Just after 2 p.m. last Wednesday, Nemat Shafik, the president of Columbia University, stepped out of an office building on Capitol Hill and into an idling black SUV.
She had just endured an intense grilling by a congressional committee investigating antisemitism on elite college campuses. Now, a fresh challenge was rapidly building back on her own turf, where pro-Palestinian student demonstrators had staked out an encampment dominating Columbia’s lawn.
For a university trying to reassure Congress that it was getting its campus under control, the timing could scarcely have been worse. With a narrow window to act, Dr. Shafik directed her car to a law firm near the White House, where she set up a makeshift command center.
The secretive deliberations that followed over 24 frantic hours have sent Columbia into a crisis over free speech and safety unlike any the campus has seen since 1968. The events also set off a chain reaction rattling campuses across the country, just as one of the most trying academic years in memory neared its end.
In theory, Dr. Shafik had a range of options to deal with the protests and protect Jewish students; in the moment, though, she saw little choice, according to three people who described the private discussions. Her testimony had pointed toward coming down hard on the protesters.
Despite brief attempts to negotiate with them and objections from key leaders on campus, Dr. Shafik ordered what she later conceded was an “extraordinary step.” She suspended the students and ordered New York City police in riot gear to arrest more than 100 activists who refused to leave on Thursday afternoon.
But instead of quelling the protests, Dr. Shafik’s decision appeared to backfire. By this week, she was besieged on all sides.
Students protesters were unbowed, and soon the encampment had regrown to be even larger than before. Dr. Shafik’s own faculty threatened to revolt over an “unprecedented assault on student rights.” At least one major Jewish donor cut off support. And while the White House voiced deep concern, the very Republican lawmakers she had set out to appeal to called for her resignation.
“It’s the most significant test Columbia has confronted since its recovery from ’68,” said Robert A. McCaughey, a longtime university professor who has written a history of Columbia, suggesting there were real questions whether Dr. Shafik, an Egyptian-born economist, could outlast it.
If the conflict was handled badly, he added, it could also contribute to a growing “crisis of confidence” in universities as engines of social progress that prepare future generations to confront the world’s most pressing challenges.
Columbia declined a request to interview Dr. Shafik.
But in a statement, a university spokeswoman said the president had remained in “constant touch” while she was in Washington, including on calls that lasted until midnight. The spokeswoman, Samantha Slater, also said Dr. Shafik was now focused on “de-escalating the rancor” on campus.
Student demonstrations for the Palestinian cause have become a constant feature of select college campuses since the Israel-Hamas war broke out. Many activists, including some Jewish students who support the movement, say they are fighting to preserve human life in Gaza, where local health officials say more than 30,000 people have died, and to end Israel’s oppression of Palestinians.
But demonstrations from the left have also included, at times, antisemitic hate speech, threats and outright support for Hamas. In recent days, nonstudent protesters gathered outside Columbia’s gates have used especially vitriolic rhetoric that has left some Jewish students feeling unsafe.
Now, with only days of classes left in the spring semester, neither side appears to have a clear endgame. University leaders are counting the days until summer, hoping to protect May’s commencement ceremonies from disruption.
Columbia faces one of the most complex balancing acts between protecting students on campus and respecting its deeply cherished commitment to academic freedom. The university is home to large Jewish and Arab student populations, and boasts a leading Middle Eastern studies department, a dual degree program with Tel Aviv University and a rich history of student activism dating back to the 1960s.
Dr. Shafik, an international finance expert with few prior connections to Columbia, has conceded the university was unprepared for the outpouring that followed Hamas’s Oct. 7 attack. She had been ceremonially inaugurated just days before. But as the protests escalated, and the presidents of Harvard University and the University of Pennsylvania lost their jobs after botching their own appearances before Congress in December, she slowly began clamping down.
In the fall, the university suspended two student groups, Students for Justice in Palestine and Jewish Voice for Peace, whose rolling protests repeatedly violated its policies. This month, it suspended students who it said had been involved in an event called “Resistance 101,” where speakers openly praised Hamas.
By the time she was called to testify before the Republican-led House Committee on Education and the Work Force this month, it looked as though Dr. Shafik might avoid the fate of the other Ivy League presidents targeted by Congress.
