Chicago police form a line to prevent protestors from entering an expressway on Tuesday, Nov. 24, 2015, in Chicago. White Officer Jason Van Dyke, who shot Laquan McDonald 16 times last year, was charged with first-degree murder hours before the city released a video of the killing. (Paul Beaty/AP Photo)

In the late 1980s, when journalist John Conroy first began investigating claims that a decorated Chicago police detective named Jon Burge was torturing criminal suspects on the South Side, he found it virtually impossible to get his hands on police misconduct records without a court order.

Conroy’s coverage of the Burge torture allegations in the Chicago Reader, the city’s alt-weekly, would lead to the detective’s dismissal from the force in 1993 — following an internal Police Department review determining that he had tortured suspects — and Burge’s eventual conviction in 2010 on felony charges of perjury and obstruction of justice for denying his use of torture under oath. (He was released in 2014 and is now living in Florida on a police pension).

Now, 25 years after publishing the first of many articles exposing Burge’s tangled web of abuse and secrecy — as the U.S. Justice Department sets out to investigate allegations of systemic violence and racism going unpunished within the Chicago Police Department — Conroy is part of a fight to stop the Chicago Police Department from destroying decades' worth of what he says are documents that could free scores of innocent prisoners.

Specifically at risk are complaints and records relating to every investigation of police misconduct dating back to 1967. The trove of data was requested by the Chicago Tribune and Sun-Times under the Freedom of Information Act last year, following an Illinois judge’s ruling in favor of journalist Jamie Kalven in another FOIA case holding that the public has a right to know which police officers have been accused of misconduct and whether and how they were disciplined.

Former Chicago Police Lt. Jon Burge arrives at the federal building in Chicago, Ill., on June 8, 2010. (Charles Rex Arbogast/AP Photo)

Somewhat unexpectedly, the city agreed to hand over the records, but the Chicago Fraternal Order of Police wasn't having it, arguing that the union’s contract allows complaints against officers to be destroyed after five years.

The police union received a temporary injunction to prevent the release of any records from before 2011 until a union arbitrator could weigh in on the matter. Last month, a labor arbitrator sided with the Chicago Police Benevolent & Protective Association, the union representing high-ranking officers, ordering that the files of lieutenants, captains and sergeants be “purged” from any city government online databases.

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Now, as the Chicago Police Department prepares to have its practices scrutinized by federal investigators, another arbitrator is expected to make a similar ruling in the FOP’s case, which calls for the destruction of decades’ worth of potentially incriminating misconduct reports.

“There are people who have been in prison for more than 20 years who may have been wrongfully convicted, who have been wrongfully convicted,” Conroy told Yahoo News, referring to the 100-plus convicts who say they were sent to prison based on a coerced confession obtained through abuse by Burge or one of the detectives under his command. Their cases are awaiting review by the Illinois Torture Inquiry and Relief Commission, created in 2009 to determine which Burge-related cases merit a retrial.

“Were all these old files destroyed, we would be consigning innocent people to prison, many of them for decades more and perhaps the rest of their lives,” Conroy continued. “This would be criminal.”

Jamie Kalven’s attorney, Craig Futterman, who serves on the commission, said justice for the victims of Burge and his associates rests on the decades’ worth of misconduct reports the police want to destroy.

“What’s at stake? Police accountability,” Futterman said. “People sitting in prison who claim that they’ve been tortured, officers who’ve been accused of abuse who are still out there. All evidence or documentation of that is at risk of being destroyed forever.”

FOP president Dean Angelo did not return multiple requests for comment on this story.

Chicago police Officer Jason Van Dyke arrives for a court hearing at the Leighton Criminal Court Building in Chicago on Friday, Dec. 18, 2015. (Zbigniew Bzdak/Pool Chicago Tribune via AP)

Last week week, Officer Jason Van Dyke was formally indicted on six murder charges and one count of misconduct for the shooting death of 17-year-old Laquan McDonald, the grisly video of which sparked citywide protests, accusations of a cover-up and calls for the mayor’s resignation when it was released by court order just before Thanksgiving this year.

McDonald was one of the 409 people who’ve been shot by Chicago police officers since 2007 — 127 of them fatally — according to the city’s Independent Police Review Authority.

According to the records Kalven has managed to obtain (he’s published 56,000 police complaints from the Chicago Police Department spanning the years from 2002 to 2008 and 2011 to 2015 in an online database at the Invisible Institute), before Van Dyke was arrested for killing McDonald, he had been the subject of at least 20 misconduct complaints, none of which resulted in discipline.

Civil rights attorney Flint Taylor argues that records like Van Dyke’s are proof of the need for public access to misconduct reports. It shows, Taylor says, that the city's history of police violence does not necessarily start and stop with Burge and his so-called “Midnight Crew.”

Taylor, who has represented several Burge torture victims and others who claim to have been wrongly convicted and sent to prison or death row, said he and other civil rights lawyers have been engaged in “a running battle for decades” against what he called the Chicago FOP’s “unremitting attack on transparency.”

