A series of sudden deaths, in which the victims spontaneously combust, has the residents of Eureka entertaining all manner of bizarre theories including Taggart's theory that solar flares caused by the eclipse, or the 'Phoenix Effect', are to blame. When Carter discovers that a blast of radiation from the artifact had penetrated the wall of the chamber and is to blame for the spontaneous combustion, it becomes a race against time to save the other two people exposed - Nathan and Kevin!

A device, known as a Multi-Application Combat Armor Alternative (or M.A.C.A.A.), disappears from a storage vault in Global Dynamics following the beginning of Global computer system's eight-hour reboot. Someone plants the device in Fargo's jacket, who then activates it, creating an expanding force field that cannot be switched off. Carter must team up with Stark to find a way to save Fargo before Allison is forced to authorize his death to avoid the force field breaching containment.

A brilliant scientist, Dr. Stephen Witicus, creates a weather machine intended to reverse the effects of Global Warming which creates an isolated deep-freeze that sets off a chain reaction of freak climate changes that soon become a critical threat to Eureka. To make matters worse for Carter, his ex-wife, Dr. Abby Carter, comes to town for Zoe's 16th birthday, and she has some interesting news for her daughter.

Carter finds himself in a parallel Eureka following a blow to the head. At first, Carter doesn't realize what has happened, but then the residents start disappearing from the town and from people's memories. Carter must figure out for himself that he is in a simulated reality, and is in fact lying in bed on the verge of death whilst the Eurekans try to figure out just what is wrong with him. Carter chooses a drastic option to stay with Zoe; but Abby suggests a more suitable option.

Falling space debris threatens Eureka and Carter suspects something at the Tesla High School Science Fair is to blame. When a specific project created to harness the sun's energy starts to attract metal objects within the room, Carter believes he may have solved it. They soon discover that someone at Global Dynamics may have been doing their own science project, turning the EM field surrounding GD into a massive magnet, attracting chunks of metal from space.

('Night of Dreams') One of the Global Dynamics tanker trucks crashes, spilling toxic waste into the atmosphere around Eureka. The driver dies after several people at Global Dynamics share the same dream of it happening. Carter believes their story because he just shared a rather embarrassing dream with several of the Eureka residents, including Jo and Zoe. The dream sharing, despite causing major problems for most, actually helps Allison see what is going on inside Kevin's head.

Pierre Fargo, Douglas Fargo's grandfather, is accidentally "defrosted" in the Global Dynamics Cryogenics lab. Pierre claims he never voluntarily went into cryogenic stasis and that a renowned scientist, Andre Sandrov, must have pushed him in the chamber in order to steal Pierre's scientific breakthroughs, which Sandrov has since used to become famous. When Pierre rapidly ages from the 30-year-old he emerged as, it becomes a race against time to claim credit for his work, and to regain his lost love.

Scientists try to recreate the "big bang" in order to study the beginnings of the universe. The highly dangerous experiment is being monitored closely until most of the Eureka residents suddenly become stupid overnight, leaving Carter as one of the smartest people in town. Together with Jo and Zane, a new genius brought to the town by GD, Carter must find the cause of the IQ plunge and a cure before the experiment creates another big bang.

Carter turns invisible following an encounter with a radioactive substance that had also turned Zoe's new car invisible. They soon come to realize that a scientist who had been working on the original invisibility project at GD may be to blame for the disappearances. Carter develops a relationship with a scientist, Callie Curie, who has become the town's Dry Cleaner following her departure from Global. Meanwhile, Zoe grows close to Lucas, her new partner on a school project, causing her to forget all about Jasper.

Mute teenage girls, glowing Global Dynamics Directors, water turning to blood and complete darkness are some of the many things causing problems in Eureka, all incidents having only one thing in common: holes melted through special reinforced glass. Has a plague of Biblical proportions struck the residents of Eureka, or is it another science experiment gone wrong? It is up to Carter to discover the answer.

Carter becomes the object of affection of all the women in Eureka. Callie feels a little bit left out, as he searches for an answer as to why all women suddenly love him. Carter soon learns, thanks to Henry, that the cause is a bacterium that has been sealed away for thousands of years has leaked into the air. When the town's air conditioning system is working again, the bacterium begins being pumped into the atmosphere, which could cause all men to become irresistible...

All metal in Eureka turns to solid gold, much to the delight of the town's residents. When the gold-turned objects start to deconstruct, Christopher Dactalos becomes the prime suspect. Meanwhile, Nathan Stark returns Beverly Barlowe to town from Guantanamo to try and get information from her about Kevin's connection to the artifact. Henry discovers her reappearance and goes after her. But a strange twist between the two becomes a huge threat towards the town... (Part One of Two)

Global Dynamics is automatically locked down when an airborne toxin is detected, sealing key Eurekans inside. Carter and Stark must put aside their differences to try and eliminate the threat before the D.o.D. does it for them and wipes everything organic out in GD in the process. Meanwhile, Henry has a plan to harness the energy of the artifact which has begun to take over Kevin's mind. Is he really helping Beverly, or does he have another agenda? (Part Two of Two)