In Lansdale, Pennsylvania, a construction crew is working on the road and listening to a radio broadcast on the recent disappearance of six local residents. One of the workers, Raymond, goes over to the nearby cornfield and notices something odd in the fields near a scarecrow. He goes into the cornfield and sees a hand-like shape in the dirt. He reaches down to dig it out and the hand grabs him and pulls him underground.
In New York City, the doctors discharge Olivia from the hospital and Peter helps her get the cane she needs to walk. As they leave, the shapeshifter using Charlie's form covertly watches them.
In Lansdale, Raymond recovers consciousness in a tunnel beneath the earth. His legs are covered with a blue liquid and badly injured, but Raymond can't feel them. Using a cigarette lighter, he finds several desiccated corpses scattered around him, some of them barely human. A humanoid creature comes at him from the shadows and he tries to crawl away. It drags him back into the tunnels as he screams in pain.
In Boston, Peter meets with Broyles, who tells him that the FBI has signed off on all of Peter's requests, including new housing for Peter and Walter. When he notes the cargo plane was hard to come by, Peter tells him that they're heading to Pennsylvania where he came up with disappearances similar to Olivia's. Broyles asks how Olivia is doing and Peter assures him she's doing fine. Broyles okays the assignment and tells Peter to watch Olivia.
Olivia arrives at Walter's lab where Walter and Astrid are recreating Olivia's car accident using frogs and a toy car. He admits he can't make the frogs disappears but believes Olivia vanished from her car and appeared in another universe for an hour. Walter explains his theory on parallel universes, and that each one is slightly different. He realizes he's discussed it with Olivia before and Olivia admits that all she can remember is that she met with someone. Walter admits that when he saw Olivia lying dead at the hospital, he doesn't know what he would have done. However, he quickly goes back to business and notes that traveling to an alternate reality could have consequences. Peter arrives to invite them to Pennsylvania.
The trio arrives in Lansdale and meets with Sheriff Golightly. He says he didn't call the FBI but admits that there have now bee seven disappearances. He tells them to stay out of the crime scene until the local investigators have finished their investigation. Once they do, Walter examines some of the blue liquid and is eager to start investigating. The team goes to the sheriff's office and Golightly is reluctant to turn over his files until he knows why they're involved outside of normal FBI protocols. They're interrupted when Olivia hears a fly buzzing. She blanks out momentarily and Peter distracts the sheriff by talking about his fly-fishing collection.
As they leave, Olivia calls "Charlie" and asks him to run the names of the victims. Coughing, he agrees but says he has to run an errand first. He goes into the shop and asks the owner to use the typewriter in the backroom. The shapeshifter informs his superiors in the other universe that Olivia still trusts him.
The trio returns to Harvard and Peter and Olivia go over the files but don't find anything to connect them. Walter discovers the liquid is a paralytic that contains male DNA. Olivia determines that one local, Andre Hughes, was at the house of several of the other victims just after they disappeared.
Andre Hughes walks through the tunnels beneath his home and finds Raymond, dead. He curses and prepares to bury him.
Peter and Olivia go to Hughes' house and find him outside. As he takes off his boots and invites them inside, Peter observes that his boots are covered with mud. Hughes explains that he spends a lot of his recent time digging out water wells. As he goes to wash the dirt off, Olivia seems to hear someone breathing and asks Hughes if there is someone else in the house. He says that there isn't and leaves them, but Olivia can still hear the breathing. She tells Peter to keep Hughes busy while she explores upstairs. Olivia finds a room with laboratory equipment and a snarling noise coming from another door. She throws it open but there's nothing inside. Peter comes in and she almost shoots him.
Olivia and Peter take Hughes to FBI headquarters and show him photos of the missing people. He explains that he's a doctor but retired nearly 20 years ago. As Peter watches, Broyles comes in and Peter explains that they didn't find anything but the lab equipment, and Walter is looking at it. Olivia points out that Hughes visited the families of several of the victims and he says he thought he could comfort them even though he hardly knew them. He explains that he lost his son and wife 17 years ago when the son died in childbirth. Hughes insists he could never hurt the victims. Olivia asks for a sample of his blood to compare to the DNA they found at Raymond's disappearance site. He refuses to give his permission. Broyles tells Peter he'll get a warrant and then asks about Olivia's shot. Peter claims it was a misfire.
