Lt. Flynn attends an AA meeting, and afterward is greeted by a young man presumably at his first meeting. He listens intently to the man's story and offers to buy him coffee and continue their conversation.
After the man turns away the offer, Flynn leaves the meeting and is attacked by an assailant in the parking lot. After putting up quite a struggle, Flynn is able to reach his gun and shoots two rounds, hitting his attacker before he flees. Flynn calls Captain Raydor to report the officer-involved incident. Determined to give his version of events before taken to the hospital, Flynn gives Raydor all the information she needs to put out a hospital alert to look for the missing assailant.
Flynn wakes up in the hospital to Chief Johnson and Provenza (holding an "It's a Girl" balloon) and shares the details of the attack. Raydor comes in with evidence and a photo of a man found dead on the side of the road in San Bernadino. She goes on to say that if Flynn identifies the victim at that point, the case becomes hers, but if he doesn't the case will be investigated by major crimes. Flynn holds back his positive identification and major crimes gets the case.
Sgt. Gabriel and Provenza go to the house of "dead Bobby Harris" to find evidence, and locate $37,000 in cash dated from the 90s. Knowing he wasn't in need of cash, they therefore determined the man had been paid to kill Flynn. Brenda asks Fritz for information about AA meetings, but he turns her down and offers a trade for information. She gets back in bed and Fritz tells her that the rumor is she will soon be offered Chief Pope's position. Brenda realizes that's why Raydor let major crimes take the case.
Flynn defies doctor's orders and comes to work to help with the case. A picture of Rick Zumen, a coke dealer whom Flynn put away for two murders in 1996 is flashed on the screen, and it's discovered Dead Bob was in the same prison facility as Rick Zumen. Zumen has a vendetta against Flynn because he told him he would make it his life's work to prove he had killed an FBI informant.
Flynn and Chief Johnson meet with Zumen and tell him he is their number one suspect in the attempted murder of Flynn. He doesn't recognize the photo of Dead Bob, and asks what his motive would be..."other than the fact that he intimidated a witness, manipulated evidence and perjured himself" to have him sentenced to death. Zumen is on appeal after his former bookkeeper found God and withdrew her statements against him. Brenda grabs him by the face and tells him that she knows he's been looking into Flynn's personal life and due to that he will eventually tell her everything he wants to know.
Raydor arrives and admits she knew about an investigation into Flynn for witness intimidation. His many charges, although exonerated, give credence to Zumen's case. If Chief Johnson can prove the witness, Floria Stenzel, was paid off to overturn her testimony, then the case against Flynn will be over. Brenda and Provenza ask Chief Pope why they didn't know about the case and ask for a protective detail (against themselves) for the witness.
The team then sets about making Floria afraid for her safety so that she goes to the police for protection and when she gets to the station she is shown the $30,000 found in her house and she gives them the information they need - she was paid to change her testimony. Floria has the cell phone number of the man, Jeff, who paid her off. Brenda dresses up as Floria to meet him. It's the young man from the AA meeting. He had paid someone to attack Flynn. Chief Johnson pretends to bribe him since she knows he drove around with Dead Bob's body and dumped it by the side of the road. Jeff then leads them to the money, thereby tying Jeff, Dead Bob and Zumen together.
Raydor has the evidence she needs to drop the case against Flynn and Brenda goes back to Zumen with information on Jeff Darby. She proves they were close, and he admits to a physical relationship. Brenda "bets" him $400,000 that she can get him to tell her everything she wants to know. Zumen says that it's not illegal to hide money in a storage locker, and Brenda tells him it was marked money was from an FBI informant who has gone missing. He spends the rest of his life on death row and Flynn is vindicated. Raydor delivers his file to Brenda, and they decide to have lunch to learn how to better share information. The episode ends with Fritz telling Brenda she needs to figure out what she wants because she will soon be offered the job of Assistant Chief of Police.