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.
What appears to be a ghost begins terrorizing people and disrupting equipment shortly after a funeral, and even more surprising, one of the recently dead reappears alive.
Occurrences of short-term memory loss begin when visiting scientists hit town, and Jack has to determine the cause while not letting down Zoe who is acting in a school play.
The presence of a crop circle leads to thoughts of an alien invasion, the future of Eureka is threatened when a congressman visits, and Jo and Jack work on their trust issues.
After Fargo triggers a device from the Cold War era, the race is on to shut it off before it starts a world war, but the only solution may lie in the depths of a demented scientist's mind.
Strange behavior exhibited by the townspeople is investigated by Carter, who has to solve the mystery before Stark makes a decision that could affect the world.
A bad day in the lab forces Carter to rethink his decision to live in Eureka, prompting an intervention from S.A.R.A.H. (the self Activated Residential Automated Habitat).