Roof, who was 21 at the time, was arrested the day after the shooting in Shelby, North Carolina, about 250 miles north of Charleston.
Opening arguments in the federal case against Roof are expected to take place Wednesday.
In the months before the shooting, Roof "decided to attack African-Americans because of their race," and he selected black worshipers at a predominantly black church "to make his attack more notorious," according to the indictment.
On June 17, 2015, Roof entered the Emanuel AME Church armed and "with the intent of killing African-Americans engaged in the exercise of their religious beliefs," the indictment states.
The parishioners welcomed Roof into their Bible study group, according to the indictment, after which Roof drew his pistol and opened fire.
Roof hoped the attack would "increase racial tensions across the Nation" and bring "retribution for perceived wrongs he believed African-Americans had committed against white people," the indictment states.
At Roof's first court appearance the day after his capture, several of the shooting victims' family members expressed forgiveness for Roof amid their grief.
"I forgive you," the daughter of victim Ethel Lance said through tears to Roof, who appeared at the bond hearing via video conferencing from jail. "You took something very precious from me and I will never talk to her ever again. I will never be able to hold her again. But I forgive you. And have mercy on your soul."
Roof was originally granted permission to represent himself in court on Nov. 28 after requesting to move forward without his counsel, according to ABC affiliate WCIV in Charleston. However, Roof then sent a letter to the judge on Sunday asking that his lawyers be rehired until a verdict is reached and that he would then represent himself in the penalty phase. The judge has agreed to this new request.
He has pleaded not guilty.
Roof is also facing a state trial, in which he may also face the death penalty. The state trial is set for early next year.