Columbia spent months preparing for the hearing. Shailagh Murray, a former adviser to President Barack Obama who oversees the university’s public affairs office, recruited a large team of lawyers, old political hands and antisemitism experts to prep Dr. Shafik. It included Dana Remus, President Biden’s former White House counsel; Risa Heller, a crisis communications guru; former Republican congressional aides; and Philippe Reines, a longtime aide to Hillary Clinton.
Many team members gathered in the Washington offices of the law firm, Covington & Burling, beginning the Saturday before the hearing for mock testimony.
Dr. Shafik was determined not to make the same mistakes as her Ivy League counterparts, according to the people familiar with her preparation. Where their testimony came off as haughty and convoluted, she wanted to project humility and competence.
The university handed the committee thousands of pages of documents, including sensitive records that almost never become public. They showed that Columbia had suspended more than 15 students and removed five professors from the classroom, including at least three facing accusations that they had made Jewish students feel unsafe.
Though her testimony on the disciplinary cases made supporters of academic freedom furious, the approach appeared to work inside the hearing room. Dr. Shafik defended free speech rights, but said universities “cannot and should not tolerate abuse of this privilege.”
Grudging Republicans largely accepted the answers.
“Columbia beats Harvard and U Penn,” Representative Aaron Bean, Republican of Florida, teased from the dais.
But as Dr. Shafik slowly dispatched one potential crisis, student organizers were carrying out a plan to escalate their own pressure on the university.
In the predawn hours before Dr. Shafik’s scheduled testimony on Wednesday, dozens of students poured out of dorms and apartments into a grassy quad outside Columbia’s main library and pitched tents. When campus awoke, a sign posted on the lawn announced the “Gaza Solidarity Encampment,” openly defying rules governing demonstrations.
Columbia administrators issued their first warning to participants to disperse at 9:30 a.m., just as Dr. Shafik was preparing to take the witness stand. But by the time she got back to Covington’s glass-walled offices to turn her prep room into a war room, the students had not budged.
“The genocide in Gaza is too unbearable for us to continue to allow our university to ignore every single democratic attempt that we have tried,” said Maryam Alwan, an undergraduate who helped organize the demonstration.
Organizers said they held hours of discussions with a senior university vice president to see if the two sides could find an off-ramp. The students were demanding the university divest from any financial interests enriching Israel and grant amnesty for all activists under investigation for protest actions, among other demands.
To some observers, though, it looked as if both sides were more interested in proving a point than de-escalating.
“You had hard-heads on both ends who wanted a confrontation,” said Dr. James Applegate, a professor of astronomy and member of the University Senate’s executive committee. “They got what they wanted.”
Dr. Shafik, meanwhile, began a series of calls with university deans, some of whom worried the university was proceeding without proper contingency plans. Around 5 p.m. on Wednesday, she formally notified the University Senate of her intention to call in the Police Department. Its executive committee replied with explicit disapproval, Dr. Applegate said.
The decision was destined to be fraught. The city’s police officers have rarely been welcomed on campus since the 1968 protests, when they helped violently remove students occupying university buildings at the height of the antiwar movement.
But Dr. Shafik was adamant that the rules be enforced. The police warned her the encampment would only get harder to root out the longer it lasted. And, with Congress and the Biden administration scrutinizing how Columbia was handling antisemitic threats, she had legal concerns about failing to act. She began making arrangements for the police to arrive the next day.
“I have determined that the encampment and related disruptions pose a clear and present danger,” she wrote to the Police Department the next day.
On Wednesday evening, Dr. Shafik did not head back to New York to be on hand when the police arrived, however. She decided to keep a longstanding plan to attend a private dinner in Washington for the Bezos Earth Fund, according to a university spokeswoman. Dr. Shafik ended up fielding so many calls that she never had time to eat, she said.
Back on campus, just before the university’s final deadline to disperse passed that night, students in the encampment gathered for a meeting. Closing their eyes for a secret ballot, they were asked for a show of hands if anyone wanted to disband rather than face repercussions.
No one raised a hand, according to a student organizer who counted the votes.
Stephanie Saul and Maria Cramer contributed reporting.
