A pedestrian walks past chalk art reading "Bring Hannah Home" on the Free Speech Wall on the Downtown Mall in Charlottesville, Va., Thursday, Sept. 25, 2014. (Ryan M. Kelly/AP)

— At the University of Virginia’s commencement exercises, graduates of the Class of 2015 received their diplomas, took pause to revel in the moment and then let out a collective sigh of relief.

The cap-and-gown ceremonies represented an emotional coda for the students, who finished their time at the elite public flagship university with a year of grief, trauma and turmoil, all while the campus was thrust into the national media spotlight.

Their last nine months at U-Va. began with the September disappearance of sophomore Hannah Graham, and the ensuing search for the 18-year-old turned into an anxious discussion about underage drinking and campus safety. Graham’s body was found in October on an abandoned property in Albemarle County, turning worry into mourning.

Just weeks later, as normalcy was beginning to return, Rolling Stone magazine published an explosive account of a brutal fraternity gang rape on campus. The article — which alleged a culture of systemic denial and coverups of sexual assaults — led advocacy groups and protesters to assail the campus as a “rape school.” Although later discredited, the story upended the campus Greek system, which signed on to new safety rules, and led to soul-searching about U-Va.’s treatment of women.

Then, in March, amid nationwide focus on race relations and police use of force, a 20-year-old African American student was bloodied in an encounter with white state Alcoholic Beverage Control officers outside a bar. Images of the student, a member of the school’s honor board, with an officer pinning him to the sidewalk spread across the Internet and led to campus protests and vigils, arousing racial tensions at the Southern school.

University of Virginia student Martese Johnson and his lawyer, Daniel Watkins, speak to the media after Johnson's hearing at the Charlottesville District Court on March 26, 2015. (Zach Gibson/Getty Images)

“It hurt like hell to be here while it was all happening,” said Jalen Ross, a 2015 graduate who served as president of the student council. “But the benefit of hindsight is, the future students here are going to be better off for what we went through there. . . . I personally have learned more in the past six or eight months than in the past four years combined.”

Students, faculty, parents and administrators acknowledge that the tumultuous year was unlike almost any other in the school’s long history. The university founded by Thomas Jefferson has a sterling reputation as a serene “academical village” of higher learning — and it is one of the most highly desired public schools in the country — but U-Va. took repeated hits as it was characterized as a campus unhinged by roaming sexual predators, fraternities gone wild and brutish police tactics.

“Many good things have happened here, and unfortunately those got eclipsed by the bad news,” U-Va. President Teresa Sullivan said in an interview last week, noting, as one example, that the university had a record number of students this year earn Fulbright scholarships. “I just regret that news got pushed to the back burners. They deserve to get recognized for it.”

Vendarryl Jenkins Sr., a U-Va. parent whose son helped lead demonstrations on campus after Martese Johnson’s arrest by ABC police, said that he believes the administration handled the events well but overall, the university’s image has been harmed. Jenkins said that people react differently now when he tells them about having a child at U-Va.

“Now even some people are saying, ‘I’m not sending my kid there,’ ” Jenkins said.

In almost every speech during graduation exercises this month, administrators, students, and even Gov. Terry McAuliffe (D) mentioned the series of dramatic events — almost all beyond the university’s control, but moments, still, that defined the academic year.

“I know this year that you have experienced what it’s like to be at the center of the public eye,” McAuliffe told this year’s 6,500 graduates. “I can tell you as someone who has been in national politics for over 40 years, I understand that feeling, and I know that sometimes it is difficult. . . . You showed the world that this university can triumph over any obstacle.”

Columbia Journalism School Academic Dean Sheila Coronel, left, and Columbia Journalism School Dean Steve Coll discuss report conducted at the school over a Rolling Stone magazine expose. (Craig Ruttle/AP)

Rector George Keith Martin, who heads the Board of Visitors, told students and faculty at graduation that “as a community, this university dealt with heartbreak and reflected upon its imperfections with honesty and resolve.”

