The university administration acknowledges that the main reason is a backlash from the events of 2015, as the campus has been shunned by students and families put off by, depending on their viewpoint, a culture of racism or one where protesters run amok.

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Before the protests, the university, fondly known as Mizzou, was experiencing steady growth and building new dormitories. Now, with budget cuts due to lost tuition and a decline in state funding, the university is temporarily closing seven dormitories and cutting more than 400 positions, including those of some nontenured faculty members, through layoffs and by leaving open jobs unfilled.

Few areas have been spared: The library is even begging for books.

“The general consensus was that it was because of the aftermath of what happened in November 2015,” said Mun Choi, the new system president, referring to the climax of the demonstrations. “There were students from both in state and out of state that just did not apply, or those who did apply but decided not to attend.”

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The protests inspired movements at other colleges. Since then fights over overt and subconscious racial slights, as well as battles over free speech, have broken out at Middlebury College in Vermont, the University of California, Berkeley, and The Evergreen State College in Olympia, Wash. Missouri’s experience shows how a conflict, if not deftly handled, can stain a college’s reputation long after the conflict has died down.

Students of all races have shunned Missouri, but the drop in freshman enrollment last fall was strikingly higher among blacks, at 42 percent, than among whites, at 21 percent. (A racial breakdown was not yet available for this fall’s freshman class.)

Black students were already a small minority. They made up 10 percent of the freshman class in 2012, a proportion that fell to just 6 percent last fall.

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Whitney Matewe, a black student from McKinney, Tex., who will be a senior in the fall, said that after the protests, her parents asked if she wanted to transfer, but she decided to stay because she is in Missouri’s prestigious journalism school.

But, she said, she understands why black students might not apply to a campus where they are all but invisible. A friend’s boyfriend obliviously told her she looked like Aunt Jemima, and she was dismayed that her friend did not object.

“Being ‘the other’ in every classroom and every situation is exhausting,” she said.

By sheer numbers, the drop in white students has caused the greatest damage, since they make up a majority of those on campus.

Tyler Morris, a white student from St. Louis, said he was afraid of being stereotyped as a bigot if he went to Missouri. So he decided to go to Missouri Valley College, “just down the road” in Marshall.

“The discrimination wasn’t against white people, but I didn’t want to be that person who I guess was stereotyped because I was white,” he said.

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College counselors said that Missouri might have a hard time recovering from protests because its reputation was largely regional. “Why would a student from New Jersey go to the University of Missouri instead of Rutgers or Penn State?” said Steven Roy Goodman, an independent college admissions counselor in Washington.

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Even in-state students for whom Mizzou is a family tradition are choosing to go elsewhere, including public universities in neighboring states, like Illinois and Arkansas, which offer preferential tuition or scholarships to Missouri students.

Aly Zuhler’s mother and cousins went to Missouri, and her mother would have liked for her to go there as well, she said. But Ms. Zuhler, who is Jewish and grew up in suburban St. Louis, said she could not stomach going to a place where blacks and Jews might feel unwelcome.

When she heard that a swastika had been smeared in feces on a dormitory bathroom at Missouri, she decided not to apply. She enrolled instead at Truman State University in Kirksville, Mo., where she will be a sophomore this coming year. “Looking for colleges is intimidating just by itself,” she said. “Adding anti-Semitism on top of that was just too much.”

A plant sciences professor, Craig Roberts, said that Missouri was suffering not because it was more racist than other places, but because the rage that had been repressed on other campuses burst into the open.

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“It was sparked at Mizzou by Ferguson,” Mr. Roberts said.

Ferguson, Mo., of course, is where the killing of an unarmed young black man, Michael Brown, by a police officer in 2014 became a national symbol of tension between the police and minority communities. Ferguson, just a two-hour drive away, was still a fresh memory in September 2015, when Payton Head, the student association president, posted on Facebook that people riding in the back of a pickup truck had continuously screamed racial slurs at him.

The post went viral and the outcry escalated through what has become known in the protest world as “intersectionality,” grievances that gain potency by being bundled together. There were demonstrations against racism, and to support Planned Parenthood, which was under attack by state lawmakers.

Days later a drunken white student jumped onstage during a rehearsal by an African-American group and used a racial slur.

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This was followed by the failure of the university president, Timothy M. Wolfe, to get out of his car to speak with demonstrators during the homecoming parade in October, drawing accusations of indifference. Then the swastika appeared.

A movement, Concerned Student 1950, commemorating the year the first black student was admitted to the university, grew out of the protests and set up a tent city. On Nov. 2, a graduate student, Jonathan Butler, began a hunger strike, spurred by the complaints of racial animosity and official inaction, as well as a cut in graduate student health care funding.

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Over the weekend of Nov. 7, the football team, led by its black players, said it would not practice or play unless Mr. Wolfe resigned. It was the last straw. On Nov. 9, Mr. Wolfe resigned as system president, and the chancellor of the Columbia campus, R. Bowen Loftin, also announced he was stepping down. Mr. Butler ended his hunger strike.

As the protests continued to boil, demonstrators tried to block the news media from the encampment, and Melissa Click, a communications professor, called for “some muscle” to oust a student taking a video of the confrontation.

In the minds of many, her outburst and the resignations became symbols of a hair-trigger protest culture lacking any adult control.

The university received a barrage of emails from alumni and families, some of which were published by National Review and Heat Street, a conservative news site.

In one, the parents of a junior wrote that while they did not underestimate the extent of bigotry in the world, “the way to effect change is NOT by resorting to the type of mob rule that’s become apparent over the past few days.”

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The university, they added, had shown a “complete lack of leadership,” and their two younger children had “all but eliminated Mizzou from their college list.”

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The email was forwarded to Ellen de Graffenreid, vice chancellor for marketing and communications, with a brief note saying, “I’m sure you already know this but you have a P.R. nightmare on your hands.” Ms. de Graffenreid, in turn, forwarded it to other administrators with a note saying, “This is pretty representative of the middle of the road people we are losing.”

While freshman enrollment has plummeted, students already at Missouri have not transferred out in large numbers — a sign, administrators said, that the protests looked worse from the outside. Christian Basi, a spokesman, said the university was formulating a marketing campaign to correct what he called “misperceptions” about the extent of the unrest.

Missouri also has appointed a chief diversity officer; promised to double the percentage of minority faculty members by 2020 and recruit more minority postdoctoral fellows; and is requiring diversity training for faculty and staff members and incoming students.

The tent city has been restored to a well-manicured emerald field of grass, but all around campus, signs of the university’s suffering are evident.

The library is asking for donations to buy 400 books that it wants, including a $5,250 copy of “Complete and Truly Outstanding Works by Homer.”

To soften the financial blow, some vacant dorm rooms — spartan suites of two rooms of two single beds, sharing a bathroom and with no TV, are being rented for $120 a night for events like homecoming, the fall family visit and the football game against Auburn University, a Southern rival.

For the Aug. 21 solar eclipse, Columbia is lucky to be one of the prime viewing locations where the sun will be completely obscured by the moon. As of early July, 35 rooms were still available for the event.

Some faculty members are still hoping that the situation can be turned around.

“I think we squandered a rare opportunity that we had to be a local, regional, national, global leader in terms of showing how a university can deal with its problems, including related to race relations,” Berkley Hudson, a journalism professor, said.

The protests could have been turned into an asset — a chance to celebrate diversity. “We still can,” he said.