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.

Taggart's theory is that solar flares caused by the eclipse, or the 'Phoenix Effect', are to blame when people start to spontaneously combust. When Carter discovers that a blast of radiation from the artifact had penetrated the wall of the chamber and is actually to blame for the spontaneous combustion, it becomes a race against time to save the other two people exposed - Nathan and Kevin!

Dr. Whiticus creates an incredible "weather machine" intended to reverse the effects of global warming which instead stirs unexpected results.

One of the Global Dynamics tanker trucks spills, potentially causing a change in everyone's sleep habits... In the course of the episode, we come to learn that Global Dynamics has developed a technology that enables them to distill six months of the town waste and by-products into one truck, an amount that would normally fill Lake Erie.

An abandoned research project on invisibility returns to haunt Eureka. Carter and Zoé become tangled in a web of strange occurrences that lead to Carter’s disappearance and the possibility that he might never reappear.

Sudden muteness, human bioluminescence and faucets running blood cause many of Eureka’s citizens to believe that they are the victims of a biblical plague.

Beverly Barlow returns to town just as a parasitic bacterium threatens to destroy Eureka, by turning everything to gold and then into rust --- people included.

Nathan Stark and Jack Carter must put aside their rivalry to stop a deadly bacteria from destroying the town and killing Allison’s son. But can Carter ignore Stark’s crimes, as well?

It's Allison and Stark's wedding day and Carter finds himself reliving it over and over. Meanwhile, Carter's sister, Lexi, visits the town.