Kate is nervous about her first day as Captain. Rick calms her nerves with a giant cupcake which contains a box with a gorgeous bracelet with the word “Always” engraved on the inside. Before Beckett leaves she gets a phone call she claims is a telemarketer. She says she has to leave to get to a meeting at 1PP and Castle heads to his P.I. Office.
The P.I. office has been completely redone to be more high tech. It even has a secret room. When Castle arrives he finds Alexis there. He once asked her to meet his contractor at the office for him and she began working cases all on her own without ever telling her father. So far, she’s solved four. She also forged Castle’s signature to make sure she gets college credit for her work.
Ryan tells Esposito that they just found out that he and Jenny are having another baby. It’s great but he’s stressing out over money and thinks he and Javi need to be thinking about moving up in their careers the same way Beckett and Gates (now Deputy Chiefs) are going.
Esposito and Ryan call Castle because they can’t get in touch with Beckett who is supposedly in meetings. Castle meets them at a mass murder scene at a theater where they stumble upon a pool of blood that has a bracelet in it. It’s the bracelet that Rick gave Kate that morning. Lanie confirms that the blood is Beckett’s and Espo calls Gates, who says Beckett had no meetings at 1PP today.
With Beckett missing, Castle, Esposito and Ryan head to an apartment rented by one of the dead men from the murder scene. They run into Hayley Shipton, who beats up Castle before being captured. She’s an independent security specialist working on a case tracking fake IDs. She won’t tell them anything more than that even when Castle begs her for help.
The boys figure out that Beckett and a man ended up at a dry cleaners. Beckett was wounded and stitched herself up. The man was ill but it was clear that Beckett was in charge. Rick wonders what she’s been hiding from him.
Later Hayley shows up at the P.I. office where she gives Alexis pointers on manipulating men in order to get information. She offers Castle her help as long as he doesn’t get the police involved. Their investigation leads to a storage unit filled with high tech weapons. A female assassin finds them and she and Hayley fight. The assassin runs off but Hayley ends up with some sort of substance on her arm. She sends it to a lab for analysis. Castle informs Esposito and Ryan, making Hayley angry.
Alexis figures out that the sick man that Beckett is with is diabetic and that he needs insulin. She tracks down a crank ambulance call and finds that Beckett stole insulin from the ambulance while no one was looking. From surveillance video she finds the cab number Beckett and the man entered. The cab later went to the prison where former Senator Bracken is incarcerated.
Castle heads to the prison to see Bracken who won’t tell him anything except that he was foolish to think that Beckett would ever be happy simply being Mrs. Castle and that she may have fallen back down the rabbit hole into an investigation. Leaving the prison, the female assassin abducts Castle and destroys his cell phone.
Alexis, who has been tracking her dad’s phone, realizes that something is very wrong and goes to Ryan and Esposito. They pick up Hayley who stonewalls them but seems to soften when Alexis begs her for help. She tells them about the assassin she fought with and the substance she had analyzed. It’s creosote which is used in making railroad ties. Ryan and Esposito begin to track it down.
Castle is being held in a warehouse filled with railroad ties. The female assassin and a male assassin want to know where Beckett is and don’t believe him when he says he doesn’t know. They put a bag full of spiders over his head. When they are finally convinced he knows nothing, they plan to shoot him but Castle has broken through his restraints. He fights back and makes a run for it but they catch him and are about to shoot him when Beckett shows up. She wounds the female assassin while the male assassin gets away. Castle, who is dizzy after taking a fall during the fight, asks where she’s been, why she hasn’t called and why she’s shutting him out but Beckett runs off as Esposito and Ryan arrive.
From a sketch of the sick man Beckett is with, they figure out his name is Vikram Singh and he’s an technical analyst for the Attorney General’s office in Washington, D.C., the same office that Beckett worked in two years ago. Turns out that Beckett’s old partner, Agent McCord was recently killed in a car accident with the three other members of her team and a fourth member was murdered in a night club.
Esposito, Ryan, and Castle bring the female assassin back to the 12th precinct but she stonewalls them, only telling him that more than one team is after Beckett. As the uniformed officers are bringing her down to booking, she breaks free, grabs their weapons, shoots LT and then opens fire on the entire precinct. Castle protects Alexis while Ryan and Esposito take the assassin down, killing her.
Meanwhile, somewhere in the city, Beckett and Vikram are in a building while an assassin team prepares to storm inside.