The episode begins, with Allison trying to guess where Jack is taking her for their honeymoon. She in the end is disappointed to see that, Jack has brought her to a cottage just 10 minutes outside town for their honeymoon. Jack wants Allison and him to work on this cottage to make it their own. Allison in the end realizes where Jack is coming from and the romantic gesture and planning behind the whole thing. Zane, Henry and Grace in the meanwhile are busy bio-printing Holly’s body. Once the body is completed Holly’s consciousness would be transferred into it. Henry tells Grace how glad he is that Grace is back home. Holly’s bio-printed body is in the meanwhile complete. Allison in the meanwhile is busy working on the cottage that, Jack has actually inherited from the previous sheriff.
Allison is a bit daunted to see the amount of work that would be required to make the cabin livable. She suggests to Jack that the engineers at GD can build them a pop up cabin according to their specifications. Jack feels there is no romance in that. He wants the two of them to polish the rough diamond that is the cabin, with their bare hands. Suddenly a few of the floorboards crack and underneath the floorboards, the two see a hidden box. Holly meanwhile is ready to be transferred to her new body. Later the transfer is complete, but much to Doug’s shock and horror Holly’s body doesn’t seem to be responding, and Grace tells him that it’s not possible to remove her consciousness from the body. Grace can’t understand what went wrong, despite Holly’s consciousness downloading into the body. Then suddenly, Holly wakes up with a start in her new body.
Andy meanwhile helps Jack open the hidden box, and inside they find a stack of old caser files. Jack hands the files over to Andy, as he is on a honeymoon. Grace meanwhile tells Holly that her body is like a newborn’s and hence she has to give her systems time to acclimatize, when Holly tells them that she has a hankering for bacon and eggs. Holly then thanks everyone present from the bottom of her heart. Doug tells Holly that he just can’t believe she is here for real. Andy and Jo meanwhile proceed to check out the files found in the cabin. It’s the files of the case where Beverly Barlow was found to be a spy. Andy believes that there was a spy consortium, so there might still be other spies in hiding. Andy and Jo meanwhile are busy studying the files.
Jo finds out that Beverly Barlow was Sheriff Cobb’s star suspect. The other suspects named in the files have either left Eureka or have been redacted. Andy then finds a disk buried in one of the files. Jack and Allison meanwhile are busy getting cozy. Suddenly the roof of the cottage collapses and somehow Jack and Allison manage to dodge the falling pieces of wood. Doug and Holly too are meanwhile busy getting cozy. Suddenly Holly tells Doug to be quite and tells him someone is listening and that, they are in a computer construct. Doug tries convincing her that they got out, but she doesn’t believe him. She then tells him that they have to get out of there. Meanwhile in the morning, Doug tells Zane that Holly doesn’t remember what happened last night, and that she is now back to normal.
Holly in the meanwhile is busy stuffing herself with food. Doug tells Zane that Holly really believed she was in virtual Eureka. Doug then tells Zane that he is afraid to let Holly leave, before he is sure that she is absolutely stable. Zane then tells Doug to bring in some of Holly’s favorite things, in order to make her feel better. Henry is meanwhile shown the disk found by Jo and Andy; he informs them that it’s a data storage device, but an old design. Jo then tells Henry that they might have uncovered evidence of possible espionage in Eureka. Doug meanwhile comes back with the stuff Holly likes, and is shocked to find her missing. Henry meanwhile tells Grace about the disk and the possible spy still lurking in Eureka. Allison meanwhile is facing her own set of problems in the cottage.
Zane and Doug in the meanwhile are busy searching for Holly. Henry meanwhile tries to play the disk and it catches fire. Vincent in the meanwhile is aware of the disk and its possible contents, and mouths its details to everyone in the café, much to Jo’s chagrin. Allison in the meanwhile is tired of things going wrong in the cottage, and tells Jack that she is tired of the whole thing and doesn’t feel it’s romantic. Allison then tells Jack it’s not a honeymoon, it’s a disaster. Jack tells Allison that he was trying to do something romantic, but things did not turn out the way he wanted them to. Allison too meanwhile receives messages about the spy. Jo and Henry meanwhile catch Grace red-handed while she is trying to steal the disk. Grace doesn’t protest or try to explain, but quietly leaves with Jo.
Later, Jack asks Henry about the whole thing, and he tells Jack that it was suspicious the way she left town after the whole artificial Eureka episode. He basically doesn’t know what to think. Doug is meanwhile surprised to find Holly hiding in his office. She tells Doug she doesn’t know what’s happening to her, as she is unable to differentiate between what’s real and not real anymore. Doug consoles Holly by telling her that she is going to be fine. Allison meanwhile asks Grace who is in captivity, if she is the one who aided Beverly. Grace tells Allison that she didn’t know anything. Allison in turn tells her that she is finding it difficult to believe her at this point. Grace then asks to speak to Henry.
Zane meanwhile tells Doug that Holly is suffering from a brain disorder, and she could soon lose touch with reality. Zane tells Doug that they have to try to reboot her brain. Holly then panics on seeing Jack, as she recollects how Jack (fake Jack) had killed her in the Matrix program. She then removes Jack’s gun from his holster when he is not looking and pointing the gun at him, tells him to get back. She with the gun pointed at Jack tells Doug and Zane how Jack isn’t real, despite Zane trying to convince her otherwise. Doug then somehow convinces Holly to put down the gun, and slowly takes it away from her; Holly then backs away crying, all the while telling them how sorry she is. Doug then begs Zane to help Holly. Holly’s brain is later rebooted. Doug and Zane then wait for Holly to wake up.
Grace meanwhile tells Henry that, there was a time when she believed in the Senator’s and Beverly’s mission to monitor GD, but when their tactics became destructive she quit. She also tells Henry she had no idea that Beverly was working with Senator Wen, and also that she had no idea what they were planning. Henry then asks Grace who she is trying to protect by trying to destroy the disk. She then shocks him by telling him that she was trying to protect him. She then tells him how they together shared classified information with Beverly, and how he is the one who introduced Beverly to her. She then tells Henry that he taught her everything she knows.
Doug meanwhile is relieved to see Holly up and running. Zane tells him that Holly’s vitals seem strong and that she seems fine. Allison meanwhile goes back to the cottage where Jack is busy trying to repair it. She tells him that, she understands his sentiment behind planning their honeymoon at the cottage. The episode ends at this point.