Mayor Green's life hangs in the balance when he goes into septic shock after suffering from severe flu-like symptoms. Jake and Eric decide to go to another town about 90 miles away to obtain the medicine the mayor desperately needs.
While traveling to Rogue River, Jake and Eric discover that the world outside of Jericho has changed immensely since the explosions took place. They pass a wrecked car whose driver is lying dead along the road. Eric wants to stop, but Jake points out skid marks and concludes that the car had been run off the road by bandits who could still be nearby. Jake also insists that they travel mainly on back roads instead of primary highways.
When they arrive in Rogue River, they discover that FEMA has apparently evacuated the town because of radioactive contamination of the water. The houses are all marked with FEMA codes indicating when the house was evacuated and how many persons in each house were found—dead and alive. Jake knows the code and explains it to Eric. (It is the same code used following Hurricane Katrina.) The town seems deserted.
At the Fillmore County Hospital, they park and approach the hospital when shots ring out. They run into the hospital lobby, which has been looted and is littered with many dead bodies, including what appear to be people in military-style gear. When they reach a stairwell, a defender lobs down a flashbang, which drives them back. Jake shouts to the guard, telling him that they are not hostile and that they need medicine. Jake and Eric leave their guns behind and slowly climb the stairs. A frightened guard meets them and takes them to the hospital's only doctor, Dr. Kenchy Dhuwalia, who is working on a patient. The doctor stayed behind trying to treat all the patients too sick to move. Many patients appear to have been shot dead. The guard, Randy Payton, explains that mercenary employees of a security company called Ravenwood were brought in to assist in the evacuation because there were insufficient National Guard troops. The mercenaries apparently wanted only to loot medicines and leave. One got impatient with the cries of the sick but unmovable patients and murdered them. Randy says that he fought the others during this atrocity and the remainder left. As Jake and Eric are getting their medicine, the mercenaries return to continue looting, and a firefight breaks out after Payton fires on them. Eric poses as a doctor and manages to lull some of the mercenaries into an ambush. In the confusion, Eric leaves his wallet behind. Randy stays and is last seen firing to cover their escape. Dr. Dhuwalia returns to Jericho with Eric and Jake.
Meanwhile, Gray Anderson and Jimmy Taylor question the Hawkins family about their curious arrival in town shortly before the attacks and their having paid for their house in cash. Before meeting with them, Hawkins gives his daughter instructions while in the basement. Gray tells Hawkins that while he was away from Jericho, the consensus of the persons he talked with was that the attacks were a coordinated terrorist attack that required many cells and collaborators in the United States. Hawkins is cool towards the investigators but largely cooperative, though the rest of his family seethes about being singled out for scrutiny. His daughter accuses Gray of suspecting them because they are black, for which Hawkins scolds her. Gray dispatches Jimmy to search the house while asking questions that Hawkins says he would've used during an interrogation. Jimmy returns a few moments later, saying he found something. He puts what at first appears to be a wallet on the kitchen counter. Gray discovers that it is a badge and credentials identifying Hawkins as an agent of the FBI. Hawkins convinces Gray that he is an undercover FBI agent who was dispatched to Jericho to investigate suspicious calls from a pay telephone in the area during the weeks before the attack. He explains his earlier disposition and his family's as being related to his desire to remain undercover since, like Gray, he is uncertain who can be trusted. Gray assures Hawkins that he will keep this information confidential, and the two agree to work together for the town's safety.
April reveals to Mayor Johnston that she is pregnant, and Gail overhears from the doorway. Later in the show, Eric confesses to Jake that he loves Mary Bailey and plans to leave April.
During all this, Heather remembers a student's science fair project to make ice, involving fertilizer. With the help of both Gail and Emily, she manages to make a small amount of ice to help bring down the mayor's fever. Eric and Jake return with the doctor and the medicine (Levaquin) and begin treating the mayor. The final scenes show the Ravenwood men back in Rogue River looking through Eric's wallet and Jake standing watch, with a shotgun, at a window of the Greens' house.