial belief or policy” at state universities — including climate change, electoral politics, abortion and immigration. The bill demands that faculty members “shall not seek to indoctrinate any social, political, or religious point of view.”

Sponsors say its purpose is to “allow students to exercise their right to free speech without threat of reprisal.” If it becomes law, universities would also be required to post all undergraduate course syllabuses online, along with the professor’s contact information and professional qualifications.

Many states have taken aim at diversity, equity and inclusion programs in university hiring and admissions. But Republicans in Arizona are going further, by trying to remove the subject entirely from the classroom. The State Senate approved a bill this month that would deny funding to any public college or university that teaches about contemporary American society through the academic framework of concepts including “critical theory, whiteness, systemic racism, institutional racism, antiracism, microaggressions.”

A bill awaiting the governor’s signature in Utah would outlaw pride flags at public schools and on government property.

In some cases, Republicans have directly interfered with campus activities. Students at the University of North Texas took down a pro-Palestinian art exhibit last month after a Republican lawmaker complained that it referred to genocide in Hebrew.

At Texas A&M University, officials banned drag performances on campus, saying it was “inconsistent” with the university’s values to host events that “involve biological males dressing in women’s clothing.”

The American education system has long been a target for conservatives, many of whom see it as hostile to their values. In the last few years, the country’s most explosive political and cultural clashes — over Covid policy, racial inequality, gender identity, immigration, Gaza — have played out with intensity on campus quads, at school board meetings and in the classroom.

Disruptive student protests have been an animating issue for Mr. Trump. In 2017, he suggested revoking funding from the University of California, Berkeley, after the university canceled an appearance by the professional right-wing provocateur Milo Yiannopoulos.

Today, Mr. Trump — who declared in his recent address to Congress that he had “brought back free speech” — continues to antagonize academia, but this time he is using the power of the presidency.

After his administration announced that it was canceling $400 million in funding for Columbia University, accusing it of failing to protect students and faculty members from “antisemitic violence and harassment,” legal scholars called the move an existential threat to academic freedom.

“Never has the government brought such leverage against an institution of higher education,” said Lee C. Bollinger, the former president of Columbia University.

Some conservatives said this kind of action is overdue and unsurprising.

“When you take federal funds, you agree to abide by all kinds of rules,” said Ilya Shapiro, director of constitutional studies at the conservative Manhattan Institute. Universities agree, for instance, to abide by certain accounting standards and anti-discrimination policies.

Those rules are not always enforced consistently, Mr. Shapiro said. Nor is the Trump administration “exactly being legally precise” in a lot of what it has done, he added.

“But part of this vibe shift that elected Trump is wanting law and order in a lot of ways,” Mr. Shapiro said. “And that includes on college campuses.”

The arrest earlier this month of Mahmoud Khalil, a green-card holder who was born in Syria and studied at Columbia, was one of the most aggressive moves yet by the Trump administration in its effort to punish pro-Palestinian demonstrators. Mr. Khalil served as a spokesman for a student group that embraces hard-line anti-Israel rhetoric and says it supports liberation for Palestinians “by any means necessary, including armed resistance.”

In announcing the arrest, the Department of Homeland Security accused Mr. Khalil of aligning himself with Hamas, a designated terrorist organization. Voicing support for such causes is not, however, a crime, and the Supreme Court has declared all manner of hateful speech to be protected by the First Amendment, including cheering the deaths of soldiers at their funerals and, in certain cases, cross burnings.

“It can’t be a crime — or even a civil offense — simply to hold and express heinous views,” said Ann Coulter, the conservative firebrand whose college speeches have been the targets of protesters and have sometimes been threatened with violence.

Ms. Coulter, an immigration hard-liner who acknowledged that she had rarely heard of a deportation that she didn’t support, said the president would be setting a terrible precedent by making protected speech — as offensive as it may be — a reason for deporting a legal green card holder like Mr. Khalil.

But Eugene Volokh, a senior fellow at the Hoover Institution at Stanford, said that the law is not always clear when the speech of noncitizens is at issue. And he said that Mr. Trump’s attempts to punish noncitizens seemed consistent in many ways with powers that Congress had already given presidents.

Does that mean that Mr. Khalil can be deported for protesting, which is a constitutionally protected act? “The only honest answer,” Mr. Volokh said, “is we don’t know.”

Conservatives have tested the scope of the First Amendment in other ways recently. Ed Martin, the Trump-appointed interim U.S. attorney for the District of Columbia, told the dean of Georgetown University Law Center that he had begun an “inquiry” into the school’s teaching and promotion of diversity, equity and inclusion — and insisted that he would not hire students from any university that continues to offer such programs.

In response, the school’s dean, William Treanor, wrote in a letter that the First Amendment guarantees Georgetown, a private, Catholic institution, “its abilities to determine, on academic grounds, who may teach, what to teach, and how to teach it.”

“This is a bedrock principle of constitutional law,” Mr. Treanor continued, “recognized not only by the courts, but by the administration in which you serve.”

President Trump signed an executive order on Thursday that directs the federal Department of Education to come up with a plan for its own demise.

Only Congress can abolish a Cabinet-level agency, and it is not clear whether Mr. Trump has the votes in Congress to do so. But he has already begun to dismantle the department, firing about half of its staff, gutting its respected education-research arm, and vastly narrowing the focus of its civil rights division, which works to protect students from discrimination.

