The men of Omega Psi Phi fraternity lead a prayer outside the Emanuel AME Church. (Stephen B. Morton/AP)

— Church is a sanctuary.

“Is something missing from your life?” Emanuel African Methodist Episcopal Church asked on its Web site, inviting one and all to its weekly Bible study. “Are you doing all you can to have a closer relationship with God? . . . Join us on Wednesdays at 6:00 p.m. in the lower level. . . .

Thirteen people accepted the invitation to the whitewashed landmark in historic Charleston on Wednesday evening. Nine of them are dead. One, the lone white man in a room full of descendants of slaves, killed them. He left one adult to tell the story. Two others — a woman and her granddaughter — escaped the murderer’s savage attentions.

The evening began with energetic prayers of devotion and a silent plot to deny humanity.

The pastor of the oldest AME congregation in the South, the Rev. Clementa Pinckney, who was also a state senator, had arrived late, having left the Capitol complex in Columbia at 5 p.m. He had a two-hour drive back to his church to lead the Bible study.

Dylann Storm Roof — 21, unemployed, using hard drugs, a white kid who made unsettling racist remarks to his friends — woke up Tuesday morning in his car, parked outside his friend Joey Meek’s house in Lexington, a suburb of Columbia, about 120 miles from Charleston.

“He told me the black people was taking over the country and he wanted it to be segregation,” Meek recalled. “He was drunk one night, and he was just talking about him wanting to hurt a whole bunch of people. I didn’t know when to take him serious. Whenever he’d say he wanted to do something crazy, I just blew it off and didn’t really pay attention to him because he was intoxicated.”

Church is no sanctuary.

Throughout the bloody history of slavery, Jim Crow and white supremacism in America, the black church has been a consistent target, singled out expressly because it served as a pulpit for those who called for justice, expressly because it organized the poor and the powerless to demand change, expressly because it was the proud home of a people who had been told they could have no such home.

Through the decades, those who sought second-class status for black Americans have assassinated religious leaders, attacked children in houses of worship, burned churches to the ground. In an 18-month period in the mid-1990s, more than 30 black and multiracial churches were set afire in the South and Southwest.

Emanuel Church sits on the edge of a neighborhood that offers “adventures of historic proportions,” according to the local tourism bureau. Here, the Old Slave Mart stands as testament to a time when people sold other people for use as animals. The last sale of slaves took place there 152 years ago. You can visit today for $7.

At “Mother Emanuel,” as the church is known, the start of Wednesday’s Bible study was pushed back to about 7:20 p.m. to accommodate a board meeting, said Harold Washington, 75, a former church trustee.

Read the victims’ stories

Polly Sheppard sat behind Washington at the board meeting. When it ended, he headed out; she stayed in the fellowship hall for the Bible study.

The group — eight women, three men and a child ranging in age from 5 to 87, elders retired from successful careers, 20-somethings still figuring out their futures — had been in session for about 40 minutes when a baby-faced white man with bowl-cut hair and piercing blue eyes walked in and sat down. It was 8:06 p.m.

The man, wearing a fanny pack, had entered Emanuel and asked, “Where is the pastor?” according to relatives of victims who spoke to a survivor.

Pinckney, 41, knew the president of the United States. His great-grandfather sued the state’s Democratic Party to force an end to whites-only primaries. His uncle sued the governor to create voting districts that would make it possible for blacks to be elected to the legislature.

Now, the pastor welcomed the stranger into his church. A white visitor at Bible study was no ordinary event. Church in Charleston, as in most of the nation, is a time when people tend to stay with their own. Emanuel Church is on a street where, for decades, blacks were restricted to one sidewalk; the other one was whites-only.

The group invited the man to join the discussion. He remained silent. One participant, Tywanza Sanders, just a year out of college and working as a barber, posted a few seconds of video on Snapchat showing congregants seated around a long table. In the corner of the screen, the white man, unsmiling, sits next to the minister.

Texts were spread around the table, Scripture and notebooks, prayers and hymns.

It was an informal group. Sharonda Coleman-Singleton, a 45-year-old high school speech therapist, took a call from her son, Chris Singleton, a baseball player at Charleston Southern University. He needed to know where she had hidden the TV remote. It’s in the closet, she whispered, tucked away to prevent Chris’s younger brother from spending too much time playing video games.

A few minutes later, at about 9 p.m., the white man pulled out a semiautomatic pistol that he had bought legally. No one saw him draw the weapon, according to law enforcement officials. They only heard the shots.

When the shooter aimed at Susie Jackson, a longtime member of the church and a soprano in its choir, her nephew, Sanders, 26, put himself between the 87-year-old woman and the gunman and sought to talk him down. But the man continued with what he later called “my mission.” He shot Sanders and then his aunt.

