When Dylann Roof sat down next to the Rev. Clementa Pinckney last month, the 21-year-old white man wasn’t there to listen to the Bible study going on that night.

He was there to kill people because of their race, according to federal court documents, and he had chosen their historic Charleston worship hall, Emanuel AME Church, to ensure notoriety for the mass murder he was about to carry out.

He revealed a .45-caliber Glock pistol and fired hollow-point rounds that have a particularly deadly mushrooming effect on their targets.

He had come carrying eight pistol magazines packed with the bullets that he used to kill nine people, including Pinckney, the documents stated.

“The parishioners had Bibles,” U.S. Attorney Loretta Lynch said Wednesday. “Dylann Roof had his gun.”

As a result, a federal indictment alleged Wednesday that Roof carried one of the deadliest racially motivated hate crimes since the Civil Rights era by targeting the 12 black people, including three survivors, and prevented them from freely exercising their religion.

The sweeping 33-count indictment by a Columbia-based grand jury, dubbed by legal scholars as unprecedented in modern American history, laid the groundwork for federal prosecutors to seek the death penalty against Roof and marked the government’s interest in pursuing justice for the nine people slain June 17 at Emanuel African Methodist Episcopal Church on Calhoun Street.

“Several months prior to the tragic events, Roof conceived his goal of increasing racial tensions and seeking retribution for perceived wrongs that he believed African-Americans have committed against white people,” Lynch said in announcing the indictment from Washington. “To carry out these twin goals of fanning racial flames and exacting revenge, Roof further decided to seek out and murder African-Americans because of their race. ... Racially motivated violence such as this is the original domesticated terrorism.”

How federal and state prosecutors would coordinate the prosecution in two different court venues was not certain. Roof was indicted earlier this month by a Charleston County grand jury on nine counts of murder, three of attempted murder and a firearms charge. Attorneys in state court also have handled it as a potential death penalty case.

While neither federal nor state prosecutors have decided whether to pursue capital punishment, Wednesday’s indictment hinted at federal prosecutors’ intentions to seek the death penalty. Citing U.S. laws on the death penalty, it stated that Roof intentionally targeted vulnerable people and meant to kill “more than one person in a single criminal episode.”

But Lynch said input from the victims’ families — whose expressions of forgiveness after the tragedy, she said, served as an “incredible lesson and message for all of us” — would play prominently into that decision.

Both governments, she added, will pursue their cases simultaneously and later assess how state and federal judges handle each one, but she noted that the state charges do not reflect the alleged hate crimes presented in this week’s indictment.

In federal court, Roof is charged with 12 violations of the Matthew Shepard and James Byrd Jr. Hate Crimes Prevention Act, which went into effect at the start of President Barack Obama’s first term in 2009, and 12 counts under the Church Arson Prevention Act of 1996. The 12 counts under each law represent the nine people who were slain and the three survivors. Each of the nine murder counts under the church arson law make Roof eligible for the death penalty. The hate crimes do not.

He also faces nine charges related to using a firearm to commit murder. “This is a very novel situation,” Miller Shealy, a professor at the Charleston School of Law who has served as a prosecutor in state courts and at the Justice Department. “This has never happened in South Carolina before, where a defendant has such infamous celebrity. ... This case is in the spotlight, and the feds want to make a statement.”

‘Almost unprecedented’

Since the night Roof walked into the church and later escaped into the night, authorities have labeled the shooting a hate crime while the Justice Department’s Civil Rights Division sent FBI agents to investigate the possible motive. But the indictment Wednesday brings that aspect of the crime that has sparked conversations about racism nationwide into the courtroom for the first time.

Such a deadly bias-motivated attack has become a rarity in modern times. In the five-year span from 2009 to 2013, American law enforcement agencies reported 34 hate-motivated homicides to the FBI. In one of the most recent instances, a white supremacist fatally shot six people and wounded four others at a Sikh temple in Wisconsin before killing himself.

Roof’s case is almost unheard of in recent times, said Jeannine Bell, a law professor at Indiana University at Bloomington and a nationally recognized scholar on hate crimes. Hate-based killings are relatively rare, and the killers have most often taken their own lives before they could be arrested or prosecuted, she said.

The two-track prosecution in South Carolina, one of five states without a hate crime law of its own, makes it even more of an anomaly, she said.

“A situation like this,” she said, “is almost unprecedented.”

