There's a dirty bomb being transported in a van somewhere in New York City. Castle and Beckett were in hot pursuit of the terrorists before they ended up trapped in a freezer. There's no way out of this subzero prison and nobody knows they are there.
As they struggle to stay alive, Beckett thanks Castle for being there for her. He responds, "Always." Beckett says, "I just want you to know how much I..." She can't finish her thought. Beckett's arm goes limp. Castle begs her to stay with him. No response. Moments later, Castle is silent, too.
Martha and Alexis return home to find a makeshift crime lab set up in the apartment. Both Ryan and Esposito believe Castle and Beckett may be conducting a rogue investigation. They are able to track down their partners and pull them to safety. Castle awakens in an ambulance to find Josh tending to him. He never went to Haiti. Castle wonders what that means to Beckett. She says, "It means we have a chance."
With less than 10 hours before the bomb goes off, Castle and Beckett relay their suspicions about cabbie Kevin McCann being the real terrorist to Federal Agent Mark Fallon. McCann was once part of an Army Special Forces unit. He's a war hero. Actually, he "was" a war hero. The real Kevin McCann is buried in Arlington. Fallon realizes the man they are seeking could be anyone, including a foreign agent.
Castle, Beckett and Fallon track down McCann's sister who recognizes the man assuming her brother's identity. His name is Radford Hayes, a disgruntled ex-soldier from Kevin's unit looking to give the country a wakeup call. The team tracks down Hayes via his cell phone. There's less than four hours before the bomb explodes. Before they enter the interrogation room, Fallon tells Beckett, "We break him no matter what."
When Fallon realizes Hayes won't talk, he takes things to the next level. He knocks the suspect to the ground and aims his gun at his head. This forces Beckett to aim her gun at Fallon. A tense standoff ends with no casualties and no usable information gained. Ryan learns that Fallon's wife died in 9/11. The team may not like the way he does his job, but at least now they know why he does it.
Castle realizes that McCann's co-conspirators are going to try to find a patsy for their terrorist actions. Fallon wants Beckett to ask Amir Alhabi's wife, Nazihah, to help them narrow down the possible choices. But when she and Castle arrive at her place, they find Fallon's surveillance agent dead and Nazihah missing. The radicals plan to frame her as their new terrorist.
Two of Hayes' old unit buddies are his accomplices. The search is on, but the clock is still ticking. Castle wants to ask for help from his Syrian secret police contact, Fariq Yusef. Fallon doesn't like it, but the meeting pays off. The team storms the hideout where Hayes' cohorts were holding Nazihah's baby hostage to do force her to do their bidding. The van is gone. Nazihah is already on her way to the target location: Times Square.
All units roll in search of a black van, but it's Beckett and Castle who get to Nazihah first. The bomb squad is en route. ETA: three minutes. That's not gonna work. There are less than two minutes left on the bomb's timer. Beckett sends a photo of the bomb to Fallon, but he can't see it well enough to tell them how to diffuse it. 15 seconds until detonation. 14...13...12...
The only thing Castle and Beckett can do is hold each other's hand. That means Castle still has one hand free. As the timer closes in on zero, Castle rips a handful of wires from the bomb. The timer stops and everyone is still there. The lesson: Never send the bomb squad to do the job of a mystery writer.
Back at the precinct, Castle and Beckett say their goodbyes to Special Agent Fallon with respect and the hope that they never have to work together again. Moments later, Castle struggles to say something to Beckett. Eventually he opts to just head home. We're guessing he never finished his thought because he saw Josh coming down the hallway. So, whatever it is Castle wanted to say to Beckett remains a mystery.