The doctor examines Olivia and says she's doing well. As she dresses, Nina Sharp comes in and notes that she went through something similar when she was first diagnoses with cancer. Nina gives her the phone number of Dr. Sam Weiss, the man who helped put her put together. When Olivia says that the FBI has psychologists, Nina assures her that Weiss isn't a psychologist.
Broyles sends Agent Jessup to check out Hughes' house. She notes the religious décor and finds a cabinet holding a cross, candles, and a Bible. Inside the Bible is an article on the mysterious deaths of Hughes' wife and child and a note from Pastor Lisburn saying that they're with God. Jessup calls Olivia to inform them of the mysterious circumstances and they order an exhumation.
In his interrogation room at the FBI headquarters, Hughes loosens the wiring on the overhead light and twists it into a noose.
In Philadelphia, the team digs up the coffins and discovers that the corpse of Hughes' son is missing, and something has dug a tunnel in… or out. Olivia goes to see Hughes, who has hung himself.
Walter examines the corpse of Hughes' wife and notes that she had an advanced case of system lupus. She was incapable of having a child. Peter mentions the empty coffin without a boy and Walter looks pensive.
Sheriff Golightly puts up police warning tape around the Hughes house, pounding the posts into the ground. Behind him, the ground starts to rise up.
Olivia meets with Broyles and starts making arrangements to have Hughes' body sent to Walter's lab. She clearly hears a man at the other end of the parking garage talking on his cell phone and remembers all the other incidents where she's impossibly been able to hear faint noises.
Walter finishes his autopsy of Mrs. Hughes and shows Peter that the afterbirth shows that her son wasn't completely human. He believes that Hughes altered his son's fetus in the womb so it could survive its mother's lupus, using scorpion and mole rat DNA. Olivia comes in and explains that she heard the boy breathing at Hughes' house and that he's hiding in the house… or underneath it.
Golightly finishes putting up the tape and goes back to his car. However, he notices the earth shifting as something moves toward him and pulls him under.
Peter and Olivia arrive at the Hughes house and find Golightly's abandoned vehicle. They go inside and Peter finds a hidden nursery. Olivia finds a storage room and calls in Peter. He finds human teeth on the floor and a tunnel leading away from the house. The tunnel is filled with human remains. Olivia looks in and the Hughes boy grabs Lydia and pulls her into the tunnels. Peter goes after him and pulls Olivia away, but the creature bites him. Olivia manages to hand him a spur of bone and Peter stabs the boy. It digs a new tunnel beneath the driveway and the sheriff's vehicle falls through, crushing him.
The authorities dig up the yard and find traps that Hughes set to trap and kill his son. Olivia describes what happened to "Charlie" and wonders if there's a part of her brain that is trying to protect her. He warns that she may not have a choice and the information she knows could be of vital importance. When he mentions parallel universes, Olivia is surprised and amused to hear him admit the theory is valid and he promises that he'll be there to help her remember.
At the lab, Peter tells Walter that he wants to go fishing. He talks of how when he was 10 or 11, he saved up his money to buy a special lure, the Night of Desirable Objects. He'd hoped to go fishing with his father, but he was never there. Walter doesn't realize Peter is talking about him, but wants to go and Peter is glad to have him.
Olivia is taking a bath at home when her heightened hearing kicks in again, letting her hear the soap bubbles pop and her neighbors talk through the thick walls. Her hearing grows more sensitive by the moment and then goes back to normal. She goes to see Dr. Weiss at a bowling alley but he's not there. The owner tells her that Weiss met a girl and moved to Atlanta. As Olivia walks away, the owner is surprised that she's giving up so easily. Olivia realizes that he's Sam, and he asks if the headaches have started yet. He warns that they soon will and then offers her a pair of bowling shoes.
The shapeshifter returns to the store, reports that Olivia doesn't remember anything, and asks for advice. His superiors send back a message that he should provoke her memories.