It's Founder's Day in Eureka and everyone is in the spirit of the celebration until Jack, Allison, Henry, Jo and Fargo are transported back to 1947 where they meet some familiar faces along the way. Will they be able to get back to 2010 or will they be stuck forever in 1947 where Eureka is not a town, but an Army base.

When the 5 get back to their time, things are changed everywhere. As the Henry tries to fix the machine that transported them in the first place, Dr. Grant is making himself comfortable as he can. Jack is still trying to wrap his mind at the fact that he asked Tess something that she says yes to and the fact that the group's positions changed. As one thing leads to another, a twist happens and things get a little dicey.

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.

Claudia Donovan visits Eureka to see if Fargo's promises of wondrous devices are true, but she finds herself in the middle of a mystery suitable for Warehouse 13 when objects begin to appear randomly around the town and GD, and it must be solved before there are deadly consequences.

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.

Love is in the air as Carter gets fed up with Grant's pursuit of Allison, Zoe conceals her love and Henry courts Grace. But all the emotions may have to be put on simmer when people in town start turning to stone.

Eureka's citizens face the return of people from the past; Global Dynamics tests a new device.

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. 

The Eureka atmosphere becomes toxic when Department of Defense auditor comes to assess the team's relationships.

The Astraeus candidates go through their final interviews while Carter and Allison appeal their relationship audit.

When an explosion in the Astraeus lab accidentally sends Andy to Titan the team must devise a plan to save him before it's too late! Eureka

In the season finale - It's chaos in Eureka when an energy beam rips through main street but the Astraeus launch must go on...with or without Eureka intact.

The Astraeus crew returns to Eureka four years later and must adapt to a myriad of changes, including a more oppressive version of Deputy Andy.

The town huddles in a last attempt to locate the vanished Astraeus before it's too late!

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.

The crew moves forward after an ordeal and Warren's visit adds to the pressure.

Jack and Allison's perfect honeymoon is interrupted when sabotage is discovered in Eureka. Elsewhere, Holly faces another hurdle to remain intact.

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

The people of Eureka are being kidnapped and replaced by body-doubles one by one unless Allison, Fargo and Zane can figure out how to avoid capture and save their town.

Wormholes randomly materialize around Eureka as the Department of Defense is set to shut the town.