The 31-year-old was charged with second-degree attempted murder and second-degree assault with a risky weapon.
Prosecutors say the bus driver was trying to navigate the Interstate 35W-Interstate 94 interchange in poor weather when the bus apparently scraped Lilly's auto. An 8-year-old child also on the bus was not injured.
According to a criminal complaint, Minneapolis police officers were called to a shooting Tuesday on Interstate 35W near Chicago Avenue. Traffic was moving slow at the time due to heavy snowfall.
The complaint does not elaborate as to why Lilly might have feared for his safety. Shortly afterwards, he begins shooting into the windshield with what authorities say was a 9mm semiautomatic handgun.
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The school bus driver, whose identity has not been made public, was rushed to hospital.
Officers recovered five discharged cartridge casings from the scene.
"The first thing we would like to do is express our concern to the bus driver and the child", Plunkett said after court.
"The actions of Mr. Lilly were outrageous and it was sheer luck that neither the bus driver nor the little girl were killed", Hennepin County Attorney Mike Freeman said in a statement Thursday.
Court records show he is being represented by St. Paul attorneys Charles Clippert and Thomas Plunkett.
He said police are still investigating the shooting, "and if we can add aggravating circumstances for a longer sentence, should we prove him guilty, we will do so".