Peter stops at a diner in Noyo County, Washington, and flirts with the waitress, Krista. She offers to burn him a CD based on her reading of his aura, and he agrees. When she wonders where he's from, Peter admits that it's somewhere she's never heard of, and he doesn't know where he's going. Krista offers to stop by his hotel after she gets off work and drop off his CD.
Later that night, Krista closes up the diner and leaves. A man approaches her and then knocks her out and takes her to a hidden operating table. As she wakes up, she discovers that the man is cutting open her skull and removing a piece of her brain.
Peter spends the night in the lobby of the hotel, barely able to sleep. The clerk informs him that Krista never came to visit him. Peter goes to his room and prepares to sleep, but the phone ring. An odd electric warbling comes out of the receiver, and no one responds when he demands to know who it is. Peter then leaves and drives on to his next destination, picking a city at random on the GPS. He passes by the diner and sees the police assembled outside, taping off the crime scene. Peter stops by and introduces himself to the sheriff, Ann Mathis. Her and her deputy, Tom Ferguson, wonder if Peter was there the previous night. When he admits that he was, they take an interest and Mathis calls the clerk to confirm his alibi. Peter notices Newton in the crowd and starts to go after him, but the First Wave leader slips away when Mathis stops Peter. She tells him that he's taking her to the station for questioning. As she and Ferguson drive Peter away, they ask where he's staying at the hotel and he admits that he's staying under an assumed name.
En route, Mathis' men radio to tell her that they've found Krista's corpse. They go to the river where the men have found Krista's corpse. Peter stays in the sheriff's SUV and hears over the radio that Krista had a piece of her skull removed. He gets out and tells Mathis to confirm if a piece of Krista's brain was removed. She checks with the coroner and confirms that Peter's hunch is correct.
Mathis takes Peter to the station where he claims he's a civilian consultant for the FBI, specializing in the weird. He explains that the killer removed a piece of Krista's temporal lobe, and that it relates to another case Peter was involved in. He figures that Newton and his soldiers are tracking him, and called him at the hotel. When Mathis wonders why Newton would kill Krista, Peter suggests that he did it to scan her memories of Peter, even the things she wouldn't normally remember.
As Mathis and Ferguson call Washington to check Peter's credentials, Peter calls Broyles. He asks the FBI head to confirm he's working with the FBI and Broyles agrees. However, Peter asks him not to involve Walter. Broyles agrees and offers to send any help that Peter needs.
Peter goes to the morgue with Mathis to examine Krista's corpse. They examine the body and conclude that due to the pinkness of the brain near the incision, she was awake and suffering an extreme adrenaline rush at the time. As they examine the body, Mathis drops her pen, which has an inscription on it about finding the crack. She explains that it was a gift from Ferguson, the only officer who supported her in the department.
Back at the station, Peter signs his statement and tells Mathis and Ferguson that he'll be checking into a different hotel. Once they're alone, Ferguson wonders if Mathis is biased because she's fascinated with UFOs and other supernatural phenomena. The sheriff says that she's a good judge of character and trusts Peter.
Peter buys weapons from a dealer and goes to his new hotel room. However, he gets the same strange electrical signal over his phone and no response. When he hangs up, Mathis calls to tell him that Ferguson has disappeared. When Peter comes to the station, Mathis figures that the same person took Ferguson and Krista, and they need the FBI to investigate. Peter insists, warning that if they come in, Newton and his soldiers will flee and they'll never find them. She wonders if he's telling the truth and Peter insists that they have to do it his way.
Back in Boston, Walter is trying to shop on his own. He picks a box of Pop-Tarts and obsesses about the potassium bromate among the ingredients. He starts snapping at people and then collapses, sobbing. He's taken to jail where Olivia and Astrid get him released and take him home. When they notice that it's a mess, Walter insists that he needs to learn how to take care of himself in case Peter never returns. He figures that he'll continue having breakdowns until he's recommitted back to St. Claire's, and Olivia promises that she won't let it happen.
