Roof, who is white, is accused of shooting and killing nine black parishioners at the predominantly black Emanuel AME Church on June 17, 2015. Roof allegedly entered the church armed and "with the intent of killing African-Americans engaged in the exercise of their religious beliefs," according to the federal indictment against him. The parishioners welcomed Roof into their Bible study group, according to the indictment, after which Roof allegedly drew his pistol and opened fire.
The 33 federal counts against Roof include hate crimes resulting in death and obstruction of exercise of religion resulting in death. If convicted, Roof faces the death penalty. Roof has pleaded not guilty.
Here are some of the key points from the government's case ahead of Thursday's closing arguments.
Survivor Felicia Sanders
Felicia Sanders, a survivor of the shooting, was the government's first witness. When Roof opened fire that June night, Sanders said she clutched her granddaughter tight and told her to play dead.
"I could feel the warm blood flowing on each side of me," she said.
"I was just waiting on my turn," she added. "Even if I got shot, I just didn't want my granddaughter to get shot."
Amid the chaos and the bloodshed, her youngest son, Tywanza Sanders, stood up and confronted the assailant: "Why are you doing this?" he asked, according to Felicia Sanders' testimony.
"And he told our son, 'I have to do this because y'all raping our women and taking over the world,'" Felicia Sanders said. "And that's when [the gunman] put about five bullets in my son."
Felicia Sanders then tearfully recalled watching her son die.
"We watched him take his last breath," she said. "I watched my son come into this world, and I watched my son leave this world."
Investigators showed pictures from the gruesome scene at the basement hall where the shooting happened. The images showed bodies with numbers labeling what investigators believe was the order in which they were shot. The images also showed streams of blood. Many of the victims were under the rickety tables. Some Bibles were still on the tables.
Roof's Video 'Confession'
In a video interview of Roof conducted by an FBI agent shortly after he was captured and played in court, Roof laughed as he admitted to the shooting.
He also said he used a .45-caliber Glock to do it, according to the video. "I didn't say anything to them before I pulled it out, not even one word," Roof says of the gun in the video. "I mean, they reacted after I shot them."
Asked in the video when he decided to do the shooting, Roof say, "I can't tell you."
Roof's voice was mostly monotone during the interview, though it was often punctuated by laughter.
"I am guilty," he says, laughing.
Roof said he did not expect to survive the shooting because he expected police to respond to the church and shoot him. Once he escaped, he said he spontaneously decided to go to Charlotte, North Carolina, because he didn't want to go home to Columbia.
After an agent tells him he killed nine people and asks how he feels, Roof responds in the video in a monotone voice, "It makes me feel bad."
Roof's Journal of Racist Language
Testimony also addressed letters Roof wrote to his parents and a journal he kept with racist entries -- all found in his car after he was apprehended.
In a note to his mother, Roof apologized and said he loved her, and he wrote, "Childish as it sounds I wish I was in your arms."
In the journal, Roof degrades African Americans and Jews, and a state law enforcement agent on the witness stand read the racist entries aloud. Some jurors leaned on their hands as they read the journal entries on monitors and appeared shocked.
Families of the victims were quiet, some wrapped in colorful blankets to stay warm in the cold courtroom.
Roof wrote that he was not raised in a racist place. He also wrote that after reading a Wikipedia entry about the Trayvon Martin case, it was obvious to him that George Zimmerman, the man who fatally shot Martin, was in the right, and he was never the same again.
Roof also wrote that one of his only regrets is that he was never able to fall in love.
Roof's Note Listing Churches
Roof had a handwritten note in his car with the names of several churches on it, according to testimony from a former South Carolina Law Enforcement Division (SLED) agent who processed Roof's car after the shooting.
Besides the note listing churches, notable items in Roof's car included a Confederate flag, a burned American flag, a gun, an empty box of ammunition and a laser attachment for a gun that helps with accuracy.
Survivor Polly Sheppard
Polly Sheppard was the government's final witness. One of the deadly rampage's three survivors, Sheppard said she initially thought the gunshots were an electrical problem. But then Felicia Sanders screamed that it was a gun, Sheppard said. Sheppard said she saw Roof shoot Rev. Daniel Simmons, then she ducked under a table.
She told the court that she listened to the gunshots ring out as she hid. She said she saw the casings bounce and roll across the ground, and watched as Roof's boots came closer and closer. When Roof got to the tables, he told her to shut up as she was praying out loud, she said.
Then she said Roof asked her if she was shot. She told him no, she said, and he replied that he wouldn't shoot her. "I’m going to leave you alive to tell the story," Sheppard said Roof told her.
Sheppard's emotional 911 call was also played in court.
Defense attorney David Bruck said in opening statements that Roof committed the crime but the trial involves understanding "who this person was and why on earth he would want to cause so much grief."
"He did it," Bruck said of Roof. "... You're probably wondering, so what we are doing here? Why does there need to be a trial? ... The practical reason is that the government has asked for the death penalty after conviction, and because of that, we have a procedure to go through."
Bruck said the jury must "go deeper than the surface with this awful crime."
"Among the elements of the crime are racial hatred. In considering that issue, ask yourself where this extraordinary degree of racial feeling came from. ... How much sense does this crime make? Does it make any sense at all? And if not, what does that tell you?" he said.
After the prosecution rested its case, Roof told the judge that he did not want to testify, and the defense called zero witnesses before it, too, rested.
Closing arguments are slated for Thursday, then the jury will begin deliberations.
Roof also faces a state trial, set for early next year, in which he may also face the death penalty.
ABC News' Steve Osunsami, Kristen McFann and Anne Emerson contributed to this report.