The FBI typically views hate crime charges only as a “backstop” to the state’s prosecution, according to its website. Defined as an illegal act “motivated in whole or in part by an offender’s bias against a race, religion, disability, ethnic origin or sexual orientation,” a hate crime against a single person is considered a civil rights violation, making it fall under federal law enforcement jurisdiction, according to the FBI.

With charges in state court, the federal authorities often offer investigatory efforts in a supporting role and later monitor court proceedings “to ensure that the federal interest is vindicated,” the FBI site stated.

But without a hate-crime law on the books in the Palmetto State, where some lawmakers’ attempts to change that have repeatedly failed, Roof’s case could play out differently.

Ninth Circuit Solicitor Scarlett Wilson told reporters days after the shooting that she planned to work closely with the federal authorities. She did not respond Wednesday to a request for comment.

“Make no mistake,” she said last month about federal officials. “We are standing shoulder to shoulder, side by side, and we will work together through this prosecution.”

‘Plowing new ground’

Both state and federal cases could proceed through their respective court systems, but one might end up taking priority, said Shealy, the Charleston law professor. With state indictments already handed down, local solicitors likely would be the first to prosecute Roof, he said.

Because the results of the case will have such broad meaning for South Carolina and the country, where discussions about race relations have persisted in recent years, the prosecutors will “definitely be plowing new ground here,” Shealy said. From what evidence has been made public, he said both sides appear to have “outstandingly good” cases.

Local prosecutors likely would be reluctant to give up the case, said Charlie Condon, a former S.C. attorney general and circuit solicitor. Based on statistics, he added, Roof would be more likely to be executed under a death penalty sentence in state court than in federal jurisdiction.

“If I had that job, I would feel strongly that it should remain in state court,” said Condon, now a private attorney in Mount Pleasant.

Wilson, the area’s top prosecutor, already has indicated in court filings that she plans to ferret out the motive for the attack while prosecuting Roof.

Investigators found handwritten letters and lists in the cars and homes that Roof used, and Wilson said in court documents that she would cite the writings to help prove his guilt and to determine what drove him to carry out the attack. The hate-crime component also surfaced publicly in the days after the attack. Roof had confided in some of his friends his plans to wage an assault in Charleston and to start a race war, those acquaintances have said. The friends did not take him seriously.

‘Sends a message’

With mentions of the Confederate flag and South Africa’s former apartheid segregation scheme, Wednesday’s 13-page indictment reflected the elements of Roof’s life that have sparked a widespread introspection on race since the attack.

It also formerly linked Roof to an online manifesto, posted at lastrhodesian.net, that surfaced shortly after the shooting. The diatribe referred to black people as “stupid and violent” and called segregation a “defensive measure” to “protect us from them.”

While it did not mention specific plans for an attack, the manifesto alluded to “drastic action” to take back the country from other races.

“I have no choice,” the Web page stated. “I am not in the position to, alone, go into the ghetto and fight. I chose Charleston because it is most historic city in my state, and at one time had the highest ratio of blacks to Whites in the country. We have no skinheads, no real KKK, no one doing anything but talking on the internet. Well someone has to have the bravery to take it to the real world, and I guess that has to be me.”

But the indictment also mentions the names of all the people whose lives and whose families’ lives were changed forever by what it says he did: Sharonda Coleman-Singleton, Cynthia Hurd, Susie Jackson, Ethel Lance, DePayne Middleton Doctor, Clementa Pinckney, Tywanza Sanders, Daniel Simmons, Myra Thompson and survivors 11-year-old K.M., Felicia Sanders and Polly Sheppard

Coupled with the state murder charges, the indictment almost guarantees Roof will face the death penalty, if he’s convicted, said Jack Levin, a criminology professor at Northeastern University in Boston who authored the 1985 book “Hate Crimes: The Rising Tide of Bigotry and Bloodshed.”

He expects the FBI’s case to take precedence because the federal government can bring more resources to bear on the prosecution.

While the state murder charges also carry a high likelihood of a death sentence, the federal hate- crime indictment carries a symbolic value that tells the nation that hate-fueled violence will not be tolerated, Levin said.

A further indicator of that: The attorney general herself signed the indictment.

“When you kill nine people in a premeditated, brutal act of murder, you wouldn’t need a hate-crime charge to get the death penalty,” Levin said. “But the hate crime law sends an important message to would-be perpetrators that we will not tolerate this type of extreme intolerance. And at the same time, it sends a message to potential victims that we are on their side, we are not bigots, and we will not tolerate hate.”

Glenn Smith contributed to this report.