The video capturing the scene is disturbing and disgusting, prompting the restaurant and the Department of Public Health to take quick action.
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Chris Brooks recorded the shocking video of a man sitting inside the restaurant with a dead raccoon on the table in front of him.
"Wow, (expletive) this guy brings a damn raccoon into the McDonalds," said Brooks on the cell phone video clip.
Brooks came to the McDonald's on Sunday to grab breakfast when he says everything went wrong.
"I'm standing at the counter, and a guy comes in yelling, 'Help, help,'" Brooks said.
Brooks and other customers were stunned to see what the man was holding as he called for help.
"I didn't know if the raccoon was dead or alive. My thought was to get out of the way," Brooks added.
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Brooks ran out, recording video through the window. On the video, someone in the restaurant removes the bloody animal, dumping it in a trash can outside.
The Department of Environmental Health says the restaurant closed for five hours Sunday to disinfect the dining room. Health inspectors say it's now safe.
"We want to assure the public that McDonald's addressed the problem appropriately. They cleaned it, sanitized it, which is the main thing for us," said Stephanie Cushing, Director of Environmental Health.
Brooks tried confronting the suspected homeless man on why he brought a raccoon into McDonald's.
SFPD officers responded, gave the man a mental health evaluation and determined he did not need to be detained.
Animal control staff removed the raccoon carcass from the restaurant property.