“I have to do it,” the man told his victims, according to Sylvia Johnson, the pastor’s cousin, who spoke to a survivor. “You rape our women, and you’re taking over our country. And you have to go.”

The shots were up close, and every victim was shot multiple times, police said. The gunman reloaded — five times, according to relatives who spoke to a survivor.

Felicia Sanders, Tywanza’s mother, fell to the floor, stayed still and used her body to hide her granddaughter, who is 5, according to Cynthia Taylor, 64, who is Jackson’s niece and Tywanza Sanders’s cousin. A 57-year-old hairstylist, Felicia Sanders was an usher at Emanuel.

The shooter spared Sheppard, 70. “I’m going to let you live so you can tell the story,” the killer said, according to those who have spoken to Sheppard.

Before he left the room, the man stood over Sheppard “and uttered a racially inflammatory statement,” according to the state’s charging document.

The pastor’s wife, Jennifer, was in his office with their 11-year-old daughter when she heard the shots. She shut the door and wedged a chair against it.

‘I think he hated humans’

Emergency dispatchers in Charleston received the call about 9:05 p.m. and immediately sent units to the church. Eight people were dead in the basement; another, the Rev. Daniel Lee Simmons Sr., a 74-year-old retiree who was one of four ministers among the victims, was transported to a hospital and died there.

Surveillance cameras caught images of a young white man at the church door. Cameras also showed his vehicle, a four-door, black Hyundai Elantra. The man left Emanuel almost exactly an hour after he arrived, this time carrying a handgun. Police sent out an alert for a man wearing a gray sweatshirt, blue jeans and Timberland boots.

By morning, the temperature was nearing triple digits. Neighbors brought ice in buckets for police who had toiled through the night. Outside the church, impromptu prayer circles formed. Friends stopped by the police command post to ask after possible victims.

Meanwhile, Roof’s sister, Amber, his father and an uncle saw the surveillance photos and called police. The father told police that Roof owned a .45-caliber handgun; police found .45-caliber casings in the church basement.

Roof’s profile began to gain focus. A Facebook photo showed him wearing a jacket festooned with the flags of Rhodesia (now Zimbabwe) and South Africa during an era when both countries were run by white supremacists.

Roof came from a family dedicated to service. Relatives serve in the Army and on community boards. An uncle is a sociology professor.

But Dylann had gone through a dark passage. He stayed in his room much of the time, said his uncle, Carson Cowles. In recent months, he had lived on and off in a mobile home that he shared with five people, including a distant high school friend, and three dogs.

In interviews Friday, two of the roommates and a neighbor described a quiet guy who listened to opera, survived on ramen noodles and Rice-A-Roni, occasionally used cocaine, often passed out on whiskey and vodka, and kept a gun in the trunk of his car. Roof would come and go, disappearing for days at a time.

Roof and Meek, a high school friend, had fallen out of touch, but several months ago, Roof reached out, saying he needed a place to stay, said Joey’s younger brother, Justin Meek. The Meeks’ mobile home became a refuge for Roof.

“He didn’t get along with either of his parents,” said Justin, who is 18. “But sometimes they’d both call him.”

Tuesday, Roof drove Joey Meek, his girlfriend, and his youngest brother, Jacob, toward nearby Lake Murray. Jacob, 15, started to move a black backpack in the back seat, but Roof stopped him, saying, “Hey, there are magazines in there.”

“I thought it was, you know, reading magazines,” Jacob said. “But now, I don’t know.”

Along the way, Roof said he wouldn’t be going to the lake. He would drop the others off because he had an AMC gift certificate and wanted to see “Jurassic World.”

The Meeks never saw Roof again.

Justin and Jacob Meek, as well as Christon Scriven, 22, a neighbor who is African American, said Roof never struck them as racist but sometimes talked about violence. “I don’t think he hated blacks,” Scriven said. “I think he hated humans.”

When they were drinking one night recently, Scriven said, Roof talked about shooting up a school. Another time, he spoke of going on a shooting spree at the College of Charleston.

“My reaction at the time was, ‘You’re just talking crazy,’ ” Scriven said. “I don’t think he’s always there.”

Scriven said Roof often slept past noon. He had worked at a landscaping company but recently either quit or was laid off.

On Facebook, upwards of half of Roof’s 88 friends are black. His education was brief and checkered; he repeated ninth grade and then dropped out. People who went to school with him recalled him as a kid with long blond hair who listened to a lot of emo, a hard-core strain of rock that grew out of the 1980s punk movement.

