People gather to protest the Confederate flag which flies in front of the South Carolina Statehouse in Columbia, S.C. (Andrew Renneisen /For The Washington Post)

— Nestled in a sea of flowers at the solemn memorial outside the Emanuel African Methodist Episcopal Church in downtown Charleston is a handwritten message to South Carolina Gov. Nikki Haley: “Take the flag down. It hurts us.”

The continued presence of a Confederate flag on the grounds of the South Carolina state Capitol has become a galvanizing cause after nine people were killed inside a black church on Wednesday.

“There is no stronger symbol than the flag flying,” said Dot Scott, president of the Charleston Branch of the NAACP. “If there has ever been a time that it was seriously considered, now is the time.”

The man accused in the killing, 21-year-old Dylann Roof, was apprehended on Thursday in a vehicle bearing a “Confederate States of America” license plate. On Saturday, law enforcement authorities said he left a lengthy manifesto on his Web site detailing how he became enamored with the ideology of white supremacy.

The flag has become a symbol of cultural identity, primarily for white southerners, while African American civil rights groups say it represents the South’s willingness to fight a war in order to preserve slavery.

A Confederate flag is still flying on the grounds of South Carolina's state capitol, even after a white gunman was accused of killing nine black churchgoers at an AME church in Charleston, S.C. Here's a closer look at why the flag isn't at half-staff or even off the grounds completely. (Jorge Ribas/The Washington Post)

The Palmetto State has for decades resisted calls to remove the flag. It first was hoisted to the top of the state Capitol in 1962, in the midst of the Civil Rights Movement, just more than a century after the start of the Civil War.

After more than 46,000 people marched to the state seat in Columbia in January 2000 to protest the flag, the legislature reached a compromise that brought it from the dome of the State House to a spot on the grounds near a Confederate war memorial.

Today, the issue is still sharply divisive along racial lines. A 2014 poll found that 73 percent of whites in South Carolina support the flag, while 61 percent of blacks say it should be removed.

State Representative Norman “Doug” Brannon said in an interview Saturday that he intends to introduce legislation to remove the flag from the grounds in honor of his friend, colleague and Emanuel pastor the Rev. Clementa Pinckney, a state senator who was killed in the Wednesday attack.

“I’m going to do it in honor of my dear friend because he was killed because he was a black man,” said Brannon, who is a Republican. “It’s something that should have been done years ago.”

Brannon said that his colleagues have been moved by Pinckney’s death, and in communications recently with fellow Republicans, “some of them are offering support for my intended bill.”

Former Republican presidential candidate Mitt Romney reiterated his call for the flag’s removal on Saturday, citing the need to honor the victims of the church attack.

Evolution of a controversial flag

“Take down the #ConfederateFlag at the SC Capitol,” Romney wrote. “To many, it is a symbol of racial hatred. Remove it now to honor #Charleston victims.”

Haley ordered the U.S. flag and the state’s palmetto flag to be flown at half mast, but said that only the legislature had the power to do the same for the Confederate flag.

In the past, some South Carolina politicians have been loath to speak out against it. In 2014, Haley dismissed the flag debate as an issue that hasn’t come up with business leaders during her term.

After the shooting, however, Haley indicated that lawmakers might take up the issue anew. “I think that conversation will probably come back up again,” she told CBS News on Friday. “We’ll see where it goes.”

Since the civil rights era, the debate about what to do with the Confederate flag has flared on and off in states including Georgia, Mississippi and Florida.

Mississippi is now the only state that still has a Confederate flag as part of its state banner. Former Mississippi governor and former Republican National Committee chairman Haley Barbour said that connecting the shooting to the Confederate flag is “beyond stretching.”

“The flag didn’t have a thing in the world to do with what happened,” Barbour said. “It is part of history, just like George Washington, Thomas Jefferson and Andrew Jackson, who were all slave owners. Are we now going to change the name of the Washington Monument, too?”

As governor of Florida, Republican presidential candidate Jeb Bush oversaw the removal of the Confederate flag from the state capitol in Tallahassee. He noted in a statement on Saturday that he is confident that eventually South Carolina will “do the right thing.”

“In Florida we acted, moving the flag from the state grounds to a museum where it belonged,” Bush said. “Following a period of mourning, there will rightly be a discussion among leaders in the state about how South Carolina should move forward, and I’m confident they will do the right thing.”

But for other Republican presidential hopefuls, the flag is a thorny issue — especially in a key early primary state such as South Carolina.

Sen. Ted Cruz (R-Tex.) said Saturday that decisions about the flag are for South Carolinians to decide, but that he understands “both sides” of the debate.

“Both those who see a history of racial oppression and a history of slavery, which is the original sin of our nation, and we fought a bloody civil war to expunge that sin,” he said. “I also understand those who want to remember the sacrifices of their ancestors and the traditions of their states, not the racial oppression, but the historical traditions and I think often this issue is used as a wedge to try to divide people.”

Sen. Marco Rubio (R-Fla.) said Saturday that it is up to the people of South Carolina, not “outsiders,” to decide whether to remove the Confederate flag from the grounds, declining to echo Mitt Romney’s call to remove it.

“This is an issue that they should debate and work through and not have a bunch of outsiders going in and telling them what to do,” he told reporters.

Businesswoman Carly Fiorina, who is also running for president, didn’t mention the shooting during a 20-minute speech Saturday at a Faith and Freedom Coalition conference in Washington.

But asked about Romney’s comments after her speech, she told reporters, “Personally, I agree with him, but I believe it’s up to the people of South Carolina.”

Robert Costa, Ed O’Keefe, and Vanessa Williams in Washington, Katie Zezima in Johnston, Iowa, and Jenna Johnson in Philadelphia contributed to this report.