“I have to do this,” Dylann S. Roof, who was 21 at the time, told his African-American victims in Emanuel’s fellowship hall as he fired 77 shots from a Glock semiautomatic handgun, “because y’all are raping our women and y’all are taking over our world,” according to survivors who testified at his 2016 trial.

Shortly before the assault on the synagogue, which the police say involved four weapons, including a Glock .357, Robert Bowers, 46, explained himself in a social media post. “I can’t sit by and watch my people get slaughtered,” he wrote. “Screw your optics, I’m going in.” After his surrender, he told a SWAT officer that he “wanted all Jews to die” because they “were committing genocide against his people,” according to a criminal complaint.

Despite what likely will be overwhelming physical and witness evidence, Mr. Bowers pleaded not guilty on Thursday to 44 federal counts, including hate crimes that will carry a possible death sentence if, as pledged, the Justice Department pursues it. Like Mr. Roof, who was convicted and sentenced to death, Mr. Bowers requested a jury trial.

Pastor Manning heard about the Pittsburgh shootings last Saturday morning when his smartphone vibrated with a news alert. He was at Emanuel, participating in a panel discussion about the Charleston massacre for a visiting group of young lawyers. His heart sank.

“Not again,” he recalled thinking.

He had become Emanuel’s pastor in 2016, tasked with the complex job of healing a deeply wounded church, which now attracts large numbers of out-of-town visitors. He filled the pulpit once occupied by the Rev. Clementa C. Pinckney, the first person shot by Mr. Roof. (As it happens, Pastor Pinckney, named for the legendary Pittsburgh Pirate Roberto Clemente, was a huge Pittsburgh Steelers fan.)