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.

Carter and Andy are jailed for trying to steal a piece of equipment to complete a device that Kevin has assembled to search for the Astraeus crew. Meanwhile, Holly comes up with a dangerous theory.

Carter and Jo continue their search for the missing Astraeus crew. A surprising source confirms the new theory of the disaster, and offers to help them rescue the crew. Meanwhile, back at the lab, lives are at risk as more of the crew comes closer to the truth of their situation.

When a smart fire experiment gets out of control, Carter and team discover that the Astraeus victims may be the cause. Meanwhile, Fargo deals with Holly's death, Grace struggles to maintain her relationship with Henry, and Allison fights her feelings about Jo.

Jack starts to swap bodies uncontrollably, which puts both his body and his consciousness in awkward situations. Meanwhile, Warren Hughes returns to GD to evaluate Astraeus crew members' reactions to their abductions. Elsewhere, Zane's quest for answers from the Matrix reveals disturbing results for both him and Fargo.

It's disaster drill day at GD and everyone must participate in order to see how well they would do in a disaster. Unfortunately the computer conducting the drill makes the simulation a reality. Elsewhere, Fargo undergoes risky interfaces with the Matrix to confirm Zane's findings.

Fargo is convinced that Holly is still inside of the Matrix computer, but the DOD is determined to wipe its hard drive clean -- losing Dr. Marten forever.

Carter's romantic surprise for Allison turns deadly when they're trapped in a sinking marine lab with time and oxygen quickly running out.

While under the influence of a smart drug, Carter becomes a genius like everyone else in town and starts to change the laws of physics. Unfortunately, his condition soon endangers all of Eureka, including Allison's brother who is in town just to meet his new brother-in-law.

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

The Department of Justice arrives to investigate Grace, while Henry struggles with his conscience and 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.

In the series finale, wormholes randomly materialize around Eureka as the Department of Defense is set to shut the town.