Edgar Maddison Welch, 28 of Salisbury, North Carolina, was arrested Sunday afternoon at Comet Ping Pong on Connecticut Avenue in an affluent neighborhood of the nation's capital, police said in a statement.
No one was injured. He was expected to make his first appearance in court Monday afternoon.
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Bartender Lee Elmore told news outlets that people in the restaurant started to panic as the man walked to the back of the restaurant.
"One of the hosts runs up and says did you see that guy? He had a big gun," Elmore said.
"His demeanor was bizarre, in that if you come in to a place to eat, you ask for a host or grab a seat at the bar," Elmore said. "Didn't make any eye contact, didn't talk with anybody."
Police say Welch told them he had come to the restaurant to "self-investigate" the fictitious online conspiracy theory that spread online during Clinton's unsuccessful run for the White House.
Upon arriving at the restaurant, he walked in the front door and pointed a gun toward an employee, who fled and contacted police, according to authorities.
Welch fired the rifle inside the restaurant, and rounds possibly hit the walls, door and a computer, all of which were damaged, police spokeswoman Karimah Bilal said.
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Authorities set up a perimeter and arrested Welch safely, Interim D.C. Police Chief Peter Newsham said. Welch was charged with assault with a dangerous weapon. Police recovered an AR-15 rifle, a Colt .38 handgun, a shotgun and a folding knife.
A telephone number listed for Welch in North Carolina was disconnected.
Comet Ping Pong is in a neighborhood of well-tended private homes and apartment buildings on leafy streets that lead to a mix of shops, restaurants and the Politics and Prose book store.
The restaurant attracted national attention after fake news stories stated that Clinton and her campaign chief ran a child sex ring out of the restaurant.
"We should all condemn the efforts of certain people to spread malicious and utterly false accusations about Comet Ping Pong, a venerated DC institution," Restaurant owner James Alefantis said in a statement. "Let me state unequivocally: These stories are completely and entirely false, and there is no basis in fact to any of them. What happened today demonstrates that promoting false and reckless conspiracy theories comes with consequences."