After Allison gets trapped on the Astreus during a hijacked launch, she's able to rouse key crewmembers just before a crash landing on Titan. At least, she thinks it's Titan… is that a humanoid life form? It looks like… no, it IS Deputy Andy! The Astreus crew is too disoriented to wonder much at why he's taking them all into custody and locking them in separate cells, but when Carter comes to collect Allison, she starts to understand just how strange things are.
He explains that Astreus never made it to Titan, but the ship and her crew were gone – no one knows where – for four years. By the time Jenna introduces herself to her mother, it's all Allison can do to keep from sobbing.
On the other side of town, Jo is trying to tell Zane something important, but the two are interrupted by pint-sized, militant hovercraft, part of Eureka's new security system, that see Zane as a threat and tase him into unconsciousness. One of the Andys – for there are now dozens of android deputies holding the town with iron fists – takes Zane to GD, where he's hooked up to a mysterious brain scanner and told to relax, but he senses that something's off and makes a quick getaway.
Meanwhile, Grace has found Henry, and after a brief but passionate embrace, he spirits her from his garage to an underground hideout. He tells her that all is not well in Eureka, that SARAH is the new head of GD, and that she and the Andys have some sort of mind suppression ray that's keeping all of Eureka's humans subdued and sheep-like.
And Fargo and Holly are on to the changes in Eureka, as well. Having lost their original posts, one of the Andys reassigns them to work with Parrish, who is initially his usual, contemptuous self, but after a close talk with Andy, becomes gentle and friendly – way too weird to be healthy. He tells them that he modified his anger ray from a few months ago, and now the Adrenaline Suppression System, or ASS, has effectively been weaponized.
Zane, with Jo's help, manages to escape from GD and is ushered to Henry's hideout, where he's filled in on all the details of this time-traveled town. But Andy is close on their heels, and when Grace and Henry try to distract him from the hideout, they're captured by Andy's giant robot and taken into custody at GD. Jo rushes to Carter to make sure he's OK, and Zane discovers another horrible truth: after four years of waiting for Allison and Zane to return, Carter and Jo have fallen in love.
Holly and Fargo arrive at the hideout, and together the six friends devise a plan to override SARAH's system and blast the Andys with their own mind-control ray. With everyone working together, they're able to accomplish the dangerous mission. Fargo resumes his post and guarantees he'll return all Eureka residents to normal, but for Allison and Zane, normal may not be possible anymore. Allison finally allows herself to shed a tear over what she's lost, not just with Jack but also with the aging of her children, Jenna and Kevin. As she does so, Beverly Barlowe looks on, satisfied that the virtual reality she's manufactured for Allison and the rest of the Astreus crew has taken hold, and they're all locked in an artificial coma. The brain power of Eureka is now hers to control, and no one in the real world has any idea what's going on.
Wormholes start popping up all over, threatening to rip Eureka apart unless Carter can stop them.