By Megan Crepeau, Dan Hinkel, Jason Meisner and Jeremy GornerContact Reporters

The Chicago police investigation of the 2014 shooting death of Laquan McDonald unfolded like hundreds of others had before it, with an officer who claimed he fired in fear of his life, fellow cops who backed up his story and supervisors who quickly signed off on the case as a justifiable homicide.

The routine way the Police Department went about clearing Officer Jason Van Dyke — who now stands charged with murder in McDonald’s death — is at the heart of what critics of the department have often referred to as the code of silence.

It’s an issue that City Hall finally acknowledged amid the fallout over the McDonald scandal. But now a Cook County grand jury has alleged the code of silence is much more than just a problem — it’s criminal.

In a move some lawyers called unprecedented, the special prosecutor appointed to look into how police handled the probe into the McDonald shooting announced that three veteran officers were indicted on felony charges alleging they conspired to cover up the details of the death to protect Van Dyke.

Detective David March and patrol Officers Thomas Gaffney and Joseph Walsh, who was Van Dyke’s partner on the night of the shooting, were each charged with conspiracy, official misconduct and obstruction of justice, according to the 12-page indictment.

At an afternoon news conference, special prosecutor Patricia Brown Holmes said the three officers lied to keep the truth from independent criminal investigators.

“The indictment makes clear that it is unacceptable to obey an unofficial code of silence,” Holmes said.

Police dashcam video of Van Dyke shooting McDonald 16 times as he walked away from police while holding a knife has caused a firestorm of controversy and led to calls for major reforms of the Police Department. The accounts of several officers dramatically differed from the video.

The indictment stopped short of criminally charging department higher-ups in the alleged cover-up even though several had been recommended for firing by the city inspector general’s office for their actions.

The charges noted, however, that several undisclosed supervisors completed or approved some of the allegedly falsified police reports.

Holmes said that the grand jury probe continues but declined to say whether others could still be charged.

“We will follow all roads where they lead, and we will seek the truth,” Holmes told reporters.

The most serious charge — obstruction — carries a maximum sentence of five years in prison, prosecutors said. The three officers are scheduled to be arraigned July 10 at the Leighton Criminal Court Building.

A representative of the Fraternal Order of Police, which represents rank-and-file officers, said it had not reviewed the indictment and declined comment. It was not known if any of the three officers have criminal defense attorneys.

But in a statement emailed through a publicist Tuesday night, attorney Daniel Herbert, who represents Van Dyke, blasted the indictment as a political effort to silence witnesses in his murder case and prevent a fair trial.

“Apparently, the rule of law is trumped by special interest groups and politicians,” he said.

Herbert also shifted blame to the police command staff, saying that if the allegations are true they must be part of the conspiracy as well because “they were aware of the reports and video when they signed off on the shooting.”

Critics who have long fought to get the city to acknowledge the code of silence said Tuesday that the charges could mark a significant milestone in ongoing efforts to reform a police culture that many have labeled among the worst in the country.

“This does really send a message that you could be charged just for sitting back even if you aren’t the primary actor,” said Christopher Smith, an attorney who represented two former officers who alleged they were ostracized for trying to blow the whistle on the code of silence. “That gives good officers the excuse to come forward and say I am not going to risk my family, risk my job.”

Civil rights lawyers who pushed for a special prosecutor in the hot-button case praised the charges, even if department higher-ups weren’t indicted.

“The indictment may not go high enough as it stands right now,” said G. Flint Taylor of the People’s Law Office. “But it certainly is a historic and significant event in terms of criminally charging police officers who engage in a code of silence.”

Prosecutors have said Van Dyke was less than an hour into his overnight shift when a radio call reported the 17-year-old McDonald had been caught breaking into trucks and stealing radios in a parking lot.

Responding first to the scene in their police SUV, Gaffney and his partner said over the radio that McDonald was walking away with a knife in his hand, according to police reports. Gaffney, who was driving, tried to block McDonald’s path, but the teen popped the tire on their squad car with the knife, the reports said.

Arriving on the scene in the 4100 block of South Pulaski Road, Van Dyke and Walsh got out of their marked Chevrolet Tahoe with their guns drawn. Van Dyke took at least one step toward the teen and opened fire from about 10 feet away within seconds after exiting the squad car, prosecutors said.

The video showed McDonald’s arm jerk as he spun around and fell to the street. As he lay motionless, Van Dyke emptied his gun and was in the act of reloading when his partner kicked away the knife and told him to hold his fire, prosecutors said.

The indictment announced Tuesday alleged that March, Walsh and Gaffney each made false police reports, ignored contrary evidence and obstructed justice “to shield” Van Dyke from criminal investigation and prosecution.

Van Dyke himself — identified in the indictment only as Individual A — was an active participant in the conspiracy, the indictment alleged.

The charges alleged the officers coordinated their efforts with Van Dyke “and others known and unknown to the special grand jury,” writing virtually identical reports to make it appear that McDonald’s actions were justified.

Among the false claims cited by the officers, according to the indictment, were that McDonald injured Van Dyke; that McDonald swung his knife around and raised his arm as if to attack; and that McDonald attempted to get back up off the ground as Van Dyke continued to fire.