Mr. Trump’s long history of attacking the Department of Education represents a revival of a Reagan-era Republican talking point. It has unified Democrats in fiery opposition. But is shuttering the department possible? And if not, how has Mr. Trump begun to use the agency to achieve his policy goals?

What does the department do?

The Education Department was founded in 1979. Its main job is distributing money to college students through grants and loans. It also sends federal money to K-12 schools, targeted toward low-income and disabled students, and enforces anti-discrimination laws.

The money for schools has been set aside by Congress and is unlikely to be affected by Mr. Trump’s executive order. But oversight of the funds could be reduced and moved to other federal agencies.

Those federal dollars account for only about 10 percent of K-12 school funding nationwide. While Mr. Trump has said he wants to return power over education to the states, states and school districts already control K-12 education, which is mostly paid for with state and local tax dollars. The federal department does not control local learning standards or reading lists.

The agency does play a big role in funding and disseminating research on education, but those efforts have been significantly scaled back by the Trump administration.

It also administers tests that track whether American students are learning and how they compare with their peers in other states and countries. It is unclear whether those tests will continue to be delivered, given drastic reductions in the staff and funding necessary to manage them.

Still, closing the department would not likely have much of an immediate effect on how schools and colleges operate. The Trump administration has discussed tapping the Treasury Department to disburse student loans and grants, for instance, and Health and Human Services to administer funding for students with disabilities.

Can the Department of Education actually be closed?

Any effort to fully eliminate the department would have to go through Congress. Republican members would most likely hear opposition from superintendents, college presidents and other education leaders in their districts; schools in Republican regions rely on federal aid from the agency, just as schools in Democratic regions do.

“They are going to run into opposition,” said Jon Valant, an education expert at the Brookings Institution. “They have a laser-thin majority and a filibuster to confront in the Senate.”

Even if Congressional Republicans stuck together to support closing the agency, Dr. Valant predicted their constituents would protest, given the department’s role in distributing money from popular programs like Pell grants, which pay for college tuition, and I.D.E.A., which provides support to students with disabilities.

“It’s a very hard sell,” he said. “And I am very skeptical that is where this administration wants to spend its political capital.”

It’s worth noting that the attempt to abolish the agency is part of a larger conservative agenda to roll back the federal role in education and direct more money toward private-school vouchers and home-schooling. Trump allies have ambitions to cut the primary federal funding stream to K-12 schools, known as Title I — although doing that, too, would most likely require action from Congress.

How much power does the department have?

Even as Mr. Trump has vowed to close the department, he has begun to use the agency’s powers.

In January, the agency announced an investigation into Denver Public Schools for converting a girls’ bathroom into an all-gender facility. It is also investigating a series of conferences for students of color in the Ithaca, N.Y., public schools, and has created an “End D.E.I.” web page, encouraging individuals to report instances of “divisive ideologies and indoctrination” in schools.

In addition, Mr. Trump’s executive order on “ending radical indoctrination in K-12 schooling” directs the department to develop and disseminate “patriotic” learning materials.

It is unclear how much those orders will change practices in classrooms, given its small role in K-12 education.

The agency does issue regulations on how civil rights laws apply to various groups of students, including disabled students, L.G.B.T.Q. students, racial minorities and girls. One of the administration’s favored strategies is to argue that when schools allow transgender students to use the bathrooms or play on the sports teams of their choice, it is a violation of girls’ rights under Title IX, a law that protects students from sex discrimination.

Mr. Trump has shown less interest in other elements of civil rights law. He has fired government lawyers who investigate schools that fail to provide equal access and services to children with disabilities, for example.

Currently, more than 70 percent of the department’s $224 billion annual budget goes to the federal student aid program, which has also become a frequent Republican target. Mr. Trump is seeking to restrict public-sector loan forgiveness, and has said fewer students should attend four-year colleges.

The agency provides more than $90 billion in new loans to students annually, which are distributed by colleges and serviced by the federal government through private contractors. It also offers $39 billion in Pell Grants annually to low-income students, which generally do not need to be paid back. It administers the federal work-study program and gives grants to students who promise to work as teachers in hard-to-staff subjects or schools.

It has had opponents since the beginning.

Opposition to the Department of Education is today associated with Republicans. But the agency began its life with fierce opponents on both sides of the aisle.

President Jimmy Carter established the department, often known simply as Ed, in 1979, fulfilling a campaign promise to the nation’s largest teachers’ union, the National Education Association. He did so over the objections of his own presidential transition team and many in Congress — including fellow Democrats.

Some staunch liberals believed all of the issues affecting children — health care, cash welfare and education — should be handled by a single federal agency, then known as the Department of Health, Education and Welfare.

Still, over the next four decades, Ed became a part of the beltway firmament, popular with Democrats and many Republicans, too. Many of the programs Ed oversees are sources of bipartisan comity, such as funding for vocational education.

Gareth Davies, a historian who has written about the founding of the Department of Education, said the revival of conservative opposition to the agency shows “just how far the G.O.P. has moved in the past two decades, from compassionate conservatism to culture wars.”

Mike Petrilli, president of the Thomas B. Fordham Institute think tank, and a former Department of Education staffer under President George W. Bush, called the gesture toward shuttering the agency a distraction from problems like the record-low reading scores of American students, released in January.

He suggested that Mr. Trump should host a governor’s summit in Washington to focus on the problem, particularly on the question of whether screen time is harming children’s academic abilities.

“If you wanted to solve this problem and show leadership,” he said, “you would talk about the real crisis.”