In a Oct. 16, 2015 photo, the Mississippi state flag and U.S. flag fly in the Circle on campus at the University of Mississippi in Oxford, Miss.  (Bruce Newman/Oxford Eagle via AP)

The Mississippi flag was taken down at the state’s public university Monday morning, after student leaders, faculty and staff called for its removal because of its prominent Confederate emblem.

It was a dramatic change for a university long proud of its southern traditions and ties to the Confederacy, a school that closed down entirely during the Civil War when nearly all of its students enlisted, and one that was at the center of a seminal moment in the civil rights movement.

It’s part of a debate playing out across the South over the Confederate symbols that for some represent Southern heritage but for others are just shorthand for slave ownership and racism.

“As Mississippi’s flagship university, we have a deep love and respect for our state,” University of Mississippi’s interim chancellor Morris Stocks said in a statement Monday. “Because the flag remains Mississippi’s official banner, this was a hard decision.

“I understand the flag represents tradition and honor to some. But to others, the flag means that some members of the Ole Miss family are not welcomed or valued. That is why the university faculty, staff and leadership have united behind this student-led initiative.”

Ole Miss police officers lowered it as the campus opened, and folded it for storage in the archives along with the written resolutions from campus groups.

Last week, the student government called on university leaders to remove the flag after a three-hour debate. Within days, the Faculty Senate, the Graduate Student Council and the Staff Council had passed similar resolutions.

[Student leaders at Ole Miss vote to take down the flag]

Student legislators voted to reject the state flag which is a symbol used by the Confederate, pro-slavery South during the Civil War. They passed a resolution asking the university to remove the flag from campus on Tuesday, Oct. 20. (Reuters)

The Mississippi Division of the Sons of Confederate Veterans did not immediately respond to a request for comment Monday.

Cornell William Brooks, president and chief executive officer of the NAACP, congratulated the students for their courage and success. “It is with confident voices and persistent action that the students, particularly the University of Mississippi student chapter of the NAACP, led the call for the flag to come down,” he said in a statement. “The lowering of the flag shows that the voices of today’s youth and leaders matter more than traditions and notions of heritage at Mississippi’s public universities.”

It hasn’t been easy to change Ole Miss; its past is deeply embedded.

In 1861, nearly all of its students left the university to fight for the Confederacy, many of them in a celebrated unit known as the University Greys. “They cast such a long shadow on this university,” said David Sansing, professor emeritus of history at Ole Miss.

The chancellor at the time pleaded with the governor not to allow these bright young students to enlist; so did Jefferson Davis. He wrote, “‘Sending these boys off to war it is like grinding the seed corn of the republic,’ “Sansing said. “We lost a generation of young  men in that war.”

During the war the campus had a hospital for wounded soldiers, and a cemetery.

None of the University Greys came back to the university. Almost all died.

When the school reopened in 1865, most of the students were Confederate veterans. Very few would have passed an entrance examination, Sansing said; they hadn’t been to preparatory schools.

In the generation after the war, as veterans aged and died, monuments were erected to honor them. One of the most prominent spots on campus has a large monument to a Confederate soldier, placed there in 1906. The band played “Dixie,” and cheerleaders and fans waved Confederate flags at football games. Even its nickname is believed by many to come from the words an enslaved person would use for the mistress of the plantation.

And then a young black man decided to force the university to open its doors.

In 1962, the governor and state legislature fought to keep James Meredith from integrating Ole Miss despite a Supreme Court ruling upholding his right to attend.

A riot broke out on campus, in the area around the Confederate monument; two people were shot and killed. The president ordered in state and federal troops.

“It was a crucial event in the civil rights movement,” Sansing said. “It was evidence that the federal government would use the Army” — thousands of troops — “to enforce the admission of one kid.”

“It wasn’t over,” he said of the fight against integrated schools. “But the end result was determined here at Oxford.”

[Former Ole Miss student sentenced for putting noose around statue of the school’s first black student]

Stansing saw the first change in 1973, when he invited Meredith back to campus to speak to his history class. There were still fewer than a handful of black students enrolled. When Sansing introduced Meredith, students rose and applauded him. After Meredith spoke, they respectfully asked him questions. One student said, “‘What do you think is the difference between the students here today who gave you a standing ovation and those 10 years ago who threw rocks at you, hurled insults?'”

Sansing recalled that Meredith responded, “‘There is no difference. If you had been here 10 years ago you would have acted like they did. If they were here today they would act like you did.

“‘Times have changed.'”

In recent years, the university has been distancing itself from the Confederate symbols that had been so central to the school’s culture.

The first black cheerleader, in the 1980s, refused to wave the Confederate flag at games. Ole Miss renamed its “Confederate Drive,” banned sticks from the stadium in a further effort to eliminate the rebel flag, and and changed its mascot from “Colonel Reb,” who evoked a plantation owner or Confederate soldier, into an animal, “Rebel Black Bear.”

This year, the debate over the flag and its message intensified across the south after a shooting at a Charleston church killed nine people in an apparent racist hate crime; the suspect had filmed himself with a Confederate flag.

[Families grieve nine victims in Charleston church shooting]

Some cities and counties in Mississippi, including Oxford, stopped flying the state flag.

At a rally in support of the flag’s removal earlier this month, Ole Miss students were confronted by people angry that the state’s history might be whitewashed, and by KKK members.

“This place, its history is such a burden to it,” Sansing said. “But it is also a place where things change.”