Will Graham, now an official special investigator with the FBI, helps Jack Crawford and the BAU unit search for a murderer who buries his victims alive to grow mushrooms. In their therapy sessions, Hannibal begins to gain Will's trust as they bond over responsibility for Abigail Hobbs, and helps Will open up about his true feelings about killing Hobbs. Meanwhile, Freddie Lounds snoops around the BAU's investigation.
Will and Crawford pay a visit to Garret Jacob Hobbs' secluded cabin in Minnesota, which is filled with decaying animal parts and has the upstairs floor covered with deer antlers. Crawford informs Will that Hobbs and his daughter, Abigail, spent a lot of time at the cabin, and suspects her to be an accomplice in the various murders. While finding a lock of hair on the floor, Jack ponders whether Abigail served as the bait for Hobbs' victims. The lock of hair belongs to Freddie Lounds, a tabloids blogger who operates the website TattleCrime.com. In her apartment, Lounds uploads pictures of Hobbs' upper floor and publishes an article about the Minnesota Shrike.
Back at the FBI Academy, Will is annoyed with the standing ovation he receives at his classroom, and lectures the class on his takedown of Hobbs. After class, Will is approached by Alana Bloom, who highly recommends him to attend psych evaluations following his first shooting. Crawford soon joins them, and arranges a therapy meeting with Hannibal Lecter, who was with Will when the shooting took place. At Hannibal's office, Will is informed that he will be declared functional to return to the field. They discuss their guilt in leaving Abigail without a parent, despite saving her life, which is why now they must look after her. When asking for his opinion, Hannibal admits that he finds Crawford's theory of Abigail's cooperation with her father's murders plausible.
Three young hikers stumble upon nine shallow graves in which nine victims were buried alive, in a catatonic state and covered with fungi, to help grow mushrooms. As Will uses his active imagination to recreate the killer's, Lounds appears at the scene, pretending to be the mother of one of the hikers, and manages to secretly take pictures of the BAU's investigation, as well as getting a detective to reveal classified information. As Will recreates the murders, a vision of Hobbs in one of the graves intrudes his mind, as suddenly one of the buried bodies grabs him arm.
Following the incident, Will agrees for Hannibal to conduct another evaluation. While Hannibal dismisses any importance to the appearance of Hobbs, Will believes that the killer uses his victims as fungi fertilizers. Hannibal suggests that perhaps the murderer is fascinated with the nature of the fungi to connect, unlike the human mind, and simply seeks someone to understand him. At the same time, Lounds huddles outside Hannibal's office and records his conversation with Will. During her scheduled time, Hannibal uncovers her true identity, and deletes her recordings.
While dining at Hannibal's house, Crawford is questioned by Hannibal about his special treatment of Will, and questions Crawford's trust in him. Crawford does not give in, and humorously assures Hannibal that he has already had his psyche evaluation. Meanwhile, at the BAU's autopsy, it is discovered that all victims suffered from and died due to kidney failure. The reveal that the bodies were fed sugar water leads to the realization that all victims were diabetic, and their unnatural comas occurred due to a change in their medication. Based on that information, Crawford locates a Baltimore county pharmacy in which 10 diabetic customers have gone missing, and narrows in on one pharmacist who works in various stores in the area, though he is not present during his shift. Will finds the suspect's car, and finds a body covered in dirt inside his trunk, though the victim is still breathing. The suspect's browser history at work includes Lounds' blog, in which she has recently posted an article about Will's instability.
Crawford and his team storm into Lounds' motel room, handcuffs her, and informs her that due to her article, the killer escaped arrest. He pulls out the lock of hair found as the Shrike's "nest," and threatens to arrest her with obstruction of justice, unless she stops writing about Will. In Abigail's room, Will awakens from a dream about the Black Stag and finds Alana reading to a comatose Abigail. While Will chooses not to talk about Lounds' article, Alana reassures him that he saved Abigail's life. Outside her motel room, Lounds is stopped by the detective from the crime scene, who tells her he has been suspended due to their earlier encounter. As Lounds offers him a position in private security, Eldon the pharmacist appears and shoots the detective in the head, splattering Lounds and the area with blood. An unmoved Eldon informs Freddie he read her article on tattlecrime.com.
A shaken Lounds is approached by Crawford, and tells him that Eldon is looking for the only person who could understand him - Will - and that she was forced to supply Eldon with the location of Abigail Hobbs. At the hospital, Eldon, disguised as a nurse, removes Abigail from her room. Will arrives at the hospital, with his gun drawn, and questions the nurses about Abigail's whereabouts. Eldon is caught by Will as he is about to leave the building, and is shot in his shoulder by Will without a warning. As Eldon begs Will to understand him, Will clarifies that he does not, nor will he ever understand him.
During another one of their sessions, Hannibal informs Will that since Hobbs did not appear when he shot Eldon, it is not Hobbs' ghost that is haunting him, but rather killing a man so corrupt that killing him feels good. Despite some resistance, Will admits that he enjoyed killing Hobbs. Hannibal likens it to God's joy in killing frequently. He surmises that it makes one feel powerful.
- The character Gretchen Speck-Horowitz appears speaking to the pharmacist. She previously appeared in one of Brian Fuller's previous shows, Wonderfalls, which also starred Caroline Dhavernas.
- Eldon Stammets is named after Paul Edward Stamets, a leading mycologist (scientist devoted to the study of fungi).
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- Will hints at his backstory, mentioning that he used to work homicide, and that he repaired boat motors in Louisiana. In Red Dragon, Will’s father was a boat repairman who frequently moved between Southern cities during Will’s childhood (“Biloxi and Greenville to the lake boats on Erie”). Will lived in Louisiana for a time working homicide for the New Orleans Police Department before going to work in the FBI crime laboratory, and then taking a teaching post in the Academy, before Jack Crawford enlisted him to help on the Hobbs investigation. After the psychological trauma of the Hobbs and Lecter investigations, Will quit the FBI and retired to fix boat motors in Marathon, Florida, which is what he is doing at the beginning of Red Dragon.
- Hannibal’s dialogue in the closing scene about his suspicion that killing Hobbs felt good to Will and about God dropping a church roof on his worshipers comes almost verbatim from the letter he sent Will after Freddy Lounds’s death in Red Dragon.