Castle and Beckett find themselves on the trail of a murder/kidnapping that involves multiple governments and a possible world war.
Tropes:
- Artistic License – Physics: Gage throws the first victim out a window. He somehow flipped 90 degrees so that he lands on a car with his head toward the trunk and his feet on the hood.
- Bag of Kidnapping: While investigating the second murder of the episode, Beckett realizes that "Gage" is still there and walks into the foyer to see Castle with a bag over his head. Someone puts a gun to her head, then a bag over it. Turns out he's with the CIA.
- Continuity Nod: While locked in the trunk of the muscle car, Castle notes that "At least this time we're not handcuffed together."
- Faking the Dead: Mathematician Blakely faked his death years ago because he knew how dangerous his work was and didn't trust the government.
- Foreshadowing: When Beckett and Castle revisit the scene of the second murder (the climate scientist), he picks up a thing and fiddles with it, clicking some buttons. It's a clock for speed chess. Later, they end up looking for a mathematician who communicates with chess codes.
- Green-Eyed Monster: Beckett is super jealous about Sophia, a beautiful CIA agent who Castle worked with for his second Derrick Storm novel. He offers to answer any questions Beckett has, and she refuses, for about five seconds.
- Hollywood Law: The CIA doesn't have authority to operate on US soil; their mandate is overseas. The intelligence agency that monitors US citizens on home soil is the FBI.
- Layout of a Season: Each of its three full seasons has a major two-parter with a big guest star representing a federal agency right about this time. In this season, we have "Pandora" & "Linchpin", guest starring Jennifer Beals, playing a member of the CIA & Soviet operative.
- New Old Flame: Beckett is really unhappy to meet Sophia, Castle's muse for the CIA agent in the second Derrick Storm novel.
- Nightmare Fetishist: Alexis gets an internship working with Lanie.Alexis: It's equal parts disgusting and cool.
Lanie: I heard that, and I agree. - Reasonable Authority Figure: Iron Gates is not happy that her people have been co-opted and thrashes her way through the command structure to try and protect them.
- Ripped from the Headlines: Blakely says that his work reduced cholera in Africa and caused the Arab Spring.
- Rogue Agent: Gage is still on the side of the US; he went rogue because someone in the CIA has betrayed the US.
- Ship Tease: "We should go to the track some time, Castle, see who laps who."Castle: [confused, aroused]
- Smart People Play Chess: Blakely communicates through chess code; Martha guesses maybe the game is a cipher for something else.
- Wham Episode: Beckett and Castle are interviewing Blakely in the back of Beckett's car. Blakely notices pigeons fleeing a random event, gets out of the car to run, and is gunned down. Then an SUV rams Beckett's car into the East River. Smash to Black, closing credits.