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!

Fargo accidentally triggers a prototype for a personal force field, which goes out of control, forcing Carter to enlist Stark's help.

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

Carter suffers a blow to the head, and after arguing with Zoe, he suddenly finds himself in a parallel Eureka, where the residents seem to be mysteriously vanishing.

Falling space debris threatens Eureka residents and Carter turns to high school science fair participants to solve the problem. Specifically, he taps a student science project created to harness the sun's energy. Also, Zoe gets an eco-friendly automobile.

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.

Fargo's grandfather awakens after 50 years in cryogenic suspension and accuses his rival of putting him there and stealing his work.

As an experiment that will recreate the first moment of the origins of the universe, the Big Bang, goes terribly awry, the town’s geniuses turn into morons, leaving the fate of Eureka in the hand of Jack Carter and an antisocial young ubergenius.

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.

Sheriff Jack Carter becomes absolutely irresistible to every woman in Eureka. But if he doesn't get his mojo under control, they might just eat him alive.

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?

The search is one for an escaped drone as Eva Thorne arrives to assist the clean up of damages which Global Dynamics has caused.

Carter and Allison investigate when a scientist mysteriously disappears from a sealed biosphere. Meanwhile, the "Fixer" tries to make Eureka's efforts more profitable.

Eureka's annual dog show is underway and is like none other. Meanwhile, Sheriff Carter experiences an earthquake; Zoe debates quitting the accelerated physics program; and Allison starts the process of fitting her wedding dress.

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.

A search for a mummy ensues after a famed archaeologist opens the tomb of an Egyptian queen at Global Dynamics.

Carter's job is made more difficult when a super hero emerges. Meanwhile, Zoe and her friends are imperiled when Thorne makes a subterranean search beneath Eureka.

The Eureka mayoral race is overshadowed by the sudden arrival of a second sun, forcing Carter, Allison and Zane to investigate it more closely.

Trust issues are produced by a scientific find, along with sinister results. Zoe's life is in jeopardy, and Eva Thorne knows what has caused the predicament.

Carter interviews for a job with the Department of Homeland Security, after being terminated as the sheriff. Deputy Lupo decides to resign after discovering that a very personable robot is the new sheriff.

Jo displays atypical behavior after a DNA scan malfunctions, unfortunately it's while she's interim sheriff because Carter is undergoing a 48-hour DOD recertification test.

Dr. Tess Fontana reopens Section 5, causing objects to become ambulatory , possibly due to poltergeists.

Carter finds himself chasing down creation of blob-ical like proportions when a series of escalating pranks turn deadly. Elsewhere, long-term rivals from Area 51 come to Eureka for a bowling tournament.

Eureka's teenagers who appear to have been manipulated while asleep, gathered in a field where they assembled a strange structure comprised of scrap metal and electronics.

Henry's ship returns causing Carter to fear it maybe linked to the town's deadly electrical anomalies.

Allison's baby shower fetches her a load of eco-friendly gifts and the discovery of a drowned scientist in a location where drowning is impossible.

Global Dynamics sonic cleaning coincides with a phenomenon in which the citizens of Eureka develop a form of amnesia. Meanwhile, Allison goes into labor.

The first day on the job as temporary head of Global Dynamics proves daunting for Tess when a new Ice Age comes to Eureka; and a familiar face returns in the process.

Tess has a job offer from Australia, Zoe is prepared to leave for Harvard and Carter has a magnetic disturbance above Eureka to contend with, in the third season finale.