CHARLESTON, S.C. » Wednesday was a busy day at the Emanuel AME Church.

The pastor, the Rev. Clementa C. Pinckney, a tall, 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 here 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. One by one, they stepped before the group to receive a certificate and applause.

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 the 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 green 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.

At about 9, gunfire and terrified cries shattered the evening calm. In the pastor’s office, Pinckney’s wife, who had been waiting patiently with their younger daughter, turned off the lights, locked the door, hugged her child close 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 stranger – identified by the police as Dylann Storm Roof, a 21-year-old high school dropout and sometime 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 of them black, before killing them, witnesses told the police.

In a matter of unforeseen moments, the future of the Emanuel African Methodist Episcopal Church and its 350 active members would be 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. And 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 open for Sunday school and services the next morning.

The massacre has reverberated far beyond Charleston, prompting fierce new debate about race relations in a nation already grappling with protests over police conduct toward African-Americans.

President Barack Obama spoke Thursday of "the heartache and the sadness and the anger" the shootings had elicited. The Justice Department opened a hate crimes investigation. And in Columbia, where Pinckney’s empty desk in the Legislature has been adorned with a black cloak and flowers, lawmakers were once again grappling with the question of whether the Confederate battle flag should fly on the grounds of the State House.

But the deepest pain was at the handsome, whitewashed old church in Charleston, now cordoned off with yellow police tape, and along the intimate tendrils that connected its members to friends and family.

The ‘Itinerant Pastor’

Pinckney, 41, was a busy man. But when he was talking to you, said Sylvia Johnson, 56, his cousin, he locked eyes intently 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." He had recently run an old car dry and bought a new SUV.

On Wednesday morning in Columbia, he was dressed, sharp as always, in a dark suit and sitting in his office with his back to a view of the Capitol dome, preparing for a Senate Finance Committee meeting. He was surrounded by framed newspaper spreads ("Leading From the Pulpit"; "Under 30 and on the Move"), recognitions of achievement (Prestigious Jaguar Award, Jasper County High School, 1991), volumes of Bibles and a poster of the Rev. Dr. Martin Luther King Jr. Next to a refrigerator bearing a "Yes! I Love My Library" sticker given to him by his wife, Jennifer, a librarian, he had rolled up a bunch of posters depicting African-American life in the South Carolina Lowcountry. He planned to take them home that day.

But first, another day of work. Pinckney, elected to the South Carolina House at age 23, had always had a sense of purpose. In seventh grade, the skinny student 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 sermons 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 of Representatives and ultimately a member, and then a senator.

Now, 12 hours before he was killed, he took the elevator down to Room 105 for another meeting on the budget, where he again pushed, in the face of an overwhelming Republican majority, for funding to fix the roads in his deprived district.

Later, he rode an escalator up from the parking lot to the Statehouse. He walked between marble columns and up a mahogany staircase lined with paintings of the Revolutionary War, and greeted friends in a lobby presided over by a statue of John C. Calhoun. In the stately Senate chamber, he greeted more friends on the floor and took a seat next to Sen. Vincent A. Sheheen, a fellow Democrat.

It was here that Pinckney made his mark that day.

When Sheheen nervously prepared to voice his opposition to a compromise reached with Republicans on their effort to introduce a voter ID bill, he was shocked to hear Pinckney’s booming voice call out, "No."

"When I heard him voting no, loud and clear, I knew I was doing the right thing," Sheheen said. They were the only two to vote in dissent.

Pinckney left another meeting early, telling colleagues that he had an appointment at his church back in Charleston.

A Wild-Talking Suspect

It is not clear where or how Roof spent his Wednesday morning. Even to his friends, there were unexplained gaps.

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

As a younger man, Roof had a rocky academic career, attending ninth grade twice at two schools, but possibly not making it any further. 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 day Roof opened the Facebook account, he went to the family trailer home of one of those old friends, Joseph C. Meek Jr., in Red Bank, in suburban Lexington County. Soon, he was sleeping there as often as four times a week, sometimes on the floor. He had a cellphone, his friends said, but no phone service. To communicate, he used Wi-Fi to send messages via Facebook, or he showed up in person.