Despite what the video captured, one report authored by Walsh stated the footage “was viewed and found to be consistent with the accounts of all the witnesses,” the indictment charged.

The defendants also failed to interview at least three witnesses to the shooting whose accounts differed from those of officers, according to the charges. In addition, the indictment alleged the officers deleted or failed to preserve communications with each other.

“The co-conspirators understood that public airing of the events surrounding Laquan McDonald’s killing, including the video recordings, would inexorably

March was slated to testify Wednesday at a hearing in Van Dyke’s murder case.

The inspector general’s office had recommended that 11 officers — from rank-and-file patrol officers to command-level personnel — be fired for making false statements exaggerating the threat posed by McDonald.

Chicago police Chief of Detectives Eugene Roy, right, gives First Deputy Superintendent John Escalante a hug outside CPD headquarters during Escalante’s retirement sendoff on Sept. 6, 2016. (Abel Uribe / Chicago Tribune)

As a result of those recommendations, police Superintendent Eddie Johnson is seeking to fire four officers — none of whom was indicted — in addition to Van Dyke. The inspector general had recommended that both March, 58, and Walsh, 48, be fired, but both resigned before any action could be taken against them. Gaffney, 43, who remained on the force, was suspended without pay after word of his indictment Tuesday, a police spokesman said.

In a prepared statement Tuesday, Johnson said the department has “fully cooperated” with the special prosecutor and reiterated his goal to put in place new and improved policies for the department.

“The shooting of Laquan McDonald forever changed the Chicago Police Department, and I am committed to implementing policies and training to prevent an incident like this from happening again,” Johnson said.

The indictments are the latest consequence of a shooting that threw policing and politics into upheaval 19 months ago.

Mayor Rahm Emanuel fought against releasing the video for more than a year before a Cook County judge ordered it publicized in November 2015. The video touched off angry, prolonged protests, particularly among African-Americans with longstanding grievances about unfair treatment by Chicago police.

A few days after the video’s release, the U.S. Department of Justice announced it was investigating whether the Police Department had systematically violated citizens’ civil rights.

Emanuel, meanwhile, newsed changes designed to get ahead of those the federal authorities were expected to seek. He has moved to overhaul the city’s main police disciplinary agency, reworked the department’s use of force rules and expanded the use of Tasers and body cameras, among other changes.

About six months ago, the Justice Department concluded its investigation, issuing a stinging report criticizing the Police Department from top to bottom, calling Chicago’s cops badly trained, lackadaisically supervised, rarely disciplined and prone to using force, particularly against minorities.

The report also alleged that the code of silence pervades the department, protecting cops from the consequences of their actions, with little threat of discipline for officers who lie.

While the DOJ sought to enter a consent decree with the city, Emanuel backed away from his pledge to do so earlier this month, instead newsing a plan for an independent monitor to oversee changes without a judge’s supervision.

Meanwhile, the city has declined to make public Inspector General Joseph Ferguson’s report on the shooting. But thousands of pages of records of that probe obtained by the Tribune months ago raise questions about Johnson’s response to the inspector general’s findings against top command officers.

Officer Jason Van Dyke in court (Chicago Tribune)

The documents revealed that Ferguson recommended firing Chief of Detectives Eugene Roy and Deputy Chief David McNaughton in addition to numerous lower-ranking officers. Ferguson found that Roy, who had supervised the department’s investigation into McDonald’s shooting, was “incompetent in the performance of his duties.”

But Johnson never acted on the recommendation. Instead, Roy quietly stepped down as he neared the mandatory age for retirement. McNaughton, the highest-ranking officer at the scene of McDonald’s shooting, also since retired.

The records of Ferguson’s investigation also detailed a meeting at police headquarters among the top brass about 10 days after the McDonald shooting. Among those at the meeting was Johnson, then a deputy chief who was later promoted to superintendent after former Superintendent Garry McCarthy was fired days after the release of the video.

Of that meeting, Lt. Osvaldo Valdez told the inspector general’s office, “Everyone agreed that Officer Van Dyke used the force necessary to eliminate the threat, and that’s pretty much it.”

Through a spokesman, Johnson has disputed that characterization of the meeting but said little more in public about the matter since it was reported by the Tribune in December.

In his interviews with the inspector general’s office, March said that the department leadership’s stance on the shooting shifted after the video was released and that no one had “voiced any reservations or concerns” to him at the time of his investigation.

“I was informed the entire command staff concurred with the findings and conclusions of my investigation,” he told investigators. He also defended his work and the accuracy of the statements of other officers, as well as McDonald’s shooting.

“Is it really being suggested that the police should have done nothing and permitted Laquan McDonald to continue on his way and not stop him?” March asked.

The inspector general also found that Walsh filed false department reports and made inaccurate statements to detectives and disciplinary investigators. Ferguson noted that Walsh told detectives that McDonald advanced on officers, swung the knife and tried to get up as Van Dyke pelted him with bullets.

He also faulted Walsh for failing to ensure that his police vehicle’s video and audio recording system was functioning; the car Walsh rode in that night failed to record audio, and its microphone was not connected to a charger.