When the ship with the Astraeus crew returns to earth, its occupants discover that four years have elapsed and time isn't the only thing that has changed.
After Senator Wen calls off the search, Kevin designs a tool to find the Astraeus ship that is still missing after four months. Unfortunately, the device's assembly stops after Andy and Carter are arrested while stealing a component for it. Elsewhere, Jo's walkabout is rocky, and at the Astraeus crew's location Dr. Marten posits a dangerous theory about their situation.moreless
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, and Carter is sent in on what may be a one way virtual rescue mission.moreless
The Astraeus crew members attempt to overcome their experiences in the matrix; Fargo deals with Holly's death, Grace struggles to maintain her relationship with Henry, and Allison fights her feelings about Jo as they share Carter's house. This all fades to background noise, however, when Dr. Parrish's latest project is accidentally released and threatens to ignite the whole town.moreless
Carter starts to swap bodies uncontrollably, which puts both his body and his consciousness in awkward situations. Meanwhile, Warren Hughes returns to GD. This time to evaluate Astraeus crew members' reactions to their abductions and any effect to their job performances. But Carter's body swapping jeopardizes jobs, relationships and, ultimately, his own life. Elsewhere, Zane's quest for answers from the matrix reveals disturbing results for both him and Fargo.moreless
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.
The Department of Defense insists on installing new security and removing all Astraeus artifacts, but Fargo resists because he believes Holly is alive in the matrix. Elsewhere, Henry recruits Carter for a brain experiment.
Carter and Allison's romantic plans run afoul of a rogue submarine, and it's up to Jo to save their lives … if she can fix the mess at Global Dynamics caused by an out-of-control prankster in time.
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.
Carter 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, and Henry struggles with his conscience. Holly receives a message that triggers a chain of events. The question is whether it's her actions or Fargo's malfunctioning signature achievement that are causing the scary incidents all over GD and the town.
The doubles steadily take over GD, which means Fargo, Allison and Zane are in a fight for their lives and everyone else's as they try to avoid capture and fix the problem.
In the series finale, the Department of Defense's closure of Eureka is delayed by random wormhole materializations.