The “independent” agency that determines whether police shootings in Chicago are justified repeatedly communicated with Mayor Rahm Emanuel’s administration after the October 2014 shooting of Laquan McDonald — including giving a top mayoral aide lists of other police misconduct cases being reviewed by the U.S. Justice Department and Cook County prosecutors.

As Chicagoans prepared to ring in the new year, City Hall released thousands of pages of emails about the McDonald case and other police-related matters in response to open-records requests from the Chicago Sun-Times and other news organizations.

The emails raise new questions about the scope of police misconduct in the city and whether the Independent Police Review Authority is truly walled off to investigate police-involved shootings without outside interference.

They also show City Hall had been communicating with both IPRA and the office of Cook County State’s Attorney Anita Alvarez over how to respond to media inquires about McDonald’s shooting.

Mayoral spokesman Adam Collins said Thursday that City Hall was never involved with IPRA’s investigation of McDonald.

“The mayor’s office obviously does not direct investigations, nor are any employees involved in those investigations,” Collins said.

“Coordinating with City agencies on press statements is completely separate from IPRA’s independent investigative work,” he said, adding that the state’s attorney’s office was looped into some of those discussions “as a professional courtesy.”

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Scott Ando, the former head of IPRA who was fired by Emanuel in December, concurred that the mayor’s office never interfered in the agency’s investigations.

But Ando said City Hall kept a tight grip on IPRA’s interactions with the media. “We were generally asked to clear every messaging or release to the press,” he said. “I really think if I’d been allowed to be more responsive to the questions that were posed, it would have cleared the air a lot sooner.”

Alvarez spokeswoman Sally Daly said any communications she had with Emanuel’s office were “a courtesy, nothing more.” She said she had “no recollection” of making any recommendations to mayoral aides, but if she did, it was “in the context and in the interest of the pending criminal investigation” into McDonald’s death.

McDonald’s shooting on Oct. 20, 2014, has put the city in the national spotlight, with a police dashcam video showing the 17-year-old being shot 16 times, apparently as he was walking away from two police officers.

In November of this year, Officer Jason Van Dyke was charged by Alvarez’s office with murdering McDonald — after a judge ordered the video to be released over objections from City Hall. Both Alvarez and Emanuel have come under fire for their handling of the situation.

The newly released emails show that IPRA notified the mayor’s office about more than two dozen potential police shooting and misconduct investigations about a month-and-a-half after McDonald died.

A Dec. 5, 2014, email from Ando to Janey Rountree, a top aide to the mayor on public safety issues, included a “list of cases pending review by either the SAO [state’s attorney’s office] or the USAO [U.S. attorney’s office].” It included the last names of the officers involved and noted which cases had resulted in charges.

That list revealed three pending cases by the U.S. Attorney’s office and Justice Department, one of which resulted in criminal charges: Aldo Brown, who was found guilty in federal court in October of roughing up a South Side convenience store clerk. The status of the two other cases is unclear; the U.S. attorney’s office declined to comment.

On top of that, there were 23 cases of possible police misconduct “pending Cook County State’s Attorney’s office review,” 20 of them regarding “officer-involved shootings.”

Only two cases had resulted in criminal charges as of the time of the email: Those involving Cmdr. Glenn Evans, who was recently acquitted of allegations that he put a gun in a suspect’s mouth, and Officer Dante Servin, who was acquitted of involuntary manslaughter and reckless conduct charges after he fatally shot unarmed Rekia Boyd in 2012. The status of the other 21 cases is unclear; Daly didn’t immediately have information on them.

On Feb. 11, 2015 — nearly four months after McDonald was shot — another IPRA official emailed Ando a link to a story in the online publication Slate by activist and writer Jamie Kalven that raised questions about the investigation.

“Took opportunity to give IPRA a quick shot, but focus is on PD,” that email said. “Hopefully SAO/USAO with [sic] be moving forward soon.” The last sentence seems to be a reference to the criminal investigation of Van Dyke, who wasn’t charged until after a judge ordered the dashcam video’s release.

Ando forwarded the email to Rountree and Collins in Emanuel’s office, writing: “Just a heads-up in case you have not seen this.”

The records also reveal communication among top Emanuel aides, officials with the police department, IPRA and the state’s attorney’s office over how to respond to media requests about the McDonald case.

Media coverage of the case was circulated widely among city officials, including Stephen Patton, the city’s corporation counsel; Ralph Price, a top attorney for the police department, and Lisa Schrader, Emanuel’s then-chief of staff.

In April, as Patton prepared to announce a proposed $5 million settlement with McDonald’s family, mayoral aides decided to craft a statement Ando would give to reporters.

“I think we should point any inquiries to IPRA, who could give the below statement from Scott Ando,” Collins wrote to Patton and Rountree on April 10. “Let me know what you think.”

The proposed statement stressed that IPRA conducts “an independent, civilian-led investigation” into each police shooting. “The shooting that led to Laquan McDonald’s death continues to be investigated by prosecutors, and as a result we cannot offer any further comment.”

Patton and Rountree signed off on the statement.

Collins also sought input from Daly, the Alvarez spokeswoman, who asked for time to review it. “Please don’t distribute until I am back in touch with you,” Daly wrote to Collins.

Other emails show the state’s attorney’s office initially wanted to remove the reference to prosecutors from the statement but eventually agreed to leave it in.

After a few more tweaks, Collins asked Ando’s office to email the statement to Sun-Times columnist Mary Mitchell, who was working on a story about McDonald. “Can you send her this statement from Scott?” Collins wrote.

Ando emailed the statement to Mitchell, who included it in her column on April 11.