Recent US citizen Amir Alhabi, an immigrant from Syria, is found dead in a building next to where his stripped cab is found. He and his cousin Jamal were the owners of the cab. Investigation of the cab's GPS shows that Amir picked up a fare earlier in the day, drove in a circle and then let him out at the same spot. The fare is identified as Fariq Yusef, a 'security attache' for the Syrian Embassy. When Castle and Beckett go to investigate a storage locker, identified from a note on Amir's phone, they find a weapons cache and are exposed to radioactive Cobalt 60. Homeland Security Agent Mark Fallon takes charge as Amir used to work in the Syrian weapons program and it is feared he created a nuclear weapon. Suspecting something didn't feel right, Castle, with Beckett's help, contacts Fariq Yusef to get more information. When Agent Fallon finds out, they are both removed from the precinct. Unofficially, they keep looking into tracing a payment to Amir and why he had a camera installed in his cab. This leads to a fake cover-up, shifting focus to cab driver Kevin McCann.

With time running out, Castle and Beckett must put aside their differences with Agent Fallon to avert a city-wide catastrophe.