Dylann Roof's request came against his lawyers' advice, and U.S. District Judge Richard Gergel said he would reluctantly accept the 22-year-old's "unwise" decision.
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Death penalty attorney David Bruck then slid over and let Roof take the lead chair. The lawyers can stand by and help Roof if he asks.
The development came the same day jury selection resumed in the case. The selection process was halted Nov. 7 after lawyers for Roof questioned his ability to understand the case against him. Judge Gergel's ruling last week cleared the way for Monday's process to begin anew.
Roof, 22, is charged with counts including hate crimes and obstruction of religion in connection with the June 17, 2015, attack at Emanuel African Methodist Episcopal Church in Charleston. He faces a possible death sentence if convicted.
Beginning Monday, 516 potential jurors were to report to the courthouse to be individually questioned by the judge. When 70 qualified jurors are picked, attorneys can use strikes to dismiss those they don't want, until 12 jurors and six alternates are seated.
The judge delayed the process of narrowing the jury pool when Roof's lawyers suggested that their client either didn't understand the charges against him or couldn't properly help with his defense. The lawyers didn't say what led them to question Roof's fitness for trial.
The decision came after Gergel wrapped up a hastily called two-day hearing to determine if Roof is mentally fit to stand trial, hearing testimony from psychologist James Ballenger and four other unnamed witnesses and reviewed sworn statements from three others.
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The judge said he took the rare step of closing the hearing to the public and media because Roof made statements to a psychologist that might not be legal to use at his trial and could taint potential jurors.
On Friday, the judge said he refrained from releasing a transcript of the hearing for the same reason, reversing an earlier pledge to release a redacted transcript. Victims' relatives complained about the secrecy surrounding the proceedings, but Gergel maintains the steps he has taken are to ensure Roof receives a fair trial and that pre-trial exposure doesn't provide grounds for an appeal.
Roof also has already been found competent in state court, where prosecutors plan a second death penalty trial on nine counts of murder.
According to police, Roof sat through nearly an hour of prayer and Bible study at the church with its pastor and 11 others before pulling a gun from his fanny pack and firing dozens of shots.
Roof shouted racial insults at the six women and three men he is charged with killing and the three people left alive, authorities said. Roof said he left the three unharmed so they could tell the world the shootings were because he hated black people.