Castle and team run to Beckett’s location and find her car with the message “Help Her” on the window. The manhunt for Beckett begins. Ryan and Castle head to Michael Boudreaux’s apartment where they don’t find Beckett but Ryan has to pull Castle out of the apartment when he goes after Boudreaux/Tyson.
Beckett calls from a payphone but is cutoff. The trace brings them to the pay phone where the call was placed but there’s only a recording there left for Castle of Beckett’s call. The call wasn’t real. It was spliced together from an interview she did when she was searching for Castle over the summer.
A witness saw Beckett, unconscious in a wheelchair and being put into a red van but didn’t get the license plate.
Castle goes back to Boudreaux’s apartment and beats the heck out of Tyson/Boudreuax. When he continues to insist he’s not Tyson, Castle holds a gun to his head just as the police storm in and stop him.
Boudreaux presses charges against Castle. He’s charged with assault with a deadly weapon but Gates lets him continue with the investigation.
Both Boudreaux and Niemann ditch their tails and run. Tyson calls Castle and taunts him. The trace makes it look as though he’s calling from inside Castle’s loft. A police team storms in, scaring the heck out of Martha and Alexis but Tyson isn’t there. He spoofed Castle’s phone number. Castle sends Martha and Alexis on a trip to Europe to get them out of harm’s way.
Castle visits Tyson’s old cellmate in prison and finds out about a place Tyson has outside of the city. Rick finds the house in the woods and finds Amy Barrett outside. She swears no one else is there but he captures her and locks her in his trunk before going inside.
Inside, Castle finds a computer monitor where he can see Beckett restrained to a surgical table, then Jerry Tyson appears and tazes him. He restrains Castle to a chair then calls Dr. Niemann who holds Kate. Jerry scoffs that he set Castle up to come out here alone and now he’ll have to watch what’s going to happen to Beckett.
Castle turns the tables and tells Jerry that his problem is that he always has to prove he’s the smarter person and that he’s in control. Then we see that Castle isn’t alone. He’s been wearing an earpiece and communicating with Ryan and Esposito. On Castle’s cue, Esposito takes a shot with a sniper rifle through the window and kills Jerry Tyson.
They trace the phone call Jerry made to Dr. Niemann and rush to save Beckett but she’s already managed to get one of her hands free. When Niemann comes towards Kate with a scalpel, saying she plans to steal her face, Beckett grabs it and stops her. By the time Castle and the team get to her, Kate is holding the scalpel and standing over a dead Dr. Niemann.
Back at the precinct, Gates tells Castle that the assault charges will be dropped as long as he does 1000 hours of community service...as Detective Beckett's consultant. The ban is lifted. Castle is back at the 12th precinct.
At home in bed, Castle wonders how Kate got through the two months he was missing. Not knowing where she was for two days almost killed him. She thanks him for coming to find her. He tells her, "Always"