The pastor, the Rev. Clementa Pinckney, would normally have stayed in Columbia, South Carolina’s capital, for his job as a state senator. But he had returned to his congregation in Charleston for an important meeting with the presiding elder of the district.

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CHARLESTON, S.C. — Wednesday was a busy day at Emanuel African Methodist Episcopal Church.

The pastor, the Rev. Clementa Pinckney, a rangy man with a deep voice, would normally have stayed in Columbia, the capital, for his job as a state senator. But he had returned to his congregation in Charleston for an important meeting with the presiding elder of the district.

There was the matter of the church elevator, long under construction. The budget needed review. And three congregants were officially received as new preachers.

The meeting in the church basement ended around 8 p.m., and the crowd of about 50 dwindled to 12 of the congregation’s most devout members, who would remain for the Wednesday night Bible study.

That was when a visitor, a young white man, came to the door, asking for the minister. It was unusual for a stranger, much less a white one, to come to the Wednesday night session, but Bible study was open to all, and Pinckney welcomed him. They sat together around a table, prayed, sang and then opened to the Gospel of Mark, 4:16-20, which likens the word of God to a seed that must fall on good soil to bear fruit.

About 9, gunfire and terrified cries shattered the calm. In the pastor’s office, Pinckney’s wife, who had been waiting with their younger daughter, turned off the lights, locked the door, hugged her child and called 911.

When the shooting was over, nine congregants were dead, including Pinckney and two of the newly ordained ministers, each shot multiple times with a .45-caliber handgun. The white stranger — identified by police as Dylann Roof, 21, a high-school dropout and itinerant landscaper — has been charged with nine counts of murder.

“You are raping our women and taking over our country,” Roof said to the victims, all black, before killing them, witnesses told the police.

In a matter of unforeseen moments, the future of the Emanuel AME Church and its 350 active members were changed forever. Church leaders were lost, along with worshippers young and middle-aged. Children were left motherless. A girls’ track team lost its coach; a university its admissions coordinator.

Residents of all races in Charleston, a city that places such value on its houses of worship that it calls itself the Holy City, recoiled in horror as one of its most storied buildings was desecrated by intolerant rage and transformed, if briefly, into a charnel house. A parishioner, Elizabeth Alston, said Saturday that the church would be reopen for Sunday for services.

The massacre has reverberated far beyond Charleston, prompting new debate about race a nation already dealing with outrage over police conduct toward African Americans.

The “itinerant pastor”

By many accounts, Pinckney, 41, was a man with serious commitments in Columbia, at home and at church. But when he was talking to you, said Sylvia Johnson, 56, his cousin, he locked eyes and listened carefully. He was especially tender toward Johnson’s blind daughter. His voice could move into a more stern, but still loving, register when he addressed his own daughters, Eliana and Malana.

With his flock in Charleston; his home in Jasper County, at South Carolina’s southernmost tip; and his job up in Columbia, Pinckney had to work to spread his love around. He called himself the “itinerant pastor.”

Elected to the South Carolina House at age 23, Pinckney had always had a sense of purpose. In the seventh grade, he endured the taunts of his classmates in Jasper County, a depressed angle of what Senate colleagues called the Forgotten Triangle, for wearing a starched shirt and tie and for carrying a briefcase instead of a backpack. He thought you needed to dress like someone to be someone.

He quickly became someone. He had begun preaching in his teens. An ambitious intern unafraid to ask his bosses to look at the county budget, he became a page in the state House and ultimately a member, and then a senator.

Wednesday morning in Columbia, he was sitting in his office with his back to a view of the Capitol dome, preparing for a Senate Finance Committee meeting. He later took the elevator down to Room 105 for another meeting on the budget, where he pushed, in the face of an overwhelming Republican majority, for funding to fix the roads in his deprived district.

Pinckney left another meeting early, saying he had an appointment at his church in Charleston.

Wild talk

Roof had dropped out of many of his oldest friends’ lives some years ago. But about a month ago he resurfaced, telling them he had gone to a public library in Columbia to open a Facebook account for the purpose of finding them.

Roof had had a rocky academic career, attending ninth grade twice at two schools. Friends recalled him as being painfully shy.

But recently, he had been showing a new side, his friends said: spouting racist comments, praising segregation and talking wildly of setting off a race war. He had also been arrested twice: once in February for possession of Suboxone, a drug used to treat opiate addiction, and a second time in April for trespassing at a mall where he had been banned for a year after the first arrest.

On the same day Roof opened the Facebook account, he went to the family trailer home of one of those old friends, Joseph Meek. Soon, he was sleeping there as often as four times a week, sometimes on the floor.

Roof told his friends he had quit a landscaping job because he could not bear working in the heat. He spent his days loafing, watching TV and sometimes calling his father, pretending to be at work, said Jacob Meek, 15, Joseph’s brother. “He said his parents kept pressuring him to get a job,” Jacob said.

He was fond of vodka and usually kept a stash. He went to the Platinum Plus strip club recently, Jacob said, and threw dollar bills at the dancers.

Amid his aimlessness, Joseph Meek, 20, and other friends said, Roof talked wildly about hurting African Americans, about doing something “crazy.” Joseph Meek, worried, hid the .45-caliber handgun Roof had bought with money his parents gave him for his 21st birthday. But Joseph Meek eventually returned the gun because he was on probation and feared having it around.

At one point, Jacob said, Roof’s parents took the gun away. “I guess he stole it back,” he said.

The massacre

The Bible study group was wrapping up when the first gunshots sounded.

Felicia Sanders, who was in the room, heard the gunfire before seeing who the gunman was, she later told a friend, Johnson.

Sanders dropped to the ground with her 5-year-old granddaughter. She saw blood everywhere. The white visitor was doing the shooting, and he reloaded his weapon five times.

Sanders’ son, Tywanza, tried unsuccessfully to shield his aunt, Susie Jackson, 87, from the gunman and talk sense to him.

“That’s when the gunman said: ‘Y’all are raping our women and taking over the country. This must be done,’ ” Johnson recalled Sanders telling her.

Then he shot Tywanza Sanders. At one point, he asked a woman if she had been shot yet. When she said no, he said: “Good. Someone has to live to tell the story, because I’m going to kill myself, too.” Felicia Sanders survived only by playing dead, Johnson said.

Soon, the gunman was gone, fleeing in his Hyundai Elantra and leaving nine churchgoers dead or dying behind.

For another victim, the Rev. Daniel Lee Simmons Sr., 74, the church had been a second home. He was a war veteran who rarely missed Wednesday Bible study, which he usually led.

On this Wednesday, as the business meeting broke up and congregants began gathering for the study group, Simmons urged Leon Alston, a steward at the church, to join. He did that almost every week. And almost every week, Alston declined.

“You need to start coming to Bible study a lot more,” Simmons said. “Maybe the next meeting,” Alston replied.