CCTV video of the weird incident shows Lilly, who is from the city of St. Paul, driving ahead of the bus in slow traffic on a snowy road.
Lilly will make his first court appearance Friday. Lilly is then seen stepping out of his auto, a black Toyota sedan, and walking back to confront the driver of the school bus.
In traffic camera video, the bus appears to be moving as Lilly is walking around, but Chief Deputy Hennepin County Attorney David Brown said the shooting appears unprovoked.
According to the complaint, the bus was trying to merge Tuesday afternoon when it apparently scraped Lilly's sedan.
"The words to describe what went on here, you nearly start running out of ways to describe this".
Video, released by the Minnesota Department of Transportation Wednesday, shows suspected gunman Kenneth Lilly pull over on the highway's shoulder, get out of his auto and walk toward the bus. As cars crept along, a Toyota pulled in front of a pickup truck and a school bus.
The complaint said Lilly was in a security guard uniform when the shooting happened. Lilly told police it was self defense.
The school bus driver, who wasn't identified, suffered a gunshot wound to the head and was expected to survive.
That's when Lilly pulled out a 9mm semi-automatic handgun and started walking toward the front of the bus, according to the criminal complaint. Surveillance footage shows Lilly then got out of his vehicle and approached the bus, before appearing to fire five shots at the school bus.
Afterward, video reportedly shows Lilly walk back toward the driver's side of the bus before calling 911.
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