In Edina, New York, State Trooper Pekarski is talking to his wife and driving along a country road when he spots a boy walking along the side of the road. He asks the boy, Teddy Falls, why he's out on the road, and he admits that his parents don't know that he's out alone. Pekarski offers him a ride and drives him toward his home. As they drive, Teddy admits he ran away and the trooper says his parents are missing him. Pekarski looks in the rear view mirror and sees Teddy transformed into an animal-like humanoid. He takes the boy back to base in Jonestown where they admit that they've heard rumors of nutjobs that look like the boy, but this is the first one they've seen. Pekarski takes Teddy's picture and enters it into the computer. The other troopers insist that people need to know, but Pekarski wants it to go through proper channels. Suddenly two men, similar in appearance to Teddy, come in and shoot down the troopers before they can respond. As they take Teddy, he apologizes to the wounded Pekarski before one of the men finishes the job.
Peter tries to convince Walter to get out of the car and into the grocery store center, pointing out that his father hasn't left the house in over a week. Peter assures him that Walter's kidnapper isn't in there, but Walter isn't convinced. Olivia tells them to meet her in Edina at the state trooper station to investigate the death of the three troopers and Teddy's disappearance.
At the Jonestown station, Broyles brings the team up to speed as they meet with the local agent, Frug. They've confirmed the troopers were killed within an hour of uploading Teddy's picture to the central database. The killers left no traces and disappeared. Broyles shows them the photo of Teddy, and Walter claims he saw a boy like that once. Peter realizes he's describing a boy from the movie Deliverance, and points out they saw it together. Pekarski's report indicates Teddy look normal when the trooper picked him up. They find 30-40 reports of people who look similar to Teddy in the photo. Some of them are 30 years old, and talk about individuals transforming from normal to deformed. All of the reports center around Edina and they begin checking out the area. As they go, Broyles warns that the individuals have been hiding for a while, and will do anything to keep their existence a secret.
The trio drives to Edina and Walter worries that there may be some kind of werewolves involved. Olivia hears a low buzz and Walter starts singing a strange song with gibberish lyrics involving an elephant. He admits that he doesn't know what he's singing, but it's related to the hum. Sheriff Velchik comes over and introduces himself, and notes that they know about the "Edina hum." He explains they come from the local military base's turbines. They go into a diner for coffee and confirm Velchik knows about the murders. They show him the photo of Teddy and he appears shocked. However, he admits that he's heard stories about similar deformed individuals. As they talk, a local man, Joe Falls, gets up and leaves. Velchik admits he's never been able to confirm the reports but offers whatever help he can.
Joe goes home and tells his wife Rose that the FBI is investigating the deaths. Rose insists they shouldn't have done it, but Joe believes they didn't have any other choice. Teddy is in the next room, working on his homework.
As they drive to a motel, Olivia calls Broyles, who informs them that the ballistic report has proven nothing definitive. Peter suggests it might be related to the military base and Broyles promises to investigate. As they drive, Walter dozes off and Peter worries that Walter hasn't been able to snap out of the shock brought on by his kidnapping. Olivia admits that she ran into a high school friend who thought she was a freak when he learned what she did for a living. A truck suddenly comes at them and Olivia swerves off the road. She's knocked off and Walter sleeps through the entire thing. The deformed man in the truck comes back and opens fire on Peter, who is unable to get his seatbelt free. He grabs Olivia's gun and returns fire, but the man has moved behind the SUV. As Walter wakes up, the man opens fire but Peter drives him off.
Later, Frug meets with them as his men secure the area. He gets a call informing him that they've found the abandoned truck back down the road. They go to check it out but discover the license plate has been taken off. Walter spots something in the nearby woods and calls Peter over. It turns out to be a butterfly, and Walter is thrilled to report that it's very rare and that Astrid collects butterflies. He goes to get his kit to collect it, humming the same tune from earlier. Olivia is more interested in the traces of blood they find on the ground. They follow the blood trail and Frug's men find Joe, dead from a gunshot wound to the neck. Frug wonders if Peter knows what he saw, but Walter realizes that Joe has metamorphic abilities.
As Joe is taken away, Olivia checks and discovers there's no ID on Joe. She assures Peter that he had no choice but to return fire, and admits that the first person she killed was a trained assassin. Olivia warns him that the first time is rough. Meanwhile, Rose watches from the woods as they take Joe away.
As the team returns to Harvard with Joe's corpse, Broyles calls and tells Olivia that the Army was in the area in the late 70s doing field research near Edina. He's put a call into the DOD but there's no indication the research involved metamorphic abilities. He sends a fax on the files to the lab. While Walter has Astrid put the butterfly specimen away, Olivia reads the files and discovers they involved "Project Elephant," the same as Walter's song. Walter doesn't remember doing any research in Edina for the military. Meanwhile, Astrid takes out the butterfly but discovers that it's now a moth with a deformed wing. Astrid opens up the corpse bag and backs away in horror: Joe has transformed into a deformed monstrosity.
As Walter examines Joe's body, he tells Astrid to feed the moth and hopes it will transforms back. He speculates that both developed the ability to transform in response to the military training. Walter explains that butterflies are one of the few creatures with the ability to transform their entire bodies. He examines a sample from Joe but discovers no indication of a metamorphic ability. Olivia runs the truck's VIN number and confirms it belongs to Joe Falls in Edina. However, the address on the registration is years out of date.
Peter and Olivia drive back to Edina and talk to Velchik. He remembers Joe as a local mill worker who does local small jobs. Olivia admits they haven't been able to make a positive ID, and Velchik says that Joe moved somewhere to the outskirts of town. She asks to look at the town records to find a photo to ID Joe, and Velchik takes them to town hall.
