US Marshall Jack Carter ends up in the town of Eureka after suffering a car accident.
The residents of Eureka mourn the death of Susan Perkins at her funeral, only when she shows up back in town, it turns out Susan Perkins isn't dead after all.
Jack shoots Henry during a short-term memory blackout and has no idea what happened, but when a respected scientitst comes to town, he may have some insights into the nature of Jack's condition.
Aliens take Spencer on a little trip and then return him to Earth one day later. Meanwhile, a congressman with a big stake in the financial affairs of Eureka pops into town.
An artifact which was secretly stashed away in Eureka is unearthed and infects Dr. Carlson, and deu to the ensuing mess, he is soon fired by Nathan Stark and asked to leave town. On the heels of his exodus, however, a desperate Carter tries to intervene.
Carter and Allison buy the services of Dr. Nobel, an old scientist who knows how to deactivate a device that could spell catastrophe which has been inadvertently switched on by Fargo and Spencer.
Stark finds himself under a lot of stress when he must complete a research project with two competing teams. Carter looks into the circumstances of a car accident. Meanwhile, Allison's son and Zoe meet one another.
Callister Raynes, a young computer programmer and Eureka's star pupil returns to town, forcing Stark to make a difficult decision. Carter tries to find Zoe who has run away.
Fargo invents a device to use the human brain like a PC mouse to control the mainframe computer.
Strange behavior is affecting the whole town except Sheriff Carter and Zoe. The father and daughter team must find the cause while Stark makes a decision that could affect the world.
S.A.R.A.H the artificial intelligence that runs Carter's house takes him and a group of residents hostage in an intervention to keep Carter in Eureka. Meanwhile her root program B.R.A.D activates and turns the situation deadly.
When Stark tests the mysterious Artifact the entire town of Eureka is time-warped into the future. It's 2010 and things are a little different: Zoe graduates valedictorian, S.A.R.A.H. gets a voice, Carter and Allison are married with a son and another child on the way, and Harry has four great years with Kim. But all of that changes when the time paradox needs to be repaired and someone needs to be sacrificed in order to do it.