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. He develops a friendly working relationship with government liaison Allison Blake and meets some of the more eccentric residents of Eureka.

Carter and the other citizens of Eureka attend the funeral of Susan Perkins. Much to their surprise, Ms. Perkins makes a return to Eureka as a woman who is very much alive!

Jack Carter accidentally shoots Henry while suffering from short-term memory loss, meanwhile a visit from a noted scientist may hold clues into to his sudden memory loss.

Spencer is apparently abducted by aliens and then returned to earth the next day inside a crop circle. Also, the town is visited by the congressman whose committee is responsible for its government funding.

After a lab accident, Global Dynamics researcher Carl Carlson is expelled from Eureka due to lack of results. Later, it is discovered that the accident has unlocked hidden abilities in Carl. Meanwhile, Jack does his best to avoid a physical.

After Fargo and Spencer accidentally activate a doomsday device, Carter must help Dr. Irwin Thatcher, an aging scientist, to shut down the device.

Carter investigates an unusual car accident. Meanwhile, Stark is under stress to produce results on a project.

When the return of Eureka's star pupil causes problems all over town, Stark is forced to make a hard choice. Carter attempts to track down Zoe who has run off with the former resident.

Fargo invents a device that bridges the gap between computers and human brains

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.

Stark is given a chance to try the top-secret Artifact. Once it's tested, Eureka warps into the future and ends up in 2010, where the town is different.