The scene opens with Kate Beckett getting into the hospital and Lanie is trying to keep Kate alive by performing chest compressions. The doctors tell her that they have it from here and that she can get off. They wheel her in the Emergency Room and Josh, Kate’s boyfriend is there as one of the doctors. Despite being in a compromising situation, he works to keep Kate alive. Castle and Lanie go in the hallway to find Ryan and Esposito there. They ask how she is doing and they tell that they don’t know. Martha and Alexis come in the hospital and console Castle. Josh is relieved from an unbiased doctor and he goes in the hall to find Castle there. He pushes him and says that this is all Castle’s fault for pushing Kate into looking for her mother’s killer. Everyone gets into a screaming match and Jim, Kate’s father, comes up and tells everyone to calm down. The doctor comes out and says that Kate is coming out of surgery and that they don’t know yet if she is going to pull through.
At the station, Ryan and Esposito look at who could have been involved in the shooting and the rifle was retrieved, but no gunman. Esposito says that the gun belongs to a Martin Holst, but he was killed in action 7 years ago. Castle doesn’t understand why people who killed Kate’s mother are still going after Kate even after Montgomery sacrificed himself to protect her. Meanwhile, a man opens a mailbox with the last name “Smith” and pulls out the folder that Montgomery sent at the end of the episode. Castle gets a call saying that Kate is out of surgery. He goes to the hospital with flowers to find Josh there too. Josh leaves and gives Castle a dirty look. Kate tells Castle that she doesn’t remember anything after getting shot. He tells her that is alright. Kate brings up the hanger situation with Montgomery and Lockwood and tells Castle that he should have let her go in there. He says that they would have killed her, but she doesn’t think so. She tells Castle that she wants a break from him and that she will call him when she is ready to continue their friendship. He says that he is alright with that, but it is clear that he is not. The mystery man goes through the files that Montgomery sent and calls the Congressional Office.
Kate walks into the station after 3 months of resting. She is welcomed back with open arms and she asks if they found anything. She asks about the Groundskeeper at the funeral. However, there were neither hits on him nor the fingerprints on the gun. Ryan and Esposito say that Castle has some theory and ask if she has spoken to him. She says that she hasn’t and that it has been 3 months since she has spoken to him. Ryan says that they have a new Captain on the squad and says that her name is Victoria Gates and she is tough as nails. Castle had leads, but she shut him down and told him to leave and shut down the investigation. Kate goes in Gate’s office and says that she is back on active duty and asks for her gun, but she tells that she needs to re-qualify first. Kate asks about her case and Gates tells her that it is over because it is cold now. However, Cate tells Gates that she wasn’t working on it and that is why there has been no success. Gates denies Kate’s request to work on her own case. Kate goes up to Ryan and Esposito and tells them that they need to get the information and they tell her that they can’t let Gates know or they all are going to get fired. Ryan gets another homicide case and Ryan and Esposito go to Sonja Gilbert’s home. She has been murdered and Lanie brings the detectives up to speed as to what they think happened. The boyfriend, Dale Landers, was the last to leave.
Meanwhile, Kate goes up to Castle at the book signing of his new book and he is not happy to see her. He walks away and says that he waited 3 months and no answer. She tells that she needed some time to work things. She tells him that she and Josh broke up. Kate says that something inside of her changed and that she built a wall that stops her from getting serious with anyone. She says that she isn’t going to be able to have one until she puts the case to rest. Castle offers his help to work with her. He says that the warehouse fire that happened had files about her mother, but faulty wiring took care of that. Kate asks if he double checked it and he says that there were none. She tells Castle that Gates won’t let him back in the precinct, but he says that he will take care of working with Kate again.
They go into the station where Gates gets a call from the Mayor demanding that Castle work with Kate. Gates tells that if he messes up anything, she will take him down. Kate is impressed that Castle showed Gates up in front on the Mayor. Kate gets her gun back after re-qualifying perfect. They look at the murder board of Sonja Gilbert. Ryan brings them up to speed, but Kate talks about the Bank that Castle looked up. They tell that Rod Halstead was the fire chief that wrote the report. She says that they need to talk to him. Gates tells Ryan and Esposito and Kate to get to Dale’s bandmate’s house because Dale has been spotted. All of them arrive and bust in. Dale runs for it and Kate goes after him. He points a gun at Kate and she freezes. Ryan and Esposito tell Dale to get on the ground. Dale says that it isn’t his gun and Kate is shaking as she puts her gun away. At the station, Castle asks if she wants to talk about it and she brushes it off and says that she is going to go find out who burned down the warehouse. Ryan and Esposito talk to Dale and he claims that he wasn’t the one who killed Sonja.
They talk to Gates and say that Mitch, Dale’s bandmate says that Dale was looking for money to get out of town. Gates asks where Castle and Kate went off to and they lie and say that they are going after another lead. Castle and Kate go to Rod and he says that there are no mistakes, but Kate doesn’t believe him. She asks who paid him to keep information. Rod tells Kate to get out of the station. Kate says that she is going to catch the person. She calls Esposito and says that she needs all the files on Halstead. At the station, Ryan says that it makes no sense for Dale to hang around six hours later after killing Sonja. At Kate’s place, Kate and Castle go through the record and Castle suggests that the fire was no accident. Kate gets emotional and says that everyone is gone who knew about this and she needs it to happen. Castle gets home and Alexis says that they missed him for dinner. She says that Castle told her that he wasn’t going back. The mystery man calls Castle and says that he needs to talk. Later, Castle tells Martha that Kate is safe only if she stays away from the case and if she doesn’t stop, they will kill her. Martha tells him to tell Kate, but he says that she will go after them with blinders on. Alexis tells Castle to grow up and stop pretending before he gets himself killed or them.
The next day, Castle comes in to find Kate looking at pictures of the warehouse. He says that Kate needs to stop so that she doesn’t get over absorbed. Kate says that she is fine and Castle says that she needs to get her bearings and says that they are going to make the people pay in time. He says that she can bring a family peace by solving the murder of Sonja. Ryan and Esposito tell that both Sonja and Dale were drugged. Kate suggests that the real killer was there the entire time. They get to the apartment and find that under the bed, there is an outline where the blood didn’t drip. They find fingerprints. They search the database and find that it is Dale’s bandmate, Mitch Yansee. They get to the loft and Mitch comes up behind Kate and aims a shotgun on her. Castle tells that she’s got this. Kate gets her confidence and makes Mitch put down his shotgun. Castle tells Gates that Mitch was the killer because he was having an affair with Sonja and that he killed them. Castle asks how solving the case felt. She says that it wasn’t enough, but it is enough. Castle gets home and tells Alexis that she is right about him needing to grow up. He says that he needs to be there for Kate. She asks if it is enough and he says that it is for now. Castle goes in his office and pulls up a case board. The episode ends with Kate meeting with the psychiatrist and says that she lied and says that she remembers everything.