Founded in 1816, the church has played an important role in the history of South Carolina, including the slavery era and Reconstruction, the civil rights movement, and Black Lives Matter.

Clementa C. Pinckney, had held rallies after the shooting of Walter Scott by a white police officer two months earlier, in nearby North Charleston.

[23][9] Dylann S. Roof, a man described as white, with sandy-brown hair, around 21 years old and 5 feet 9 inches (175 cm) in height, wearing a gray sweatshirt and jeans, opened fire with a Glock 41 .45-caliber handgun[24] on a group of people inside the church at a Bible study attended by Pinckney.

[30] According to the accounts of people who talked to survivors, when Roof walked into the historic African-American church, he immediately asked for Pinckney and sat down next to him, initially listening to others during the study.

[34][35][36] Dot Scott, president of the local branch of the NAACP, said she had heard from victims' relatives that Roof spared one woman (Polly Sheppard),[37] saying that she could tell other people what happened.

[48] Dylann Storm Roof[49] was named by the Federal Bureau of Investigation (FBI) as the suspected killer after his father and uncle contacted police to positively identify him upon seeing security photos of him in the news.

[51][52] According to then FBI Director James Comey, a police report detailing Roof's admission to a narcotics offense should have prevented him from purchasing the weapon used in the shooting.

[60] In this manifesto, Roof says he became "racially aware" as a result of the 2012 killing of Trayvon Martin, writing that when he learned about the incident, he read about it, concluding that George Zimmerman had been in the right.

[26][69] On the morning after the attack, police received a tip-off from a woman who recognized Roof and his car, a black Hyundai Elantra with South Carolina license plates and a three-flag "Confederate States of America" bumper decoration,[70] on U.S. Route 74, recalling security camera images taken at the church and distributed to the media.

[35][74][75] At the jail, his cell-block neighbor was Michael Slager, the former North Charleston police officer charged with murder after shooting Walter Scott following a traffic stop.

[91][92] On September 3, Ninth Circuit solicitor (i.e., district attorney) Scarlett Wilson announced that she intended to seek the death penalty against Roof in the state proceedings, based on more than two people being killed in the shooting and others' lives put at risk.

[102][103][104][105] On December 4, Roof made a handwritten request of Gergel, asking for his defense team for the guilt phase of his federal death penalty trial.

[126] Heidi Beirich, the director of the Intelligence Project for the Southern Poverty Law Center, a non-profit that seeks to identify American hate groups and confront their activities, said that the gunman's reported motive has frequently appeared on white supremacist websites.

"[131] At Morris Brown African Methodist Episcopal Church in Charleston, numerous people of different races and religions attended a ceremony commemorating the victims and they proclaimed that the attack would not divide the community.

[133] On June 25, 2015, at Emanuel AME Church, funerals were held for victims Ethel Lance and Sharonda Coleman-Singleton and they were attended by several political figures and civil rights leaders.

[16] Clementa Pinckney's funeral was held in the basketball arena of the College of Charleston on June 26, 2015, with President Barack Obama delivering the eulogy.

[139] The artists who were involved in the memorial included Ricky Mujica, Mario Andres Robinson, Lauren Tilden, Paul McCormack, Gregory Mortenson, Catherine Prescott, Terry Strickland, Judy Takács, and Stephanie Deshpande.

[141] In 2020, Allen University in Columbia, South Carolina announced that their renovation of the Good Samaritan Waverly Hospital would include a memorial that will prominently feature the names of Clementa C. Pinckney and the other eight individuals slain at Emanual African Methodist Episcopal Church in 2015.

[144][145] At the 2019 historical marker unveiling at the Dr. Cyril O. Spann Medical Office in Columbia, South Carolina, a planting and dedication ceremony for a Tree of Peace and Resistance held that day in conjunction with the Visanska Starks House recognized actions of mutual support between members of Emanual African Methodist Episcopal Church and Tree of Life _ Or L'Simcha Congregation after the Pittsburgh synogogue shooting, and expressed a commitment to public health and non-violence.

Some churches considered hiring armed security guards and installing metal detectors, but conversations in support of these steps have currently not gained traction.

[152] The FBI underwent a 30-day review to examine the lapses in the background-check system that allowed the suspected shooter to legally purchase the gun used in the shooting.

"[166] On June 19, the United States Department of Justice fast-tracked a Crime Victim Assistance Formula Grant of $29 million to the South Carolina government.

[204] Calls to remove the Confederate flag from statehouse grounds, as well as debates over the context of its symbolic nature, were renewed after the attack[205][206] by several prominent figures, including President Barack Obama, Mitt Romney, and Jeb Bush.

[208] At a statehouse press conference on June 22, Governor Nikki Haley, flanked by elected officials of both parties, including U.S. Republican senators Lindsey Graham and Tim Scott, and former Republican Governor Mark Sanford, called for the flag to be removed by the state legislature, saying that while the flag was "an integral part of our past, it does not represent the future" of South Carolina.

Clementa Pinckney on June 26, 2015, before 5,000 congregants at the College of Charleston, President Barack Obama acknowledged that the shooting had catalyzed a broad movement, backed by Republicans and Democrats, to remove the flag from official public display.

He based this conclusion on a racist political motivation that "seems likely" and his "intimidation of a wider audience" criterion was met when "... the shooter reportedly left one person alive to spread the message".

[228] An article by CNN National Security Analyst Peter Bergen and David Sterman on June 19 says, "By any reasonable standard, this is terrorism, which is generally defined as an act of violence against civilians by individuals or organizations for political purposes.

[230][231][232] The journalist Glenn Greenwald wrote that Almost immediately, news reports indicated that there was 'no sign of terrorism' – by which they meant: it does not appear that the shooter is Muslim ... other than the perpetrator’s non-Muslim identity, the Charleston attack from the start had the indicia of what is commonly understood to be 'terrorism'.

(emphasis in original)[233]Speaking at a press conference in Baltimore on June 19, FBI Director James Comey said, while his agency was investigating the shooting as a "hate crime", he did not consider it an "act of terrorism", citing the lack of political motivation for the suspect's actions.

"[234] Heidi Beirich, who leads the Intelligence Project at the Southern Poverty Law Center (SPLC), pointed to the discovery of a website attributed to Roof, which featured a manifesto and sixty photos as an example of why federal agents "don't have themselves together on this issue".