At the Lab, a group of excitable Woodchuck Scouts proudly present a decomposed corpse they discovered in a riverbed to HODGINS, CAM and BRENNAN. Hodgins and Cam are impressed, but Brennan reprimands the young girls for disturbing a crime scene, setting off tears and protests.
Cam begins an autopsy on the oozy, gangrenous corpse. She and WENDELL inventory anomalies on the body, including a sulfuric stench and missing toes and finger tips. The absence of fingerprints and the stench cause them to suspect that the deceased was involved in a secret government experiment involving suspended animation. They decide to report their suspicions to Booth. Hodgins takes Wendell to the site where the body was discovered to search for the missing digits.
Back in Angela's Office, BOOTH interrupts ANGELA and Brennan with information on Hodgins' conspiracy theory. He presents Angela with a file on DARPA, the defense agency rumored to be creating genetically-enhanced super soldiers. Angela's facial reconstruction of the victim, showing an eerily chicken-like visage, only makes their theory seem more plausible.
In the Autopsy Room, Brennan, Wendell, Cam, and Hodgins discuss the possibility that the victim was some kind of animal-human hybrid super soldier engineered by DARPA. Quelling their chatter, Cam notes heavy deformities to the body's nasal cavities. Hodgins finds a gapeworm, a chicken parasite, in the victim's neck, only fueling more chicken-soldier speculation.
Booth's search for missing DARPA employees turns up empty, but scanning through the DMV photo database results in an uncanny match: a man named NICK RABIN, the head of personnel at Clucksten Farms, a chicken processing plant. Booth and Brennan head to the farm to investigate and encounter a mob of animal rights activists and community members protesting the farm's practices.
Inside Clucksten Farms, Booth and Brennan interrogate Nick's wife, GAYNOR RABIN. They learn that both Nick's nasal deformities and odd smell were caused by the hazardous conditions at the farm. When his wife learns that Nick was murdered, Mrs. Rabin suggests that one of the "anti-chicken fanatics" is to blame. Meanwhile, back at the lab, Angela updates Hodgins on her ongoing celibacy. He's not interested in breaking her fast, but she insists she was merely making conversation.
At Clucksten Farms, Head of Security JOHN COLLINS takes Brennan and Booth to meet the protesters when they witness a farm worker, GINA MCNAMARA, being confronted by the angry mob. Used to this sort of altercation, John quickly breaks up the fight. He points out JOSH PARSONS, the protesters' ringleader, as a potential suspect in Nick's murder. When Booth and Brennan approach Josh, the protesters fight back, "tar and feathering" them with corn syrup and paper feathers.
In the Interrogation Room, SWEETS and Booth confront Josh Parsons with a video he made documenting the mistreatment of the chickens at Clucksten Farms. They propose that Nick interfered while Josh was filming his latest video, and he killed Nick for getting in the way. Josh adamantly denies the claim, saying he didn't film the tapes. Booth threatens him with an assault charge, and Josh suddenly produces the raw footage on a USB drive.
Cam and Wendell examine the X-rays and discover that the victim was killed due to his neck being wrung. Elsewhere, Angela is visibly upset by Josh's graphic chicken footage. Brennan cannot empathize, instead reminding her colleague to focus on the murder. After extracting data from the video file, Angela determines the footage was shot from a camera purchased by Gaynor Rabin, the victim's wife. Still upset by the mistreatment of farm animals, Angela asks Brennan for a donation to save a piglet from slaughter. Finding such effort to save a single pig illogical, Brennan declines. Angela is infuriated, putting their friendship in peril.
At the Diner, Booth and Brennan confer with Sweets about Gaynor Rabin's possible involvement in Nick's death. Noticing she looks upset, Booth asks Brennan what's wrong, and she mentions her fight with Angela, but quickly changes the topic. She remembers a recent news story about human fingers found in chicken meals at a local restaurant. Brennan suspects those fingers may belong to their victim, and asks Booth to see about obtaining them. Worried, Booth assures that her feud with Angela will be resolved quickly.
