Beckett is doing surveillance on a man named Jason Marks. She snaps photos of him in an alley at 1:14 in the morning. It's impossible to see who is inside the black town car that picks him up. This surveillance is all part of a secret project she's been working on with Castle, who is on a book tour in Chicago. The remainder of the tour is being postponed until after the wedding which is just two short weeks away. Beckett's phone chat with her fiance is cut short when work calls. There's been a murder. The victim: Jason Marks.
Ryan reveals that Jason Marks ran a political consulting firm in DC. He was shot around the time Beckett was watching him. Surveillance video shows Vulcan Simmons was the driver of the town car that picked up Marks. Beckett believes Senator Bracken is behind this. Castle wants to take advantage of the fact that Vulcan Simmons is the prime suspect. Too bad Captain Gates pulls Beckett off the case. That doesn't mean she's going to stop investigating though.
Beckett tracks down the town car. Vulcan Simmons is waiting for her. He knows that bloody evidence she found covering the car's interior is inadmissible. Simmons instructs her to leave the premises. That's not going to happen until she gets some answers. A short time later, Castle gets a call from Esposito who says Gates is putting Beckett back on the case. The reason: Vulcan Simmons has been murdered. He was tortured before he was killed.
Beckett admits to Castle that she was at the crime scene but she didn't kill Simmons. Lanie discovers a bullet in the victim's spine. Ballistics determines it came from Beckett's backup gun. Suddenly, Beckett is on the run from Internal Affairs. Castle is asked to leave the precinct but not before Esposito and Ryan assure him that they are in this, too. They discover that Jason Marks met with Captain Montgomery's old friend Smith, who was thought to be dead. In other news, Captain Gates wants to know why Beckett is being set up. Ryan and Esposito give her the full backstory.
Beckett meets Castle at the park where he proposed. Bracken knows she was bluffing about having evidence against him. Beckett questions the doctor who signed off on Smith's death. He refuses to admit he helped the guy to disappear. Beckett's face appears on the TV news. She's being branded as a fugitive cop. She's on the run when Castle gets a call on his burner phone. It's Smith. He's alive. He tells Castle and Beckett there's a recording out there where Bracken admits to murder. No one knows where it is.
Smith advises Beckett to run, to disappear. If she doesn't, Bracken will kill her. Castle knows they need a plan. He leaves to contact a friend who can help. While he's out, Senator Bracken shows up at their safe house. Armed gunmen hold Beckett at gunpoint. She dares the senator to pull the trigger himself. He leaves his thugs behind to do his dirty work. They force a pill and alcohol down her throat. The plan is to make her murder look like a suicide.
Beckett struggles to stay lucid as one of the thugs tries to make her point her gun to her head. SMASH! BANG! BANG! Beckett takes out the two thugs. She never swallowed the pill. The alcohol, however, is making her woozy. The second thug smashes her head with a bottle. Beckett shoots him dead. Castle returns a short time later to find her. Beckett realizes Montgomery is the one who made the incriminating audiotape. Johanna Beckett's notes suggest her mom hid the tape. This revelation occurs just as the police swarm in. Beckett is arrested, as are accessories Castle, Ryan and Esposito.
When Beckett is brought back to the precinct, she realizes that her mother hid the incriminating tapes in the elephant decoration on her desk. She frantically tries to find it as Internal Affairs officers aim their guns at her. The tape falls out. The recording has Bracken speaking of multiple crimes he's committed and threatening several more. It's proof that he's a killer. Beckett steps into the middle of a live TV interview to place Bracken under arrest for the murder of her mother. Justice has finally been served. Beckett is finally at peace. She lets Castle know that she couldn't have done any of this without him.