Roof studied the church's long history in the black community, found out what time a Bible study class would be held, loaded his gun the night before, packed extra ammunition and drove more than an hour to the church, Assistant US Attorney Jay Richardson told the jury of nine whites and three African-Americans.
He was welcomed into the Bible study and displayed a "cold and hateful heart" by sitting with the group more than 30 minutes, Richardson said.
As the 12 people stood to offer prayers and close their eyes, Roof opened fire with a Glock .45-caliber pistol, firing 70 rounds, Richardson said. Nine people were killed.
Tywanza Sanders, one of those killed, told Roof that he didn't have to shoot them, saying "we mean you no harm," the prosecutor said, recounting the story of one of the survivors. Roof, who is white, replied, "Y'all are raping our white women, y'all are taking over the world," Richardson said.
After he was captured, authorities learned Roof had written a "manifesto" of his racist beliefs and posed for photos with the US flag burning in one hand and the Confederate flag in the other, Richardson said.
Roof also designed his own logo that included his initials, a swastika and the number 88, which for white supremacists stands for "Heil Hitler," the prosecutor said. "He created the symbol to reflect who he was, what he thought and what he had done," Richardson said.
Opening for the defense, attorney David Bruck told the jury, "you're probably wondering why there has to be a trial."
Authorities previously said Roof had confessed to the killings and told the FBI that he hoped to provoke a race war.
The practical reason for the trial, Bruck said, is that the government has asked for the death penalty.
Bruck said the jury will decide guilt or innocence in the first phase of the trial. In the second phase, the jury will decide on punishment.
Bruck reminded the jury of Roof's youth and urged them to try to understand him. Roof told the FBI he didn't have any friends, Bruck said.
Jurors should ask where Roof's feelings of racial hatred came from, Bruck said.
"How much sense does this crime make, does it make any sense and if any at all, what does that tell you?" he asked.
Bruck ended by saying he probably would not call any witnesses.
Roof sat mostly motionless in his state-issued, gray-and-white striped jumpsuit throughout both opening statements, barely looking up from the defense table.
Tywanza Sanders came to Bible study
Felicia Sanders, who survived the shooting, was one of seven prosecution witnesses to testify. Sanders' 26-year-old son, Tywanza, and 87-year old aunt, Susie Jackson, were victims.
Sanders teared up recalling her close friends and members of the church, including the Rev. Daniel Simmons, 74, a church staff member and former pastor of Friendship AME Church in Mount Pleasant, South Carolina.
Simmons, who was killed, "was the backbone of the church," Sanders said.
Richardson showed pictures of all nine victims as Sanders spoke. They looked happy, smiling.
Asked about her aunt, Sanders said: "First of all she was my best friend. ..." Jackson would organize hair appointments for members of a senior citizens home and made sure they took their medicine, Sanders said.
Sanders said she was also close with her son.
She said the last text he sent was to ask her: "Are we having bible study?"
She texted him back, "yes." And he came to the church.
She screamed, 'He has a gun'
At Bible study, Sanders recalled the church's then-pastor, the Rev. Clementa Pinckney
, who was killed in the shooting, gave Roof a copy of the page they were studying in the group.
Sanders said Roof hung his head down during their group "just as he's doing right now."
Roof also appeared to have his eyes closed throughout Sanders' testimony.
Sanders recalled the group in the Bible study shutting their eyes.
Then, "a lot of sound went off," she said.
She said she screamed, "He has a gun." But Roof had already shot Pinckney.
She said Simmons stood and said, "Let me check on the Pastor, just let me check on the Pastor."
Sanders was under a table. She said she thought it was a machine gun.
"There were so many shots," she said.
Her granddaughter, who was with her, said, "Granny I'm so scared."
"Play dead, play dead," Sanders recalled telling her.
"I muzzled her face to my body so tight, that I thought I suffocated her," Sanders said.
Sanders said Roof asked Polly Sheppard, a retired nurse at the Bible study, "Have I shot you yet," Sanders said.
Sheppard replied, "No."
Sanders said Roof wanted her to tell his story.
'Evil as can be'
Motioning to Roof in the courtroom, a sobbing Sanders said: "The defendant over there, with his head hanging down, told my son I have to do this."
"My son said 'you don't have to do this, we mean you no harm,' " Sanders said.
But Roof told him that black people were raping white women and taking over the world, she said.
"Then, he put five bullets in my son," she said.
She said she felt the sting. "There was a lot of shots, 77 shots in the room."
She added: "He just sat there the whole time, evil, evil. Evil as can be."
As Roof left, her son screamed: "Aunt Susie, Aunt Susie."
Sanders said she implored her son to lay still. As he lay bleeding and dying, he asked his mother for water.
Sanders begged: "Miss Polly, 'please help my son.'"
"I watched my son come into this world and I watched my son leave this world," Sanders said.
Earlier Wednesday, eight white women, two African-American women, one white man and one African-American man were seated on the jury, according to a pool report from the US District Court in Charleston.
Two white women, two white men, a black woman and a black man were picked as alternates, the pool report said.
All 18 panelists will listen to testimony and arguments without knowing whether they are jurors or alternates.
Roof was granted the right to represent himself during the questioning of potential jurors, but US District Judge Richard Gergel granted Roof's motion on Monday to have attorneys assist him during the guilt phase of his trial. Roof has asked that he act for himself in any sentencing proceeding.
In another order Tuesday, the judge rejected the defense motion to restart the jury questioning. Gergel wrote that Roof actively participated in jury qualification questioning.
Last week, the judge deemed Roof was competent to stand trial
Roof faces 33 federal charges: nine counts of violating the Hate Crime Act resulting in death; three counts of violating the Hate Crime Act involving an attempt to kill; nine counts of obstruction of exercise of religion resulting in death; three counts of obstruction of exercise of religion involving an attempt to kill and use of a dangerous weapon; and nine counts of use of a firearm to commit murder during and in relation to a crime of violence.
If convicted, he could face the death penalty.
Roof, 22, also faces nine counts of murder and other charges in the state court system. His trial in that case is scheduled to start in January.
The trial resumes Thursday morning.