Sgt. Isaac Lambert was assigned to investigate the August 2017 shooting of Ricardo "Ricky" Hayes by Sgt. Khalil Muhammad who was off duty at the time. Hayes, who is black, was 18 when the shooting happened.
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In his lawsuit filed electronically in Cook County Circuit Court, Lambert says his bosses dumped him from the detective division last month, days after he refused to change the report, the Chicago Tribune reported.
"They wanted me to have some reports changed to fit the narrative that they wanted," Lambert said at a press conference Monday. "They wanted this kid to be charged with aggravated assault, and the elements just weren't there."
The lawsuit is against the city of Chicago. City officials could not be reached for comment Monday.
Surveillance video was released in October by the Civilian Office of Police Accountability that shows Muhammad shooting the unarmed Hayes, contradicting an initial police description of an armed confrontation. The grainy video was from a security camera on a home on Chicago's South Side.
Hayes' caretaker had called police to say Hayes had wandered away from home and that he has developmental disabilities.
Before the shooting, Hayes can be seen running along the sidewalk then stopping. Muhammad pulls up alongside, with parked cars between them. Hayes takes a few steps toward him and shoots Hayes in the arm and chest. Hayes turns and runs, despite his wounds.
In a federal lawsuit filed on Hayes' behalf, Muhammad has denied any wrongdoing, court records show. He was placed indefinitely on paid desk duty after the shooting.
Lambert's lawsuit alleges Muhammad called Hayes over to his personal vehicle after spotting him "skipping and running" near his residence about 5 a.m. Hayes, who was about 20 feet (6 meters) from the vehicle, took about four steps toward Muhammad's vehicle when the sergeant opened fire.
Video from the home security camera shows Hayes never did anything to threaten Muhammad or give him any reason to open fire, Lambert alleges.
Later, at Area South detective headquarters, Muhammad "was not able to provide a coherent or believable explanation" for why he shot Hayes, according to Lambert's lawsuit.
WLS-TV contributed to this report.