Astrid confirms the moth has a germline mutation, and Walter confirms Joe has the same disorder. The mutation makes them deformed, but he doesn't know what makes them transform. Walter seems to recall seeing the mutation before, but can't remember when. He hums the song again and realizes that he saw the mutation at the military base near Edina. Walter wonders if he did work on Project Elephant and can't remember it. Astrid writes down the words and realizes that the first letters spell out "Harkness." Walter realizes that it's a mnemonic that he created on purpose, and Harkness is the name of a law school library. They go to find out what's there.
Peter and Olivia go through the records and discover the entire "F" section is missing. They go to check the federal records.
As Walter opens up a vent at the library, Astrid asks what happened to him in Edina. He explains that he used work to overcome his grief when Peter was sick. He finds one of his hidden caches in the vent, and a box containing U.S. Army files and photos of deformed individuals. Dr. Edward Cobb was the head of research, and Walter realizes what it all means.
Olivia and Peter fail to find anything but Peter notices that the census numbers don't add up. Velchik calls and Olivia informs him that the "F" files are missing. The sheriff suspects who is responsible and tells them that the local tax collector has told him that Joe moved to the outskirts of town with his wife and son, and his son was the same age as Teddy. He agrees to meet them out on the edge of town. He then goes outside and tells the assembled townspeople that Olivia and Peter don't know anything. Rose disagrees, warning that they have proof. Velchik says he'll take care of it and make it all go away.
Walter and Astrid drive to Edina, and Walter describes how the Army experimented with electromagnetic pulses as a means to scramble the optic nerve of the enemy, making their soldiers invisible. Walter left and the Army realized that the pulse caused genetic disorders. Joe and the moth are the descendents of individuals affected by the pulse. They arrive at the outskirts of Edina and Walter shows Astrid the moth. As they watch, it transforms back into the butterfly. He explains that their perception of the man and moth are what changes.
Walter calls Peter and explains that someone perfected the pulse and used it to conceal the persons with the deformities. Anyone within range of the pulse will see a deformed individual as normal. Walter explains that no one but Cobb would have the imagination and know-how to perfect the pulse. Peter tells Walter and Astrid to go home so they're out of danger. Once he hangs up, Walter lies to Astrid and tells her that Peter wants them to go into the town and find the source of the pulse.
Velchik and his deputy are loading up their guns when Rose comes in and insists that they have to stop before any more innocent people are hurt. Velchik warns that there is a lot at stake, and that when they killed a Federal marshal a few years earlier, no one came looking for the man. He tells Rose to stick to her job and tend the machine.
As they drive through Edina, Walter explains that a large capacitator bank or compression generator would be necessary to transmit the pulse. She suggests that a satellite dish might be responsible and many of the townspeople have one, but Walter figures they simply watch a lot of television. Astrid suggests a big antenna like the one behind a house they're passing. They pull over and knock at the door. As they wait, Walter notices the names Joe and Rose on the door, and remembers that Cobb had a daughter named Rose. Teddy answers the door and Walter confirms that Teddy's grandfather was Cobb. He introduces himself as a friend of Cobb and convinces Teddy to let them in.
Inside, Walter finds a photo of Cobb and his young daughter Rose. When Teddy explains that they have no photos, Walter realizes that a camera wouldn't be fooled by the pulse. Teddy says they have to go but Walter asks to use the bathroom first. He winks at Astrid and leaves, while Astrid makes small talk and offers to play a game of Operation with him.
Olivia and Peter are driving and figure that Joe's father was one of the mutated soldiers. Peter reviews the census data again and notes that the population only goes down when someone dies: no one ever leaves the town. They realize that everyone in Edina is involved. They arrive at the trailer as Velchik drives toward them. Peter realizes what's going on and pulls Olivia down as Velchik opens fire. They run toward a nearby barn as Velchik and his deputy drive after them.
Walter goes into the basement and finds the generator. Meanwhile, Astrid and Teddy are playing Operation when Walter turns off the generator. He comes upstairs as Teddy is revealed in his mutated form.
Velchik and the deputy, their real forms exposed, charge the barn. Olivia shoots the deputy down but Velchik gets the drop on them. He orders Olivia to drop her gun, but a deformed Rose comes up with a shotgun. When he refuses to listen, she shoots him down.
The next day, Rose explains that her father couldn't live with himself after his experiment caused the deformations. He resigned, came back to Edina, perfected the machine, and then offered the townspeople a choice. They could live in Edina where the pulse would allow them to hide in broad daylight, or leave and find their fortune in the world. They all chose to stay in Edina. Cobb stayed there to be with his daughter. The Army never told Cobb they were expanding the scope of the test. Walter says that he remembers Cobb fondly and explains that he believed invisibility would solve lives. Rose tells them that her father succeeded in creating a good life for them.
Walter goes outside where Astrid is waiting with Teddy. Broyles arrives and Walter goes to meet him. He tells Broyles that they need to let the townspeople keep their secret. Walter points out that the two killers were brought to justice, and the population will be subject to experimentation and humiliation. He begs Broyles to spare the people any further harm, and Broyles tells him that if he didn't find the machine, there's nothing to report. Walter realizes what he means and thanks him.
Later, Teddy is standing on the city limits as Walter, Olivia, and Peter drive out of town. Walter admits he admires Rose for exposing her secret to right a wrong. Peter says that he admires his father for speaking up for the townspeople, and admits that he's proud of him. Walter is glad he chooses to see him that way.