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Police escorted Dylann Roof from police headquarters to the Cleveland County Courthouse Thursday afternoon for his first appearance.
Roof waived extradition, an attorney told Channel 9. It is unclear when he will return to Charleston.
The appearance was closed to everyone but law enforcement officials.
Roof is accused of walking into the Emanuel AME Church and opening fire during Bible study Wednesday night.
Nine people were killed. The shooting happened around 9 p.m. Police said Roof told one of the three survivors he let her live so she could tell others what he did.
Details on Roof's arrest
The Shelby Police Department received a call from the Kings Mountain Police Department at 10:32 a.m. that a business had contacted them of a possible sighting.
At 10:43 a.m., officers spotted Roof's vehicle on Dixon Boulevard. He was pulled over at 10:44 a.m. Roof was the only person in the car. He was taken into custody at 10:49 a.m. and taken to the Shelby Police Department.