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

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!

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.

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.

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.

When a prototype sets everyone into bad temper mode, the issue escalates and gets worse beyond the control of what Jack can handle. As Jack and Allison and Tess are the only sane people at Global Dynamics they have to devise a plan that will make everything calm and happy again. Meanwhile, Henry is helping Dr. Grant re-build the bridge that got them back to the new world except everything they touch disappears.

When Sara gives Andy a (as Zane calls it ) an EMO download to give him emotion, she inadvertently affects all Level 6 AIs. Including Tiny. She escapes while being transported to NASA and is on the loose. Meanwhile, Jack takes Kevin camping with Fargo and Grant and Jack is not happy that Grant is there. They argue on who is with Allison and who is not and they are interrupted by Tiny who has an attachment to a certain object of Kevin's.

When mites threaten to take down Global Dynamics, Jack is called into action since Jo is in the middle of training. Allison is struggling with the fact that everyone things that her brain doesn't work and she is determined to prove that she is back in action again. 

Beverly Barlowe resurfaces in Eureka seeking Carter's help to free the Astraeus crew, and the rescue plan lands Carter in the crew's virtual world.

Eureka is cut off from the world by a malfunctioning experiment that threatens to eradicate the town's populace.