SLIDESHOW – Protests in Chicago over police shooting of black teen

CLICK IMAGE for slideshow: demonstrators continue to protest the fatal police shooting of Laquan McDonald December 18, 2015 in Chicago, Ill. (Joshua Lott/Getty Images)

This October, Taylor filed a lawsuit on behalf of three men who say they were wrongfully imprisoned after being “physically and psychologically” abused into providing false confessions by Chicago police officers at the Homan Square interrogation facility. An explosive investigation published by the Guardian newspaper in February describes Homan Square as more like a CIA “black site” than a police precinct, a secretive warehouse where suspects are allegedly subjected to beatings and prolonged shackling, are denied the right to legal counsel and are not booked in any official CPD databases.

Taylor’s lawsuit — the third of its kind relating to alleged abuses at Homan Square since the Guardian published the first in its series of exposes — alleges that clients Atheris Mann, Jessie Patrick and Deanda Wilson were denied access to water, food and bathrooms, as well as the right to contact their families or an attorney, while being interrogated at the facility. Wilson says an officer held a knife to his throat. Mann and Patrick, Mann’s stepson, say they were subjected to full strip searches, shackled to a bench and berated with a series of threats and racial slurs.

The Chicago Police Department has repeatedly denied the allegations made about Homan Square in the Guardian and elsewhere, maintaining that suspects interviewed at the West Side facility are treated no differently than anyone else arrested by Chicago police. Department representatives denied an invitation to testify at a Cook County Commission hearing about the alleged abuses at Homan Square last week.

Taylor said he was disappointed when, in response to a reporter’s question at a press conference last week, Attorney General Loretta Lynch said the Justice Department’s forthcoming investigation of the Chicago Police Department would not include the recent allegations of unlawful detention at Homan Square.

While the claims of abuse at the facility “are extremely important, they’re not at this time in the purview of our investigation,” Lynch said. “At this point in time it is a use of force investigation.”

Attorney General Loretta Lynch, right, and U.S. Attorney in Chicago Zachary Fardon, left, speaks during a conference at the Justice Department in Washington, Monday, Dec. 7, 2015, about an investigation into the patterns and practices of the Chicago Police Department after recent protests over a video showing a white Chicago police officer shooting a black teenager 16 times. (Susan Walsh/AP Photo)

For Taylor and other civil rights attorneys who had previously called on the U.S. Justice Department to investigate unlawful patterns and practices within the Chicago Police Department, in 1999 and again in 2010, to no avail, last week’s announcement that the DOJ would finally be investigating the department was long overdue. Still, Taylor said, the investigation’s apparent narrow scope and lack of interest — at least initially — in the kinds of extensive allegations that have arisen from Homan Square, leaves him with only “guarded optimism” about the DOJ’s ability to effectively weed out systemic wrongdoing and enforce accountability.

“You can’t look at a city in pieces like that,” Taylor said. “You can't look at the police department and its misconduct and compartmentalize. You have to look at it across the board in order to have any kind of meaningful reform.”

Taylor and others, including Craig Futterman and attorneys with Northwestern University’s Roderick and Solange MacArthur Justice Center — where John Conroy now works as an investigator — followed up on Lynch’s announcement with a complaint to the Justice Department. The complaint applauds the DOJ probe and urges investigators to specifically “examine the failures of the disciplinary system to respond seriously to not only shootings but all acts of police brutality in general.”

The Justice Department also declined to comment on whether it plans to intervene in the police unions’ effort to destroy the misconduct records that Conroy, Taylor and other reform advocates are seeking.

At this point, Futterman said, there’s not really anything else the public or the press can do to obtain those records. Earlier this month, he and Kalven called on Illinois Circuit Court Judge Patrick Flynn to overturn the union arbitrator’s decision, arguing that the records are not a labor issue but a matter of public concern.

Flynn declined, but did issue an emergency order requiring the Chicago police to notify activists and press before destroying misconduct records.

“They have to give us two weeks' notice, but that doesn't mean we can stop it,” Futterman said. “We will just know.”

“The best thing that can be done would be for the Illinois Legislature to act and simply amend the Local Records Act to say government agencies shall not destroy records related to complaints of police misconduct and their investigations,” Futterman said.

A barricade blocks a sidewalk outside an alleged police warehouse that has been reported to house a detention and interrogation facility known as Homan Square in Chicago, Ill., on Feb. 28, 2015. (Tannen Maury/EPA/Corbis)

But, he added, “it's critically important that they act before the records are gone.” So far, no bills have been proposed to make this change.

In the meantime, the city could appeal the first arbitrator’s decision within 90 days of the ruling but, with just over 60 days left, has not indicated any plans to do so.

A spokesperson for the city did not respond to repeated requests for comment on whether Mayor Rahm Emanuel’s office plans to take legal action to prevent these police misconduct records from being destroyed.

“It’s ultimately the mayor’s call,” Futterman said. “The clock is ticking.”