In recent months, Roof had run into trouble with the law. He had been poking around at Columbiana Mall in the state capital. In February, Roof, dressed in black, creeped out employees at the Shoe Department and Bath and Body Works by peppering them with questions about their work hours and staffing levels.

Mall security called police and an officer questioned Roof, who said that “his parents were pressuring him to get a job,” according to the police report. But Roof hadn’t picked up a job application at any store.

The officer found an unlabeled bottle in Roof’s jacket pocket containing orange strips. Listerine breath strips, Roof said. But they were Suboxone, an opiate that is prescribed to heroin and opiate addicts as a therapeutic aid. Legally, it’s used to wean addicts from their cravings.

Roof had no prescription. He was charged with possession of a controlled substance. (A law enforcement source said the state’s social services department referred Roof for drug or alcohol treatment as a minor, but he never showed up for sessions.)

Two months later, on April 26, Roof was arrested at the same mall for violating the one-year ban imposed after the first arrest. This time, the ban was extended to three years.

Some of Roof’s friends said he had been making more racist comments of late. Police say he was collecting racist writings and skinhead videos — materials that are readily available in the area. Ten miles from Roof’s home, the League of the South supremacist group has a retail outlet, the Southern Patriot Shop, featuring Confederate paraphernalia, racist books and pro-slavery histories. The head of the Aryan Nations group moved its headquarters to Roof’s home town a decade ago.

“My family is not like this,” said Cowles, Roof’s uncle. “He did this, and he’s going to pay for it. I’d be the executioner myself if they would allow it. He left us with something we’ll never be able to escape.”

Spotting the fugitive

Two hundred and forty four miles from Charleston, Debbie Dills was on her way to work Thursday morning when she pulled alongside a car and saw a driver with a distinctive haircut.

She continued driving, pulling off Interstate 74 toward her job as a florist at Frady’s Florist in Kings Mountain, N.C. But the image of the guy with the bowl cut nagged at her. It was, she decided, the guy she had seen in the news photos.

Dills, too, had spent Wednesday evening at Bible study, at her Baptist church in Gastonia. “Those people were doing what I had just done,” Dills said. “They were studying His word . . . and they lost their lives doing that.”

Dills punched up her boss, Todd Frady, and got back on the interstate, zipping about 10 miles before she saw that same car again. Keeping the car in view, she got her boss to patch her through to the Shelby Police Department and relayed the tag number. The police told her they would take it from there, and Dills turned around to get to work.

Before she reached the shop, Frady called with the news: Police had arrested Roof in Shelby, three miles from the home of Michael Tyo, a recruiter for the Army Reserve who is engaged to Roof’s sister, Amber. Amber and other relatives were in Shelby, preparing for the wedding, which was to take place Sunday.

In custody, Roof told police that he chose Emanuel Church because he wanted to be sure he wasn’t killing white people. He said he “almost didn’t go through with it because they were so nice to him,” said a state lawmaker who was briefed by police.

Roof reportedly called the killings “my mission.”

‘I forgive you’

What remains is a new chapter in an old story of racial difference and human sameness.

It is a story of symbols: On the same day that the U.S. Supreme Court ruled that Texas could reject a license plate featuring the Confederate flag, that flag flew atop its pole in South Carolina’s capital. Nearby, the American flag and the state banner were lowered to half-staff to honor the shooting victims. But South Carolina law requires that the battle flag of the Confederacy always flies high.

And it is a story of labels: The killer saw not people but a dehumanized race. On the day of the shooting, it was reported that the U.S. Census Bureau would experiment with eliminating questions about “race,” instead asking Americans to describe their background however they wished.

Finally, it is a story of faith in humanity. At a bond hearing in a Charleston courtroom Friday afternoon, relatives of those killed at Emanuel looked into a video screen at an image of Roof broadcast from the detention center.

There was no yelling. There were no accusations. Instead, people who had lost the loves of their lives blessed the accused murderer.

“I forgive you,” said the daughter of Ethel Lance, 70, who was among the dead. “You took something very precious from me. I will never talk to her again. I will never, ever hold her again. But I forgive you.”

Felicia Sanders, the survivor and mother of one of the victims, spoke directly to the shooter.

“We welcomed you Wednesday night in our Bible study with welcome arms.” Her voice cracked. She kept on. “You have killed some of the most beautifulest people that I know. Every fiber in my body hurts, and I’ll never be the same. . . . But as we say in Bible study, ‘We enjoyed you, but may God have mercy on you.’ ”

Jeremy Borden in Lexington, S.C.; Ken Otterbourgh in Shelby, N.C.; Abby Phillip in Charleston; and Sari Horwitz, William Wan, Alice Crites, Julie Tate and Jennifer Jenkins in Washington contributed to this report.