It happened around 12:10 a.m. at the McDonald's on Tower Boulevard.
Police said two armed, masked men used the drive-thru window to get inside the fast-food restaurant.
Officials said the suspects demanded money and roughed up the manager, causing serious injuries.
At least one shot was fired during the holdup.
Authorities said the incident is not connected to a string of violent events that happened early Tuesday morning in Durham and Wake counties.
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