The scene opens with a fight going on with distinct sounds inside a room. There are crashes and sounds of gun fire, after which a man is pushed out of a window. Meanwhile, Castle is busy in the kitchen, and happy that his mother’s students used her studio, and not the living room for rehearsing the boxing sequence in Who’s Afraid of Virginia Woolf? Martha is excited to find Castle making her favorite pasta, but Castle intends to share it with Alexis as well. Martha lets on she is not home, and has taken up an internship. Yet another one? And what sort of an internship could it be that keeps her out at 9 o clock? It is the type that Martha has personally approved. That is no reason for Castle to be satisfied.
When Castle and Beckett arrive at the crime scene, they discover that the men who apparently fell from the fourth floor window, does not have an ID, but as Dr. Parish lets on, he has a number of reasons to have died. Shot, stabbed, as well as jammed with a pencil in his throat. Castle sees how the word ‘overkill’ could have a new meaning. Before long, he finds Alexis at the scene. She is wearing a medical examiner’s jacket, and Castle wonders what she is doing there. This is her internship work, and she thought she will have a greater chance in entering med school if she exposed herself. However, as Castle later tells Becket, he is worried about Alexis’ presence harming the wonderful synergy between them as partners. When Beckett hears about the suspect having limped of the building, it turns out there are blood drops trailing towards a car. Beckett points out they should be able to get some help from the surveillance camera positioned at the place where he might have gotten into the car.
They find he has taken a hostage when they see the video, when Beckett tells the detectives to find out where the car might have gone from the number plate. Before long, they are at an apartment, where the killer is sitting calmly in the face of armed forces. When brought into interrogation, Thomas Gage says he won’t need an attorney, and whatever they think they have, is going away. Esposito reports the man’s real name is not Thomas Guage. His driver’s license is baloney, and his fingerprints do not match anything on the criminal database. Before long, they are interviewing the girl who was held hostage – Tina Masse. She lets on that Gage did no chit chat – “get in the car, or I will kill you,” he said. He promised not to kill her if she attended to his wound. He had a bad gash. Said he was stabbed with a knife while killing someone. But he also said that the victim does not exist.
Beckett wonders how Dr. Parish has not been able to ID the victim. Well, no fingerprints in criminal database, although he sure is some kind of criminal – fracture marks, karate and martial arts signs… And when they get to the mortuary, Parish’s John Dough is gone. Later, they find out Thomas Gage has escaped as well. Castle tries finding out how that happened, but all he can conclude, as he explains to Alexis, is that Gage disappeared after orchestrating the disappearance of John Dough’s body. Back at the police station, Capt. Victoria Gates doesn’t want to know where Gage was, but where he is, and how did he manage to escape through the back door while he was under Esposito’s watch. Ryan hands her a photograph showing that Gage escaped through the front door, and that too in a uniform. Castle and Beckett find out the man also accessed the police station database. For what? For who, says Esposito, as he shows them what he has discovered. The profile of a Tracy McGuire.
When they are headed to McGuire’s, Beckett regrets the phone calls are only reaching her voice mail. They knock on the door and realize some one is already inside – the door is ajar. Before they find anyone, Tracy is lying dead with a shot at the back of her head. The carpet is drenched in blood. They call up Parish. Before long, Beckett is horrified to find Castle’s face covered with a black blinder. Before she says anything, she has a gun pointed at her head, and has to surrender her weapon. When Parish and Alexis arrive, they cannot find Beckett or Castle. Neither is the dead body to be seen anywhere. Just a patch of blood on the carpet.
Moments later, Beckett and Castle have their blinder taken off. They are in an elevator, when Castle points out they don’t know where they are, but they are going more than 15 stories under below the basement. When the door opens, they wonder place might be. Castle is at a loss for words. Before long, arrives Sophia Turner with a pleasant smile. Hello Rich, she says, Welcome to the CIA! Meanwhile, Ryan and Esposito are interviewing a man from the Newton institute. That is where Tracy worked. It turns out she was a classic car buff, and a brilliant mathematician. She was working out a model for climate change. Yesterday, she left abruptly, which the man tells them is very unlike her. However, he can access her mail server from the police station, when the cops need access to her accounts.
Meanwhile, Castle cannot hold his excitement down feeling he is the middle of a James Bond movie. However, he is not answering Beckett’s question about who Sophia Turner is. How does he know her? It’s a long story, Castle hesitates. Beckett would like the short version, which Turner is ready to let on. It is the woman who inspired Castle to write his novels, and they know each other since he wanted to have an up close research into the life of a female CIA agent. Later, they learn that Gage was one of the best CIA had. They sent him into a number of countries, failed states, he knows eleven languages, but went rogue. Now he is planning to trigger a major catastrophe, by which damage to the United States could be imminent. Castle guesses – so the man he pushed out of the window was CIA? Yes, Gary Harper. They sent him after Gage after they got a tip on his whereabouts, but obviously things didn’t go as planned. Beckett and Castle also learn that if they are going to be on the mission to help CIA, they will have to maintain complete secrecy of their activities. Turner is the only one to be reported to.
After Castle and Beckett get back, they are not talking about anything with the detectives, or even the Capt. Although she is livid, Beckett points out the Chief of Detectives will back her on this one. Castle and Beckett go investigating in the house, and find nothing to get cracking. However, when they find the car manual on the table, they figure out they have to find out the car belonging to Tracy. Ryan gets on investigations, and finds out that she had been paying $100 a month at a long term parking lot. Castle and Beckett get there, and discover a military phone kit in the hatchback, but also find themselves in the face of a fearless Gage. Beckett points her gun at him, but he quickly snatches it out and now really has the upper hand. Next, Beckett and Castle are inside the hatchback, but Castle has managed to press the panic button before Gage crushed it. However, Beckett is not willing to be save by who she thinks is Castle’s ex-girlfriend. So she manages to crank the hatchback out. However, the CIA man arrives with the blinders again.
At CIA basement lab, Sophie lets on they can find out the number Tracy called from the military phone. When Castle wonders how, Sophie lets on they can do it with the coolest toys. Before long, hi tech programming allows them to shortlist numbers called by Tracy to people who would have picked up payphones. And then, with a little help from map evaluations and surveillance cameras they are watching a man pick up the phone. Sophie knows him – but he is supposed to be dead. Nelson Blakely – a genius and mathematics professor – consulted for the CIA. He had a Lynchman theorem – something that could be used to predict big events from small ones. Using lip reading technology the CIA specialists are also able to find out what Blakely might have said in the conversation. However, it is three chess moves involving two bishops and a pawn.
After spending hours trying to decode what the chess moves could mean, it turns out he was telling Tracy to meet him at a particular place. Beckett and Castle figure out the place is Brooklyn Bridge Park. When they reach the place, Blakely arrives after a while. Castle and Beckett break the news about Tracy’s death – which surprises him – not as much as the fact they know who he is. He gets in their car voluntarily, and asks them to drive to Pier 32. He lets on Pandora is the name of his whitepaper – the one that talks about a domino collapse. The worse thing one could do is to trigger it. After they reach, he is about to explain what Lynchman Theory is, when he notices a flock of pigeons and panics because they do not fly in flocks unless being attacked by some predator. He refuses to listen, and jumps out of the car. Before they know it, he falls to a shot in the head. Wham comes a car from behind, and pushes Castle and Beckett’s car into the water. The episode ends with to be continued.