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The fallout in Chicago continues as Mayor Emanuel pledges change

The Justice Department launched an investigation into the city's police just as a second officer was cleared in a separate, caught-on-camera killing.

The city of Chicago is on fire. And day by day, the kindling of police-involved killings and alleged cover-ups is piling higher.

U.S. Attorney General Loretta Lynch on Monday announced a federal investigation into the Chicago Police Department amid ongoing fallout from video released last week of a police officer shooting a young black man, Laquan McDonald, 16 times. That officer, Jason Van Dyke, was charged with murder.

“The city needs answers in what happened to Laquan McDonald, his tragic and avoidable death. But this is bigger than one incident."'

But the ripples continue to shake the frame of Mayor Rahm Emaneul’s administration, the police department, and the broader law enforcement apparatus in the city.

Last week Emanuel fired Police Superintendent Garry McCarthy, and on Monday, ahead of Lynch’s announcement that the DOJ would be conducting a far-reaching investigation into the patterns and practices of the Chicago PD, Emanuel also fired the head of Chicago’s Independent Police Review Authority, which investigates allegations of police misconduct. At the same time, the police department’s head of detectives resigned.

News of a federal investigation was welcome news for many as the trust gap between the city’s most aggrieved communities and the administration and police has grown depressingly wide. Emanuel, who just a week ago appeared adamant that a Justice Department investigation was not warranted or wanted, on Monday enthusiastically embraced the intervention.

“We are going to welcome this investigation, we are going to cooperate with it and it’s in our long-term interests,” Emanuel said on Monday afternoon. “The city needs answers in what happened to Laquan McDonald, his tragic and avoidable death. But this is bigger than one incident."

RELATED: When cops kill, are murder charges enough?

It has been a tumultuous couple of weeks in Chicago and for this mayor, in the first year of his second term, one of pain, protests and no doubt, political posturing.

Just five days ago Emanuel said the DOJ would be unhelpful in getting to the bottom of the issues in the McDonald case and in the police department; now he’s supporting their efforts. After the video of McDonald’s killing was released, he defended former Superintendent McCarthy -- then he fired him. Just a week ago, Emanuel described Van Dyke as a rogue officer who didn’t represent the department; now he’s saying there are deep systemic and cultural problems in the department that have lingered for far too long.

Emanuel has appointed a new task force to take a deep dive into the issues facing the police department and will lean on that group to offer a report and recommendations. On Monday, he said the three main bodies responsible for police oversight – police internal affairs, IPRA and the police commission— have not worked to adequately address the accountability of officers who’ve done wrong.

In his press conference on Monday, as reporters pelted him questions and skepticism over his handling of this moment, Emanuel said he takes full responsibility for what has gone down not only on his watch, but also in the future. “I’m taking responsibility for what happened and I’m taking responsibility for fixing it,” he said.

As he spoke, protesters were already gathered outside of City Hall.

RELATED: DOJ to probe Chicago Police after Laquan McDonald death

Allegations of a cover-up in the McDonald case span from the mayor’s office to the police department, and finally to the office of Cook County State’s Attorney Anita Alvarez. Alvarez charged Van Dyke with murder a full 13 months after the October 2014 killing and only after a county judge ordered the release of video. That footage completely contradicts the initial police accounts that say McDonald was moving toward officers when he was shot. It is clear in the video that McDonald was moving away from officers, not toward them.

New reports have surfaced that suggest that officers on the scene the night of the McDonald killing fabricated their official post-incident reports. In at least five of those reports, officers offered versions of the events that echo Van Dyke's -- that McDonald raised his knife and came toward the officer, that Van Dyke fired out of fear and that after McDonald was struck down he appeared to be trying to get up.

At least 13 of the 16 shots fired into McDonald struck him after he’d been knocked to the ground.

“When community members feel that they are not receiving that kind of policing, when they feel ignored, let down or mistreated by public safety officials, there are profound consequences for the well-being of their communities, there are profound consequences for the rule of law and for the countless law enforcement officers who strive to fulfill their duties with professionalism and integrity,” Lynch said.

