“We cannot make sense of what has happened, but we can come together,” said the Rev. George Felder Jr., pastor of the New Hope AME Church.

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CHARLESTON, S.C. — The mass slaying of nine people who gathered Wednesday night for Bible study at a historic black church has shaken a city whose history from slavery to the Civil War to the present is inseparable from the nation’s anguished struggle with race.

Fourteen hours after the massacre at Emanuel African Methodist Episcopal Church — in which the Rev. Clementa Pinckney, the pastor and a prominent state senator, was among the dead — police arrested Dylann Roof, 21, a white man with an unsettled personal life and a recent history of anti-black views.

Roof was charged Friday with nine counts of murder and a weapon-possession charge in connection with the attack, police said.

The killings, with victims ranging in age from 26 to 87, left people stunned and grieving. Roof sat with church members for an hour and then started venting against African Americans and opened fire on the group.

At the Morris Brown African Methodist Episcopal Church in Charleston, blacks, whites, Christians and Jews gathered to proclaim that a racist gunman would not divide a community already tested by the fatal police shooting in April of an unarmed African American, Walter Scott.

“We cannot make sense of what has happened, but we can come together,” said the Rev. George Felder Jr., pastor of the New Hope AME Church.

Gov. Nikki Haley fought back tears at a news conference. “We woke up today, and the heart and soul of South Carolina was broken,” she said. “Parents are having to explain to their kids how they can go to church and feel safe, and that is not something we ever thought we’d deal with.”

President Obama, once again having to confront the nation’s divisions, saw systemic issues of guns, violence and race in the tragedy in Charleston. “We don’t have all the facts, but we do know that, once again, innocent people were killed, in part, because someone who wanted to inflict harm had no trouble getting their hands on a gun,” he said at the White House.

Even amid calls for calm and compassion, at least three bomb threats were made Thursday that forced the evacuation of buildings around Charleston, including churches where prayer vigils were being held for the shooting victims. And while the racially mixed crowds inside those churches linked arms and appealed for harmony, the tone among black people gathered on the city’s streets was not so conciliatory.

Jareem Brady, 42, said the shooting was only an extension of what black people face daily. “We’re not worth the air; they don’t want us to breathe,” he said of Charleston’s white citizens. Of those killed, the most prominent was the church’s leader, Pinckney, 41.

“He was very gentle,” Mayor Joseph Riley said. “He spoke thoughtfully and deliberately. He had a big job, because that’s a big, important church.”

Pinckney was holding a Bible study session with a small group Wednesday when, surveillance video shows, the suspect arrived after 8 p.m. He sat down with the others for a while and listened, and then began to disagree with others as they spoke about Scripture, said Kristen Washington, who heard the story from relatives who were in the meeting and survived.

Witnesses said the gunman asked for the pastor when he entered the church, and sat next to Pinckney during the Bible study.

They said that almost an hour after he arrived, the gunman suddenly stood and pulled a gun, and Washington’s cousin, Tywanza Sanders, 26, known as the peacemaker of the family, tried to calmly talk the man out of violence.

“You don’t have to do this,” he told the gunman, Washington recounted.

The gunman replied, “Yes. You are raping our women and taking over the country.”

In an interview with NBC News, Sylvia Johnson, a cousin of Pinckney’s who also spoke with a survivor, gave nearly the same account of what the gunman said: “I have to do it. You rape our women and you’re taking over our country. And you have to go.”

The gunman took aim at the oldest person present, Susie Jackson, 87, Sanders’ aunt, Washington said. Sanders told the man to point the gun at him, instead, she said, but the man said, “It doesn’t matter. I’m going to shoot all of you.”

Sanders dived in front of his aunt, and the first shot struck him, Washington said, and then the gunman began shooting others. She said Sanders’ mother, Felicia, and his niece lay motionless on the floor, playing dead, and were not shot.

The gunman looked at one woman and told her “that she was going to live so that she can tell the story of what happened,” said Councilman William Dudley Gregorie, a friend of the female survivor and a trustee in the Emanuel church.

The gunman left six women and three men dead or dying, including a library manager, a former county administrator, a speech therapist who also worked for the church, and two ministers.

Greg Mullen, the Charleston police chief, called it a hate crime, and Attorney General Loretta Lynch said the Justice Department was investigating that possibility.

The massacre had a particular resonance in a city that offers perhaps the sharpest contrast in the South between its cosmopolitan, tolerant present, and its antebellum past, when Charleston was the capital of the slave trade. It was in Charleston that a state convention adopted the “ordinance of secession” in December 1860, putting South Carolina on a path to become the first state to leave the Union, and the first shots of the Civil War were fired four months later, on Fort Sumter.

But if the church shooting prompted comparisons to the 1963 bombing of a black church in Birmingham, Ala., by white supremacists that killed four girls, it also illustrated how much has changed. The earlier bombing took place as black people struggled to secure basic civil rights, at a time they were barred from voting, much less holding office. Alabama’s governor at the time, George Wallace, was the public face of white resistance, and no one was charged with the crime until 12 years later.

The shooting Thursday took the life of a black state legislator, an arrest was made in hours, and some of the most emotional expressions of mourning came from Haley, whose parents are from India, and who is not only the state’s first female governor but also the first who is not of European descent.

Local, state and federal law enforcement started a manhunt for the suspect, distributing pictures of him entering the church, and asking people to be on the lookout for him or his 2000 Hyundai sedan. By midmorning Thursday, he had been identified as Roof.

A short time later, someone reported possibly sighting him some 200 miles to the northwest, in Shelby, N.C. Jeffrey Ledford, the Shelby police chief, said officers there pulled Roof over, arrested him at 10:49 a.m. and found a gun in the car.

Roof waived extradition and was flown to South Carolina late Thursday and, amid extraordinary security, walked into the jail in Charleston County.

As Roof, who was wearing a striped jail jumpsuit, entered the jail through a secured entrance, a police dog barked and cameras clicked.

Nearby, a 15-year-old boy from North Charleston held a handwritten sign: “Your evil doing did not break our community! You made us stronger!”

In Charleston, nicknamed “Holy City” for its large number of churches, many houses of worship held prayer vigils, for the dead and for survivors, that drew people from different communities, races and denominations together.

Hundreds of people packed the pews of the white-columned Second Presbyterian Church on Thursday evening in a vigil to remember the victims of the shooting. Pastors read Scriptures, the congregation sang and the Rev. Sidney Davis delivered a rousing sermon, screeching at times. After reading a passage from the Bible, he said: “Last night, Satan came again. Satan came to say white and black cannot raise God.”

Later, he told the racially mixed congregation that the bullets were not simply penetrating the people who died in the church. “It was all of us dying last night,” he said.