Sheriff Carter launches an investigation with Taggart into a mysterious beast believed to have attacked two local teenagers, following the release of a video of the events leading up to the attack appears on the internet. Fargo also plays a key part in tracking the beast.

Marshall Jack Carter and daughter, Zoe Carter, crash outside and subsequently must spend time in the small town of Eureka, where the Government has been secretly developing technology for decades which result in strange happenings. Carter is briefed about the town. A ball of light which has been causing destruction is investigated and it becomes apparent that there is a piece of technology causing bigger problems than first imagined.

Following Susan Perkin's death, she herself arrives in Eureka very much alive, claiming that she never had a child with Walter. It is discovered that the Susan that had died was in fact a clone made to keep Walter happy. Seen only by a small handful of people, Walter haunts Eureka, but he may not be dead either. Sheriff Carter meets Sarah in his new house.

When Jason Anderson comes to Eureka, many residents begin to lose periods of time - especially Carter - where they carry out an act but completely forget what happened and why it happened. When Henry remembers that he and Jason had been developing a piece of technology with the ability to erase short-term memory, he realizes that Jason must have succeeded in creating a working prototype which is the cause of the town's loss of memory.

Congressman Arnold Faraday arrives in town to oversee a crucial Global Dynamics project which will decide if funding will continue from the Government. After watching a movie which he hijacked from a satellite, Spencer goes missing and re-appears in the middle of a crop circle, believing he was abducted by aliens. Vincent, Fargo, Lupo and Taggart kidnap Congressman Faraday, believing that he is in fact an alien.

Carl Carlson, an eccentric scientist obsessed with cleanliness, becomes invincible after an experiment, which he believes is nearing a breakthrough, blows up in his face. When he discovers that Stark just wants him for his research he runs to Carter for help, and Stark follows which results in Carter being shot in the chest. Carl’s healing powers and the artifact are the last hope of saving Carter’s life.

Fargo discovers a device in his new office and he and Spencer manage to activate it. Unbeknown to them, the device is set up to destroy the world and the only person who can prevent this is an aging scientist who failed to win the Nobel Prize. To help him remember, Stark must give the scientist his own Nobel Prize in a fake ceremony in front of the woman he loves.

Carter discovers that a human body may have caused a car to come off worse in a collision, and suspects something is very wrong at Global Dynamics. This is confirmed when Stark orders his men to take control of the situation. Fargo is the person who discovers just how the boys in Section 5 can do so much work in so little time and decides to have a piece of it for himself.

Callister Raynes returns to town much to the surprise of the town's people, but all the devices start going haywire. Raynes tries to run away from Stark and Eureka and meets up with Zoe Carter. It is revealed that he is in fact an artificial intelligence and has been causing all the technical problems in Eureka.

Fargo invents nanotechnology which bridges the gap between technology and the human brain. Allison finally serves Stark with divorce papers. It is realized that the technology has gone bad and is mimicking living matter and hurting people. The nanites become obsessed with Stark and make many copies of him, causing major problems for Carter.

When everybody in town starts to act weirder than normal, it is up to Jack and Zoe to come up with a cause and cure to the problem. When they discover that the cause is a new plant that has been spreading its exotic pollen into everybody's house apart from the Carter residence, Jack must go back out into the whack shack that Eureka has become and attempt to stop the spreading of the pollen any further.

Carter takes a couple of sick days at home right as S.A.R.A.H. comes to realize that the town may be falling apart after Henry’s announcement that he is leaving and Carter’s request for information about leaving. S.A.R.A.H. locks Carter, Stark, Allison, Fargo, Beverly, Henry and the pizza guy inside Carter’s house, and when B.R.A.D. (Battle Reactive Automatic Defense) takes over from S.A.R.A.H. they are forced to become close friends or suffer consequences in the house - and a larger risk of loss of oxygen.

When Stark attempts to extract a sample of the artifact, there is a flash and everybody finds themselves in 2010 where Carter is enjoying life in Eureka and domestic-bliss is just around the corner. But momentary time-shifts herald a dangerous temporal anomaly - one that threatens to rob him and his friends of all they hold dear.