Hours after Lynch’s announcement, Alvarez released video footage in a second police-involved killing that took place just days before McDonald’s. This one shows an officer shooting Ronald Johnson, 17, in the back as he appears to run away from approaching officers. Johnson was armed with a gun, police and Alvarez say. Officer George Hernandez fired five shots at a fleeing Johnson, striking him twice.

RELATED: Why did it take 13 months?

After releasing the video, Alvarez announced that her office would not charge Hernandez in Johnson’s death. And in an extraordinary exhibition, Johnson detailed much of the evidence she used to arrive at her decision not to charge the officer, including several audio recordings of 911 calls, digitally enhanced video of the killing, and witness testimony. She said he resisted arrest, was armed and posed an immediate dange,r and as such, lethal force was warranted.

“Based upon an objective review of the evidence and the law, we have determined that the prosecution could not establish beyond a reasonable doubt that the actions of Officer Hernandez were not reasonable and permissible under the laws of the state of Illinois,” Alvarez said.

In the video, Johnson is seen running into frame, across the street and toward a park, when three officers hop from an unmarked car with their guns in hand, firing as Johnson stumbles back out of frame.

Alvarez said that Johnson was in an area where residents had called 911 to report gunfire not long before he encountered police. She said that earlier in the night, Johnson was sitting in the backseat of a car that was involved in an earlier shooting, having its back window shattered by gunfire. Johnson and the others in the car circled back to the scene where the car had been shot. That’s around the time police, responding to reports of gunfire, came across Johnson.

Last year, police said that Hernandez shot Johnson after he lifted a handgun over his shoulder and aimed it at police. The newly released video is dark and grainy, and does appear to show Johnson lifting his arms at all. Seeing an object in his hand at all is difficult given the quality of the video.

RELATED: Rahm Emanuel buckles on new police shooting video as family alleges cover-up

About 30 minutes before Alvarez’s press conference, Anthony Guglielmi, a police spokesman, said that Johnson was shot after aiming his gun at officers. Guglielmi said “[Johnson] leads them on a brief foot chase, the gun is in his right hand and after numerous commands to drop the gun he doesn’t drop it.”

“The reason police opened fire,” he said, “you see him running and he has the barrel of the gun pointed behind him in the direction that the cops are chasing. Once they see the barrel of the gun, they opened fire.”

“This is a cover-up from the beginning."'

Alvarez, during her press conference, refuted those allegations, that Johnson aimed his gun behind him as he ran. But she did say that because that is a legitimate fear police were still justified in using lethal force. She even went as far as to show video of an unrelated case in which a fleeing suspect pointed a gun behind him as he ran and fired at a police officer who was chasing him. The officer was struck by a bullet and limped across the scene.

Michael Oppenheimer, a lawyer for Johnson’s family, described Alvarez’s press conference as “a joke,” a 25-minute infomercial, and a game of three-card Monte.

“This is a cover-up from the beginning,” Oppenheimer said during a news conference of his own.

Oppenheimer criticized Alvarez for saying that she leaned heavily on the investigation into the shooting by IPRA, whose integrity and independence has been called into question in the wake of the McDonald and Johnson investigations. He said they had not interviewed several key witnesses including police officers and said that investigators manipulated the testimony of a witness referred to several times by Alvarez as Witness A, whom Oppenheimer said in a deposition that he was coerced by police investigators to say that he had seen and heard a gun in Johnson’s hand not long before the police killed him.

Oppenheimer also noted that in a six-hour deposition that Officer Hernandez sat for just a month ago, Hernandez told Oppenheimer that he had not been contacted by Alvarez’s office. The lawyer said that the fact that Hernandez sat for six hours and spoke openly and freely and intimated that he doubted that he’d be indicted spoke volumes about the manner in which the State’s Attorney was investigating this case.

"How in the world does he know he's not going to be indicted unless someone in Alvarez's office told him?" the attorney said.