An accident leads a U.S. Marshal and a teenage girl (who later is revealed to be his daughter) to a peculiar town populated by scientists and their families where 10-year-old boys are in 11th grade, the local diner doesn't believe in menus, and E=MC² was just the beginning. Just as the Marshal starts to get settled into the swing of things, a local scientist develops a bomb that seems to appear anywhere and eats all the matter around it.

The citizens of Eureka attend the funeral of Susan Perkins, only to find out that she is in fact alive. Meanwhile the Sheriff moves into an underground bunker that is actually a 'smart house' controlled by a computer dubbed 'S.A.R.A.H., and begins to investigate a 'ghost' that has been appearing in town.

Something starts to steal the townspeople's memory...

After hosting a movie party, Spencer is found the next day in the middle of a crop circle, claiming he was abducted by aliens; and then other people who attended the party start to go missing as well. Elsewhere, the legislator responsible for Eureka's funding visits the town, and gets dragged into a Sector 5 experiment...

An unpredictable researcher accidentally unleashes a dangerous artifact which was previously hidden by Nathan Stark.

A sleeping weapons system is accidentally awakened by Fargo and Spencer. Henry tries to avert the pending catastrophe with the help of a retired, nonsensical scientist.

Carter investigates an unusual car accident. Meanwhile, Stark, under the stress of completing a project on time, pressures two research teams to produce results.

A former resident returns to Eureka and creates mayhem which threatens Global Dynamics, prompting Stark to take action.

Taggart achieves a medical breakthrough while Fargo invents a device that bridges the divide between computers and human brains.

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.