For a moment, President Obama stood alone on the stage.

With an audience of about 5,500 people looking on at the College of Charleston TD Arena, the president then passionately burst into song.

“Amazing Grace, how sweet the sound,” he began, singing the 18th-century hymn solo.

The ministers beside him smiled, stood up and joined in.

Then a church organ was played and the crowd added their voices as they held hands.

The stirring scene took place June 26 at the funeral of the Rev. Clementa Pinckney, the pastor who was slain along with eight church members at Emanuel African Methodist Episcopal Church in Charleston, S.C., during a June 17 Bible study by a white gunman. Dylann Roof, 21, a white supremacist, was arrested the next day and is now behind bars awaiting trial.

After the hymn, President Obama called out the names of the Charleston shooting victims into the microphone. The crowd responded, “Yes!” to every name.

In a speech likely to be considered one of the most memorable of his presidency, President Obama paid an emotional tribute to the pastor and his flock.

“Blinded by hatred, the alleged killer would not see the grace surrounding Reverend Pinckney and that Bible study group,” President Obama told the audience.

Speaking in the language and cadence of the black church, President Obama argued that the massacre and God’s grace “allowed us to see where we’ve been blind” and has given America a chance to face up to the scourges of racism and gun violence.

He said the removal of Confederate flags across the South was “a modest but meaningful balm for so many unhealed wounds,” but that the United States needs to go further.

“I don’t think God wants us to stop there,” the president said.

He urged the audience to use the killings as a spur for reforming a criminal justice system that jails one of three black men at some point in their lives and for confronting “the unique mayhem that gun violence inflicts upon this nation.”

“It would be a betrayal of everything Reverend Pinckney stood for, I believe, if we allow ourselves to slip into a comfortable silence again,” President Obama said.

The shootings sparked an intense dialogue over the legacy of slavery and its symbols after photos showing the alleged gunman posing with the Confederate flag surfaced on a website that also displayed a racist manifesto.

Politicians and businesses quickly scrambled to distance themselves from the Civil War-era battle flag of the Confederacy amid calls for the flag to be lowered from the grounds of South Carolina’s State House.

President Obama called the flag “a reminder of systemic oppression and racial subjugation.”

Republican Gov. Nikki Haley, who added her voice to those calls last week, brought a Charleston congregation to its feet Tuesday at the last funeral for one of the victims when she declared: “That Confederate flag will come down.”

Gov. Haley broke down a day earlier in a service to honor church member Myra Thompson, 59, who earned her minister’s degree on the day she was killed.

“This is a woman who I want to strive to be,” Gov. Haley said of Ms. Thompson. “She wanted every person she came in touch with to make them better.”

Gov. Haley and the Rev. Jesse Jackson attended funerals for victims Saturday and Sunday.

During last Saturday’s funeral for Tywanza Sanders, 26, and his aunt, Susie Jackson, 87, Gov. Haley promised, “We will make this right.” The governor did not say what actions she planned to take.

Hours before the funeral for DePayne Middleton Doctor, 49, began on Sunday, Vice President Joe Biden made a surprise appearance at the church’s morning service to speak and worship.

Vice President Biden gave his condolences to the families of the victims and received a standing ovation after reading a selection of scripture.

The vice president’s son, Beau, died May 30 of brain cancer. He narrowly avoided death as a young boy in a 1972 car crash that killed the vice president’s first wife and his daughter.

“The reason I came was to draw strength from all of you,” he said. “I wish I could say something that would ease the pain.”

Since the church murders, outrage and fear have spread with reports of seven fires at predominately black churches across the Southeast. Arson is suspected in three cases so far.

The latest: A blaze that burned down Mt. Zion AME Church in Greeleyville, S.C., Tuesday night. The same church was torched by Ku Klux Klan members in 1995.

Fire officials have ruled the church a total loss.

A federal law enforcement source told the Associated Press Wednesday morning that preliminary indications are the fire does not appear to be the work of an arsonist.

The federal Bureau of Alcohol, Tobacco, Firearms and Explosives investigates fires at houses of worship. The FBI has joined the investigation as well.

Separately, an African-American woman scaled the flagpole in front of the South Carolina state house last Saturday and removed the Confederate flag.

“We can’t continue like this,” the climber, Bree Newsome, 30, said in statement about her bold move. “It’s time for a new chapter where we are sincere about dismantling white supremacy and building toward true racial justice and equality.”

Ms. Newsome was arrested and charged with defacing monuments on state Capitol grounds. The offense carries a possible fine up to $5,000 and up to three years in prison.

The flag was flown again on the pole about 45 minutes later.

The Loyal White Knights chapter of the KKK, based in Pelham, N.C., said it will hold a rally at the South Carolina State House on July 18.

“We’re standing up for the Confederacy,” James Spears, the chapter’s “Great Titan,” said on Tuesday.

He said speakers would address slavery, then hold a cross-burning ceremony on private property.

Gov. Haley said the group was not welcome in the state.

In Virginia, the Sons of Confederate Veterans has vowed to oppose Gov. Terry McAuliffe’s order to remove the Confederate flag from state-issued license plates, a move he announced last week.