CHICAGO (CBS) — Chicago Police Cmdr. Paul Bauer gave up his life in service to the city, and his brothers and sisters in blue were paying tribute to their longtime friend Wednesday morning, a day after he was gunned down by an assailant in the Loop.

Bauer spent the last two years of his 31-year career commanding the 18th District, spanning the Streeterville, River North, Lincoln Park, Old Town, Goose Island, and Gold Coast neighborhoods.

Bauer was working near the Thompson Center downtown Tuesday afternoon, when he heard police radio calls about a suspect who had run away from tactical officers, police said. The commander spotted the suspect and engaged him in a physical confrontation, and fell down a staircase. It was at that point the suspect shot Bauer in the head, police said.

Police Department spokesman Anthony Guglielmi said the gunman was carrying a semi-automatic handgun, which was recovered, and was wearing body armor. The officers who initially tried to stop the suspect were not aware he was wearing body armor. They wanted to stop him because he matched the description of a suspect in a shooting earlier this month.

Bauer leaves behind a wife and a 13-year-old daughter. Police have asked anyone who wants to make a donation to the officer’s family to send their contribution to the Chicago Police Memorial Foundation.

“His family paid a huge debt to keep the citizens of this city safe, and we owe them,” Police Supt. Eddie Johnson said.

18th District Cmdr. Paul Bauer (Chicago Police Department)

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The suspect who shot Bauer was taken into custody, and police have said they expect to file charges by Thursday afternoon.

Because he ran toward danger and not away from it, Bauer became the first Chicago police officer shot and killed in the line of duty since 2011, when Officer Clifton Lewis was slain during an armed robbery at a convenience store.

Bauer was set to appear next week at a “Coffee With The Commander” event, a monthly meeting he held with people who live and work in his district. Instead, he will be buried after his final call on Feb. 20.

Overnight, mourners left flowers and balloons outside the 18th District station, where a black and purple flag adorned in a gold star flew at half staff in tribute to Bauer.

“I think now it’s important that we focus on Commander Paul Bauer’s legacy, and what he meant to the city of Chicago,” Johnson said.

Johnson and Mayor Rahm Emanuel both visited the station Tuesday night for an emotional roll call with the men and women reporting for their first shift without their beloved commander.

“This is like a gut punch to the Police Department. It’s a gut punch to the city. I ask you to take a moment of time, remember what they do for us, and find a place and a time to thank them,” Emanuel said.

Mayor Rahm Emanuel, Johnson, and other top police brass gathered at Police Headquarters on Wednesday to discuss the case. Emanuel and Johnson patted each other on the back, and said little to each other as they walked into the building around 10 a.m.

The mayor also delivered flowers to Bauer’s family home in Bridgeport on Wednesday.

The entire 18th District escorted Bauer’s body from Northwestern Memorial Hospital to the Cook County Medical Examiner’s office Tuesday afternoon, saluting their former commander as the ambulance arrived at the morgue.

It was a procession marked by blue police lights and the arched ladders of two fire trucks raising the American flag above the intersection of Harrison and Leavitt.

Detectives have been working through the night combing through evidence and building a case against the suspect. Police spokesman Anthony Guglielmi said detectives expect to file charges by Thursday evening. Guglielmi said detectives have been combing through a vast amount of video evidence from various cameras downtown, including police surveillance cameras, taxi cameras, social media posts, and cell phone videos from witnesses.

Officers also returned to the Thompson Center on Wednesday morning, showing commuters a photo of the suspect.

“Thank You CPD” signs adorned nearby windows, and flowers marked the spot of Bauer’s death.