Anna comes to the police station to see a suspect who has been accused of killing someone in a bar brawl. In the holding cells, another man, Wilkes, is lying there shivering and the suspect claims he puked on him.
Later, Anna finds out that the suspect rejected a deal. Her conversation with Peter about her chairing a homicide case is interrupted by news that Wilkes died.
Wilkes' mother and her priest want a full investigation. Laura and Antonio start at the hospital. They learn Wilkes was not on the top of the triage list, that the paramedics left him in the ambulance while they picked up another patient... and that Atwater made the arrest.
Laura and Antonio go to talk to Atwater. He is offended by the suggestion he did something wrong. He claims to have used reasonable force to subdue Wilkes and walks off.
Carerra comes with his lawyer and says he will claim Wilkes told him a cop hit him in exchange for a reduced sentence. Stone rejects this idea. Meanwhile, Wilkes and Fr Frick go to Jeffries with cell phones containing footage of the arrest. It is impossible to tell whether or not Atwater strapped Wilkes into his seat properly.
Antonio talks to Atwater who says he should have let the guy go poison people with dope. Later, Antonio disagrees with Stone that Atwater did anything wrong.
Stone wants to indict everyone involved, from the cops to the paramedics to the doctors in the hospital. Jeffries isn't sure about this strategy.
Antonio tells Voight he is doing his best to protect Atwater. Voight says if Atwater killed Wilkes, Wilkes needed killing.
Stone and Valdez run into Stone's old mentor, Robinette, who is representing Atwater. Robinette presents a motion to suspend grand jury proceedings that is sure to go nowhere. He argues in court that he had to do it this way because of prejudice against cops. The judge denies his motion and Jeffries wonders if Robinette filed the motion to find out how many people are involved in the investigation.
Atwater is indicted for murder and Jeffries orders an arrest warrant. Antonio takes Atwater and Trudy is very upset. Later, Antonio angrily confronts Stone about ruining Atwater's life but Stone reminds him he's no longer CPD.
The trial begins and a doctor claims that it took 7 to 8 hours for Wilkes to die, possibly longer. Robinette tries to sneak in that other people were made to go before a grand jury but the judge doesn't allow that.
A woman testifies that Wilkes looked hurt after her arrest. She also tells the defense attorney that her brother was unfairly arrested by a bigoted cop.
Atwater tells Antonio he feels like he is being looked at as a traitor to his people and their history of oppression.
Carerra testifies that Wilkes says Atwater hit him. Afterwards, Stone makes a deal with Robinette. Atwater gets one year in jail. When Atwater confesses, Wilkes' mother is satisfied.
Antonio is upset about Atwater. He realizes no one ever proved that Wilkes was drunk and that a drunk person couldn't have outrun Atwater. He and Laura confront Carerra and get him to confess. Stone apologizes in court to Atwater, whose conviction is vacated.
Stone gives in and calls his father after all is said and done.