The residents of Eureka attend Walter and Susan Perkins' funeral. Henry leads, giving a speech in which he states how Walter and Susan will be missed. Jack is the last person left at graves, after the residents begin departing. Meanwhile, Jack is blurrily viewed from a distance. Jack tries to get his car under control, after the technical parts of it all suddenly turn on, and then suddenly out the corner of his eye he notices something, though he shrugs it off.
At the police station Jack talks to his courier service, which is holding up the arrival of his belongings. Jack switches to another line to listen to an "urgent" report...about a reported ghost sighting. Jack is disgruntled as the courier service has hung-up while he was listening to the ghost report, and he blames Jo for "setting him up". Shock dawns on Jack and Jo, when Susan Perkins walks into their office wondering where Walter is.
Allison and Jack talk to Susan; they tell her that they attended her funeral that morning. Susan tells Allison and Jack how her parents rang her in hysterics, after they received an invitation to her funeral, and news she apparently had a child. They reveal to Susan that Walter is dead. Jo brings up the question as to who they buried that morning at the graveyard, and Susan tells them how she and Walter got married after they graduated from MIT, and how one morning Walter was offered a top-secret job, which Susan was not interested in – thus they separated.
At the graveyard, Susan is excavated from the ground by Henry, who reveals he is also a coroner (and he even has a title badge to affix to his jump-suit).
Allison takes Jack to Global Dynamics to get authorization to use their molecular bio-scanner. Allison is shocked to discover that Nathan Stark is Global Dynamic's new director. Allison talks to Jack about her history with Nathan, and reveals that Nathan is her ex-husband.
At Allison's home she readies Susan and Walter's son Brian for bed. Allison comforts Brian, telling him how it's hard to lose a loved one, but things do get better. Late at night in Brian and Kevin's room, electrical things, such as toys and an alarm clock begin acting strangely. Having been awoken, Kevin looks in fear at something, while flashes of light surround the room.
Fargo visits Jack late at night, Jack believes Fargo to be breaking in – at first – but soon discovers that Fargo is there to "help" him. Fargo takes Jack to an abandoned nuclear disaster bunker, Jack's new house…that has a name, S.A.R.A.H. (Self Actuated Residential Automated Habitat). Fargo takes Jack inside the house, a smart house that speaks.
Jack is in bed when he is wakened by S.A.R.A.H. playing loud music. Jack rings Fargo, wondering why the house is "yelling", and Fargo tells him that a power surge reset the clock, throwing off the settings.
Jack attends Global Dynamics for Susan's bio-scan; Henry tells him that a bio-scan is more accurate than a DNA scan. Once the scan is complete, Henry tells him that both Susans are exactly the same, in a different manner to a clone.
Nathan is hospitalized, and he tells Allison it's due to an electrolyte balance. Jack arrives to pick up Allison, as Henry told Susan about the "alternate" Susan. Nathan asks Jack to stay behind; he tells Jack that something was in his office – something non-corporeal, a "ghost".
Jack and Henry visit Eureka's cold storage facility. Henry tells Jack that the mortality rate in Eureka is "twice the national average". Jack's phone rings, it's S.A.R.A.H., his house. S.A.R.A.H. tells Jack that his daughter Zoe didn't return home the previous night.
Allison talks to Susan about her life. She queries Susan about Walter and her clone's son. Susan decides that she does not wish to have anything to do with Kevin, her biological child. Allison offers to drive Susan to her car.
Jack, Henry and Jo visit Global Dynamics to see Fargo. Jack asks Fargo to bring up video footage from the previous night while he was sleeping – specifically the time around the power surge. They discover the "ghost" that had been plaguing the town.
Allison drives Susan to Eureka's school where she points out Brian to Susan. Tearfully Susan decides that she still wishes to have nothing to do with her biological son. Allison's car begins going crazy, she and Susan view the ghost as it walks across the school grounds – walking into the school. Inside the school the ghost heads for Brian. Allison and Susan rush to save Brian as the ghost continues to draw closer, but Allison is knocked unconscious when she comes into contact with the ghost. Susan, her maternal instincts taking over, rushes to protect Brian. The ghost is shown to actually be Walter while it phases in and out.
At Global Dynamics, Henry tells Jack that Walter wasn't actually killed, but rather shunted into an alternate "time-stream". Walter is placed inside a sphere, which Henry states will help stabilize him.
At his home, Jack angrily bangs on the door of his house, which will not let him in. He discovers that S.A.R.A.H. is mad at him for not being home at the right time for his tea. Inside he asks S.A.R.A.H. to turn on the lights and some music. He sits in a recliner chair, which begins to massage him as he relaxes. He hears a knock on his door, at the door he discovers Jo with his daughter who immediately walks in wondering where her room is.