Back at the lab, Cam and Brennan handle the finger and toe nuggets, confirming that they do in fact belong to the victim.
At the FBI, Angela approaches Sweets about a donation to save her piglet, but he is more interested in the psychology behind her devotion to the pig, as it relates to her feud with Brennan. He believes her strong attachment to the animal is a rerouting of her libido as a result of her celibacy. Angela leaves, not amused.
Booth interrogates Gaynor, who admits to shooting the Clucksten Farms video, but denies killing her husband, insisting her intent was the opposite. Gaynor was trying to get the farm shut down to protect his health and safety. She wanted to defend her husband from threats and harassment. When asked about how his fingers could end up in restaurant meals, she says they had to have been thrown into a food shipment, meaning the killer likely worked at the farm. Gaynor also suggests another possible suspect, Roy Meyers, a nearby baker whose business suffers from Clucksten's widespread foul odor.
Continuing her fundraising efforts, Angela approaches Wendell for money to save the piglet. Initially he's hesitant about the cause and parting with his meager savings, but sensing her devotion, he sympathetically empties his wallet for her. Touched and thrilled, Angela kisses him, and he passionately kisses her back.
Booth and Brennan visit ROY MEYERS at his bakery, and he admits he's been trying to get Clucksten Farms shut down. The stench is ruining his business. While talking, Roy cuts a cigar with a cutter that could easily remove fingers. Brennan is more interested in Roy's cigar cutter than his story.
In the Bone Room, Angela and Wendell work together and discover data on the damage to the victim's skull. They present their findings to Cam. The images show a strange pattern of injury on the skull, caused by some sort of machine. The pictures also reveal an anomaly in the pattern that indicates something blocked the weapon's strike.
Hodgins enters, stating that results show Roy Meyers' cigar cutter wasn't used to remove the victim's fingers, but he did find evidence of electricity in the victim's digits, indicating a self-cauterizing blade as the method of removal. Even more pertinent, he also found traces of Beak and Feather Disease Virus in the removed thumb. The instrument that cut off Nick's fingers must have been used for beak removal, likely something found at the chicken processing plant.
"Beak Clipper" Gina McNamara is brought in for questioning. She was demoted after charging Nick with sexual harassment. She admits to fantasizing about hurting Nick, and even asks for some jail time just to get out of work, but it's clear she's not the murderer.
Meanwhile, Brennan meets with Sweets about her fight with Angela. Sweets suggests she give up reason for once to make her friend happy. Brennan hesitates, but admits that Angela's piglet is very cute.
In the Ookey Room, Hodgins experiments on Wendell to demonstrate the parameters of the murder weapon. Twirling him in his chair with paintbrushes mimicking the weapon strikes, the three discuss what may have caused the injuries as Wendell's head is smeared with paint. Brennan suddenly realizes the answer.
Per Brennan's request, Booth retrieves the Chicken Plucking Machine from Clucksten Farms and wheels it into the Lab. An inspection finds human blood and necktie fragments. Confirmation needed, Brennan uses Booth's tie to show how one caught in the Plucking Machine could have strangled the victim. The murderer's hand in the machine likely caused some of the strange markings on the skull. If they find a Clucksten employee with a broken hand, they'll have the killer.
Booth and Brennan interview Head of Security John Collins, whose medical records show a recently broken hand. John reveals he fought with Nick over a gas allowance. He admits he was there when Nick was killed by the Plucking Machine, but that he tried to save him. Booth is ready to believe his story until Brennan reminds him that the murderer pushed Nick's head into the machine. Realizing he's been caught, John confesses.
At the Founding Fathers bar, Booth is embarrassed about being duped by John, lamenting that his brain tumor cost him his ability to sniff out liars. Brennan assures him that he's still sharper than most people. Booth feels a bit better. Brennan brings up Sweets' advice about Angela, and Booth concurs with Sweets' opinion. Brennan writes Angela a check for the piglet, and the two make up. Across the bar, Booth spies Wendell touching Angela lovingly. Booth and Brennan toast to each other.