Roof told his friends that he had quit a landscaping job because he could not bear working in the Southern heat. He spent his days loafing around the place, watching television 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 around. He went to the Platinum Plus strip club recently, Jacob said, and threw dollar bills at the dancers.

But amid his aimlessness, Joseph Meek, 20, and other friends said, Roof talked wildly about hurting African-Americans, about doing something "crazy." Meek, worried, hid the .45-caliber handgun Roof had bought with money his parents gave him for his 21st birthday. But Joseph 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, too. "I guess he stole it back," he said.

On Tuesday, Roof agreed to drive his friends to Lake Murray. He said he was pressed for time, because he wanted to make the 2 p.m. showing of "Jurassic World" at the AMC theater. He showed Jacob the movie coupon he had in his car. He carried a $7 pack of American Spirit cigarettes and wore a long-sleeve gray shirt with a Border Patrol logo on one side and a sleeve stained with battery acid. He wore that shirt all the time, Jacob said.

He was not acting jumpy or out of the ordinary, his friends recalled. He was acting like a guy who had a movie to catch.

"He did seem like he was in a rush," Jacob said. "He was like, ‘Come on, let’s go.’"

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, Pinckney’s cousin.

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 Sanders, tried unsuccessfully to shield his aunt, Susie Jackson, 87, and talk sense to the gunman.

"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. 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." 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.

Tywanza Sanders, 26, who recently graduated from college, had been cutting hair and hoping to get a better job. In his final Instagram post, he quoted Jackie Robinson: "A life is not important except in the impact it has on other lives."

Then there was Ethel Lance, 70, a mother of five. She was a sexton at the church and had worked as a custodian at Charleston’s Gaillard Center for 35 years until her retirement.

A fan of gospel music, Lance was in charge of the backstage area there, including the dressing rooms, a job she loved because of the procession of performers who filed in and out. "She got a kick of that," said Cam Patterson, a former co-worker.

Cynthia Graham Hurd, a Charleston County librarian, had spent much of her last day in meetings at work before going to church. One of the presentations had been about civility, said her colleague Cynthia Bledsoe.

"She was so vocal and excited and happy about what was going on," said Darlene P. Jackson, manager of the main county library. "She was happy about how we were going to set policies to help people."

In a 2003 feature in the local newspaper, The Post and Courier, Hurd said marrying her husband, Steve, had been one of the greatest joys of her life. Steve Hurd, a merchant seaman was making his way back from Saudi Arabia, when Cynthia Graham Hurd was killed. Sunday would have been her 55th birthday, and Steve Hurd had arranged a surprise, a delivery of pizza and cake, another co-worker of Cynthia Graham Hurd’s said.

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.

A Suspicion Confirmed

Up in Red Bank on Wednesday night, the Meek brothers heard the news about a mass killing in Charleston. Roof immediately came to mind, Jacob Meek said. They waited until they saw the surveillance photos to be sure.

There was a familiar figure, wearing a recognizable Border Patrol shirt stained in black.

They called the FBI. The authorities quickly arrived at the trailer and went through Roof’s things, taking his vodka and his two shirts, one that said "Myrtle Beach" and another with a picture of the Hulk, Joseph Meek said.

The Charleston police say Roof’s father also called the authorities that night when he saw photographs of the suspect. He told them his son owned a .45-caliber handgun. Law enforcement officials had found .45-caliber casings at the scene.

At home in Summerville, half an hour northwest of Charleston, Johnson received a call Wednesday evening from Pinckney’s wife, who told her that there had been a shooting.

"I said, ‘Where’s Clementa?’" Johnson recalled.

Her cousin’s wife, distraught, replied: "I don’t know. I don’t know."

© 2015 The New York Times Company