Roof's attorney, David Bruck, said that the 22-year-old's actions were clearly senseless, but he described them as the actions of someone unable to perceive the world as it is.
"Why did Roof do this? Why was he motivated?" Bruck said, calling on the jury to try their best to consider who Roof is and what led him to commit such a violent act. He called Roof an immature young man who gave himself over to the "mad idea that he can make things better by executing those kind, virtuous people".
Much like in the Boston Marathon bombing trial last year - the last case that saw the Justice Department obtain a rare federal death sentence - Roof's guilt has been effectively unquestioned. Prosecutors played video footage of Roof admitting his guilt to FBI agents, and Roof's attorneys did not argue that he was innocent.
Instead, the larger question surrounding the trial has always focused on the expected next portion of the case, which will deal with whether Roof is sentenced to death or life in prison. Federal death sentences are rare, but the government has opted to seek one in this case, even though it has caused some unease among relatives of the victims.
For Bruck, a widely-recognised death-penalty lawyer, his closing arguments represented perhaps his last chance to address the jurors. US District Judge Richard Gergel agreed to let Roof represent himself during the penalty portion of the trial, though Bruck and his other attorneys will remain as standby counsel to assist him.
While prosecutors will outline the aggravating factors that they believe warrant a death sentence, it is unclear what Roof will do in his own defense. Bruck had previously indicated in a court filing that he would raise the issue of Roof's mental health, which could be a mitigating factor to avoid a death sentence.
Authorities said that in his FBI interview and manifestos, Roof had said he "had to do it" because he believed nobody was putting a stop to what he had read online about "black-on-white crime." Roof believed that it was "not too late to take the country back from blacks," prosecutors said during the trial.
During the closing arguments, Roof did not look up while Williams recited details of the case.
"A church is a sanctuary, a place of worship, a place of safety," Williams told the jurors. Roof shattered that peace, Williams said, with a carefully-plotted attack, visiting the church numerous times before the shooting.
Prosecutors had previously said that they believed Roof self-radicalised online, drawing bigoted beliefs from the Internet rather than any personal experiences. They had also said that Roof had two handwritten manifestos along with a list of churches. Williams said that this was a group of predominantly black churches, and "the one that he chose was at the top of his list."
"A person's actions tell us what they are thinking and what is in their heart," Williams said as photos of Roof's victims were shown in the court.
Each victim was shown gunned down on the floor of the church's basement, depicted as they were at the time of their death. Above each graphic photo was a portrait of the victims as they were during their lives.
"There is no bravery in this defendant. There is no bravery in his actions. But there is bravery in this case," Williams told the jury before recounting the courage shown by the victims at the time of the shooting and the survivors who took to the witness stand to recount the massacre.
Jurors began deliberating the case at 1.15pm. Last year, it took the jury in the Boston Marathon bombing's case about 11 hours to deliberate before finding Dzhokhar Tsarnaev guilty on all 30 counts. The jurors returned to the courtroom shortly after 3pm.
Roof is also facing a potential death sentence in a state trial, set to begin on January 3 next year, on charges of murder and attempted murder.
