After a strange accident sidelines Eureka's sheriff, U.S. Marshal Jack Carter takes over the investigation into the mysterious phenomenon that led to the death of a resident. Carter learns about the secret purpose of the town while trying to re-establish a connection with his angry and bitter daughter, Zoe. 

Jack Carter accidentally shoots Henry while suffering from short-term memory loss, and the visiting scientist whose wife is Henry's old flame may hold the only clues into that incident and the increasing memory losses occurring both in town and at Global Dynamics just as an important military contract comes due.