The episode begins at a crime scene where during an under cove operation, the Boston homicide detectives opened fire in a warehouse. Maura’s father, Paddy Doyle is shot. He is an Irish crime boss. Cut to flashback, we see that Maura is at the warehouse talking to a man, when he draws his gun at her. in order to save his daughter, Paddy shoots the man. Paddy is also shot by him. Just then Rizzoli arrives and shoots Paddy. Maura is upset about the entire thing. Maura is furious with Rizzoli and doesn't want her help. In the present, Rizzoli tells Vince that Maura hates her and that she lost her best friend. Rizzoli tries to explain but Maura tells her that Paddy shot the guy who tried to run her over the previous day and who sent his mother to the hospital. Rizzoli tells her that the man was their suspect. She tells Maura that she didn’t know that Agent Dean was following her.
She tells Maura that Paddy shot Dean in the leg and hence she had to shoot Paddy. But Maura tells her that if Paddy wanted dean dead, Dean would have been dead. But Paddy had no such intentions. Rizzoli thinks that Maura is naïve and Maura walks away. Rizzoli tells Vince that they shouldn’t have let Maura to the undercover operation. Cut to flashback, Rizzoli wires up Maura for the sting and Maura is all excited about it; but Rizzoli looks worried. In the present, her thoughts are interrupted by Sean who takes away her gun from her as it is evidence and also informs her that Internal Affairs is going to investigating the shooting. Next, a man wearing a hood walks into a departmental store and shoots two men. Meanwhile, Rizzoli is being interrogated by Tom.
She admits that she knew that Maura is Paddy’s daughter for the past two years, but she doesn’t know what Dean was doing at the warehouse. She is then questioned about her relationship with Dean. Vince is surprised and upset to learn about it. At the hospital, Maura declares that Paddy is her biological father. Meanwhile, Vince pulls Rizzoli out of the interrogation as she needs to be at a crime scene; a homicide. Vince tells Rizzoli that she needs to train Maura as to how to play this interrogation as Maura is totally incapable of lying. Rizzoli is cross with Dean for following Maura and also for telling Internal Affairs about their sexual relationship. At the hospital, Maura asks her mother as to what she wasn’t told that she was paddy’s daughter. Angela walks in with flowers. Next, Rizzoli arrives at the departmental store, where the shooting took place.
The officer identifies the victims; Ralph, the store keeper and the other man was Officer Wally Wisniewski. Rizzoli tells Frost to check the security footage. She is unhappy to see Pike replacing Isles. Rizzoli examines the victims and the surrounding and she is sure that it wasn’t a typical robbery. She wonders whether the gunman knew that Wally was a cop. Meanwhile, Maura tells Angela that paddy kept telling her something; “Hope”. She is not sure what it meant. Maybe it is the name of her biological mother. Rizzoli arrives at the hospital to warn Maura that the Head of Internal Affairs is going to interrogate her and that she needs to answer the questions correctly as the department thinks that they are dirty cops. Maura is angry that Rizzoli isn’t sorry about shooting her father. Just then John arrives and reprimands Rizzoli as isn’t allowed to talk to Isles; Rizzoli leaves.
John asks Maura about a book that paddy kept as it might contain the names of the dirty cops. Maura isn’t aware of any such book. Paddy, who is out of sedation, warns John to stay away from isles. Rizzoli tells Angela the story of how she met Isles; it was during an undercover operation, where she was a hooker and Maura had offered her money to buy some food at a restaurant. Just then Maura arrives and tells Rizzoli that she isn’t supposed to be at her place as the investigation is still on. They leave. The next, morning Dean arrives at Rizzoli’s place with flowers. But she throws them in the bin and tells him that she is late for work. Dean tells her that it appears that there are some people in the department who are working for Paddy and it looks like Rizzoli has been set up.
Dean tells her that he might be moving to Washington. Maura is back at work and Rizzoli and Maura get into an argument. Pike informs the authorities about the cat-fight and Sean arrives and transfers Rizzoli from homicide to evidence management. Maura resigns. When Maura arrives home, she finds her entire house ransacked. She informs the department. Vince arrives with the team. He asks her if her father mentioned about a book to her. Vince orders Frankie to stay with Isles. He tells Maura to get hold of that book as it could give them th names of all the corrupt people on Paddy’s payroll. Vince tells Maura that Rizzoli didn’t know that Dean was going to be at the warehouse; he assumes that she resigned because of the fight.
But Maura tells him that she resigned because she is a mobster’s daughter and that the whole department is under investigation because of her. Meanwhile, Rizzoli tests few guns from the evidence section; a way to kill time and also have some fun. But then she notices that the bullet of the “dessert eagle” is similar to the one that was recovered from Wally’s back. This means that the gun from the evidence department was used to kill Wally. Someone from BPD killed him. Rizzoli goes to Sean to report it; it appears that Sean was waiting for the news, as they were already suspecting that Paddy had someone working for him in evidence and that is why Rizzoli was transferred so that she could keep an eye.
Sean, Frost, Vince and Rizzoli go to Wally’s house. They figure out that Wally was going to hit a big score before he got shot. it appears that Wally was supplying paddy the guns that the cops seized during their investigations. While searching for weapons in the barrels, they find John’s partner, Cliff’s body in one of the barrels. Just then John arrives. Rizzoli figures out that Wally hid the guns in Paddy’s evidence box. They find the weapons; but they also find a surveillance report and also find pictures of some girl. Rizzoli rushes to her mom and she wants to see the painting that Maura gave her. The painting is a replica of one of the photographs from the file. She goes to Maura’s mother and asks about the woman in the picture.
She tells her that it is Maura’s biological mother. Paddy was a student of hers at Harvard drawing classes. He disappeared and then after several months returned with a new born in his hands. She tells Rizzoli that paddy feared that his father would kill the baby and the mother, so he told everybody that the baby and the mother died during childbirth. Rizzoli and Angela go to the cemetery to visit the graves; and Rizzoli finds the book that Paddy had hidden under Maura’s grave. She finds a photograph in it. It is a photograph of Wally, Paddy, John and Cliff standing together. John is the dirty cop.
Sean arrives with Frost and the team and arrests John. Maura asks her father if he would have shot Rizzoli and paddy says a yes. Rizzoli takes Maura to her grave. Maura now knows why her mother never looked for her. Maura wants Rizzoli to tell Pike that she wants her chair back. Rizzoli walks away with a smile. The episode ends.