Paul Reeves' murder in the park leads the detectives to search for Jared Stone but when Esposito tries to talk to Jared on a subway car, he pulls the emergency stop on the car, takes a gun off of a transit police officer and then reveals that he has a bomb strapped to his chest. He holds the subway car and all of its passengers hostage.
Jared says he wants Erin Wilson released from prison. Erin was his girlfriend. They were both hackers and Erin is doing 7 years in prison for felony computer trespassing. Jared wants her flown to the Maldives, a non-extradition country.
Tory is able to pull up a camera feed of the subway car so that the detectives at the 12th precinct along with Lanie can watch. The Hostage Response Team plans to breech the car but Jared figures out they are watching him through a hidden camera and shoots it out.
While watching the video feed, Lanie figures out that Jared is very sick. Esposito worries that Jared may pass out and let go of the dead man's switch. He and Marissa, the transit officer manage to take down Jared and secure the switch. But Jared has been infected with a deadly strain of flu virus. Everyone on the car is taken to the hospital for quarantine.
Castle and Beckett figure out that Jared was being used as a pawn to spread the deadly virus. Paul Reeves boss, Ms. Jervis had concocted the plan to spread the virus and then make money off of the stock from the pharmaceutical company that made the vaccine.
When everyone from quarantine gets a clean bill of health, Marissa points out to Javi that just before they took down Jared, he said Lanie's name. Earlier, Javi had confided in Ryan that Lanie was happy with their relationship as it was but he wanted to move things forward.