The incident happened around 7:30 PM at 34th Street and 10th Avenue.
Witnesses said about three dozen people were inside the McDonald's when shooting started.
Sources told Eyewitness News that the investigation was drug related.
ICE agents investigating an international narcotics ring set up a buy where ICE was posing as sellers delivering drugs in the McDonald's parking lot.
After cash was paid from one suspect vehicle, sources said a second vehicle pulled up and tried to get/steal cash back after getting the drugs. The second vehicle was driving straight at the ICE agent.
Officials said the agent fired three shots in self-defense at the approaching vehicle, which then fled the scene.
No one was injured, officials said.
Other agents pursued the suspect's vehicle. It was found a few blocks away at 38th Street and 9th Avenue in Midtown.
One person was taken into custody. Authorities would not say whether it was the driver of the fleeing vehicle or someone else.