The Rolling Stone article, which alleged that campus fraternity culture was part of rampant sexual abuse at U-Va., led to calls for stringent control, or even the closing, of campus Greek houses amid rousing protests against the university’s administration. Some fraternity members said they were embarrassed to wear their letters for fear of ridicule, and a campus dean has said her entire life’s work was called into question. The pressure eased when the article was discredited and later retracted.

Brian Head, a 2015 graduate and Phi Gamma Delta fraternity member who served as president of the all-male sexual-assault-prevention group One in Four, said the episode allowed him to more closely examine the school and Greek life.

“I have been telling people that you can simultaneously love something and think that there is something wrong with it,” Head said. “As a U-Va. student and Greek man, it would be cowardice to just leave something instead of trying to change it.”

As part of the graduation events, comedian Ed Helms — of “The Hangover” and “The Office” fame — cast the Rolling Stone ordeal in a humorous light.

Helms joked, to tremendous applause: “It has been said that a rolling stone gathers no moss. I would add that sometimes a rolling stone also gathers no verifiable facts or even the tiniest morsels of journalistic integrity.”

But Annie Forest, a 2015 graduate and sexual assault survivor, said the article rocked the campus and left a lasting impression that may not be negative in the long run.

“It has exposed a rape culture that really is rampant on grounds not only at U-Va. but also at college campuses across the nation,” Forest said. “There are so many people who have it on the forefront of their minds now.”

The university has taken those concerns to heart and is implementing changes, including enhanced safety features on campus such as improved lighting and new programs to support sexual assault survivors. McAuliffe also formed a review panel to improve ABC law enforcement.

Residual effects to the university itself are still not clear.

The number of applications to U-Va. had grown significantly and continuously for a decade, peaking at 31,021 last year. That total was up 7 percent over one year and 40 percent over four years. But this year, the growth stopped, with the application total for the incoming fall class virtually unchanged, dropping less than 1 percent.

“After years and years of growth, there was a very, very small decline this year in applications,” said U-Va.’s admissions dean, Greg W. Roberts. “It’s quite possible that we simply experienced a natural leveling off this year, like you find in many markets.”

Other elite U.S. public schools — including the University of California at Berkeley, UCLA, the University of Michigan and the University of North Carolina at Chapel Hill — saw all-time record numbers of applications this year, as did Virginia’s William and Mary (up 2.7 percent) and Virginia Tech (up 7.6 percent). Perennial top-ranked schools Harvard, Princeton and Stanford all saw increases that set all-time highs this year, although a small number of exclusive schools, including Cornell, Yale and Duke, saw their numbers drop slightly.

Sullivan said that donations to U-Va. are up and that alumni remain enthusiastic about the university’s future.

“Students ask me why all these things are happening at U-Va., and what I say is that U-Va. matters,” Sullivan said, noting that the media chose not to cover other student abductions from colleges this past year, even one at a school just 50 miles from Charlottesville. “Rolling Stone could have done a story about sexual assault at any school in the country. Why did they do us? Because U-Va. matters. U-Va. is a significant institution in this country, and when things happen here, their significance is magnified, especially when it’s bad things that happen here.”

Eva Alvarado, who will be a U-Va. sophomore in the fall, said she recognizes that hers was not a typical first year of college.

“U-Va. attempts to create this sense of a very nice undergraduate paradise,” Alvarado said. “I think the students really wanted to preserve that second semester, but it’s hard when the outside world keeps coming in and taking that way from you. . . . We kept getting hit with different tragedies and problematic things. People were able to manage, but at the same time, when the year ended, there was definitely a sigh of relief.”

Rennie Mapp, an English professor who is Alvarado’s mother, said that U-Va., because of, and not in spite of, its reputation as an elite public school, was well prepared for the harsh criticism this year.

“These things were horrible, but if they had to happen, U-Va. was the right institution for them to happen at,” Mapp said. “We’re an easy target for resentment. . . . Everyone loves to hate U-Va.”

Jenkins, whose son attends U-Va., said that he’s optimistic that the school will move forward and that the memory of the difficulties of the past will fade.

“ I don’t know how much of a stain it would be,” Jenkins said. “Two years from now, will anybody remember?”

Nick Anderson contributed to this report.