Mathis takes Peter to the bridge where Ferguson called in his last position. They look around and Peter hears an electric signal from the surrounding woods. Newton and a shapeshifter are there and fire a dart at him. Peter ducks and returns fire, chasing them into the woods. Mathis runs to investigate the gunshots and points out that there's no sign of the two intruders. Peter notices that her hand is bleeding and suspects that she's a shapeshifter. She has no idea what he's talking about, and he tests her identity by asking her about Ferguson's pen. Once she confirms she is who she appears to be, Peter explains about the shapeshifters. Mathis thinks he's nuts and suspects that he's suffering from hallucinations because he can't sleep. Peter realizes that she and Ferguson are having a private relationship. Mathis admits that his hunch is true, and insists on maintaining hope until they confirm he's dead.
The sheriff's men radio to tell her that they've found a body in a quarry. She and Peter go there and discover that the body is a girl, Gwynn. Peter has never seen her before. They talk to the dead girl's sister, Heather, and Peter starts to harass her as he tries to figure out if he and Gwynn crossed paths. Mathis tells him to stop and get control.
In Boston, Walter and Astrid are cleaning up the house. She finds a double-decker car model that Walter found in the building that transitioned over from the other Earth, and Walter gets an idea. He tells Astrid to gather all the objects from the building and from Jacksonville and bring them to the lab. He plans to use the glimmer caused by their presence in the other universe to home in on Peter's own extra-dimensional glimmer.
Mathis drives Peter back to her house, insisting that he's too important to be left alone. They spot Gwynn's truck on the road and confirm that she willingly pulled over, and figure it must have been a policeman that pulled her over. Peter wonders if a shapeshifter disguised himself as Ferguson to capture Gwynn. Mathis wants to call in the FBI but Peter comes up with an idea. He has her drive to the morgue so he can check both bodies. Gwynn has the same indications of an adrenaline surge, and Peter determines each one suffered from two adrenaline spikes: one when they were captured, and one when they died. Peter shoots a bullet into the ceiling to startle Mathis and get a comparative tissue sample with adrenaline. He then proposes that they time the intervals between the victims' adrenaline spikes to place their position when they died.
Olivia goes to see Broyles and tells him that Walter is worried that Peter will disappear for good. When Broyles hesitates, Olivia realizes that he's talked with Peter.
Peter calculates vehicle speed and compares it to the time of the spike intervals, and pinpoints an arc on a map. He figures that the murders would have taken an operating theater, and that both murders must have taken place at the same point. Mathis points out that there's an isolated dairy farm in the area that would be perfect for someone setting up for surgery. They go there and meet with the owner, Craig. Once Mathis asks him about his high school history and confirms he's not a shapeshifter, they ask him for maps of the dairy farm. While Mathis goes to radio for reinforcements, Peter goes inside Craig's house to get the maps. He notices a CD with his name on it, the one that Krista burned for him. Craig realizes that Peter has caught on and attacks him. Peter fights back, pins him down, and demands to know where Newton is. As Mathis comes in, Craig tells them that he just couldn't stop and that he was trying to become closer to the girls. They search the house and find Ferguson, strapped and ready for Craig's next operation.
Later, Peter apologizes to Mathis about how he was wrong to suspect Newton. She figures he doesn't owe anyone an apology, since his theory saved Ferguson and brought a killer to justice. She wishes that she could help him like he helped her, and Peter admits that he doesn't know who he is any more. Mathis tells him that a killer murdered her family while she was in college, and she still hopes to find him someday. The sheriff admits that she was alone for a long time, but finally found someone to share her life and hopes that Peter will as well.
At the lab, Walter is preparing to track Peter. However, Astrid realizes that he's entered the wrong numbers. When she confronts him with the fact, Walter admits that he's not sure if he wants to find Peter, and that he doesn't know what will happen if Peter won't forgive him. Olivia arrives to inform them that she has located Peter and invites Walter to come along with her to collect him.
Peter goes back to his hotel room and listens to Krista's CD. With the help of the music, he finally dozes off. However, he wakes up suddenly when Newton enters the room and holds him captive at gunpoint. The extra-dimensional leader asks the Secretary to come in. A man enters the room: Walter Bishop from the other Earth.
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