Episode 1 is called Kaiseki. Jack Crawford visits Dr. Hannibal Lecter at his home and immediately attacks him. A protracted and brutal fight ensues, ending with Dr. Lecter stabbing Crawford’s neck with a piece of broken glass. Bleeding profusely, Crawford manages to lock himself in Lecter’s pantry. Twelve weeks earlier, Kade Pruell, an investigator for the Inspector General’s Office, warns Crawford of his misconduct, while pressuring Alana Bloom to recant her complaint, namely about Crawford’s mishandling of Graham’s instability. Bloom refuses, stressing that the truth must go on record. Dr. Lecter gets to walk in Graham’s shoes when six partially preserved bodies are found in a river. Dr. Lecter theorizes that the killer is preserving the bodies to create a human model collection and that those in the river are imperfect castoffs. In the Baltimore asylum, Graham is determined to uncover how Dr. Lecter sets him up and enlists Alana to help him recover lost memories through hypnosis. While not immediately successful, he later has a flashback of Dr. Lecter forcing Abigail Hobbs’ ear down his throat with the use of a plastic tube. The killer strikes again, kidnapping a young man and taking him, alive, to an empty silo where his collection is revealed: an interconnected collage of naked bodies.
Episode 2 is called Sakizuke. The young man Roland Umber, escapes from the silo, but is chased by the killer through a cornfield to the edge of a cliff and dies attempting to jump into the water below. The BAU team recovers his body but assumes he was discarded and dumped like the others. Dr. Lecter picks up the scent of corn on him, which he keeps to himself. Dr. Bedelia du Maurier terminates her relationship with Dr. Lecter, having come to the conclusion that he is a dangerous man. Beverly Katz continues to use Graham to help with the case and, using photos of Roland Umber’s body, Graham realizes that he had in fact escaped and was not discarded. In return for his help, Katz promises to look into Graham’s possible innocence. Dr. Lecter finds the silo without informing the BAU and kills the murderer, adding him to his own mural. Prunell visits Graham in the asylum and offers him the chance to avoid the death penalty by pleading guilty, which Graham refuses. Bedelia du Maurier visits Graham, standing close and whispering “I believe you” before being forcibly removed by orderlies. Dr. Lecter goes to Bedelia du Maurier’s house, seemingly to silence her, only to find the furniture covered and the house empty.
Episode 3 is called Hassun. Graham’s trial begins and the prosecution paints him as an intelligent, creative psychopath. Crawford puts his job at risk by testifying that he may have pushed Graham too far by keeping him on the investigative team, though the admission allows him some relief. Graham’s lawyer receives a severed ear in the mail, cut from a corpse within the previous forty-eight hours, causing doubts to stir among those who believe in Graham’s guilt. Katz, Price and Zeller determine that the ear was severed using the same knife that cut off Abigail Hobbs’ ear, which was signed out of the courthouse evidence room by the bailiff in Graham’s trial, Andrew Sykes. A large fire is triggered when the FBI raid his apartment, but it does not destroy a key piece of evidence: Sykes’ body mounted on a stag’s head, missing an ear, face cut into a Glasgow smile and set on fire: all of the things Graham supposedly did to his victims. Dr. Lecter presents the forensic reports to Graham, who deduces that Sykes was killed in too different a manner from the others to be the same killer. Dr. Lecter agrees, but urges Graham to lie about who he thinks killed Sykes in order to exonerate himself. The prosecution picks up on the dissimilarities as well, and succeeds in having the bailiff’s murder deemed inadmissible. The next day, the judge in Graham’s trial is found brutally murdered and displayed in the courtroom. This prompts a mistrial and saves Graham from conviction, for the moment.
Episode 4 is called Takiawase. Graham agrees to an intense stimulation with flashes of light by Dr. Chilton, during which time he realizes that Dr. Lecter was tacitly encouraging his encephalitis. Dr. Chilton confronts Dr. Lecter about this, but is not hostile, relating to Dr. Lecter as another physician accused of manipulating his patient into murder. An acupuncturist lobotomizes suffering patients, leaving them to die in meadows. Her first victim is found with a beehive occupying his half-empty skull; the second is found still standing, brain dead but physically alive. After the second victim is discovered, he is immediately connected to the first as patients of the acupuncturist. When Crawford visits her, she turns herself in without a fuss. Bella Crawford talks to Dr. Lecter about the possibility of suicide in the face of her lung cancer, something which he encourages, citing Socrates and describing death as a “cure”. Later, Bella visits Dr. Lecter’s office after taking an overdose of morphine, and falls unconscious. After flipping a coin, Dr. Lecter saves her life with a naloxone shot. Later, he visits her and Crawford in the hospital, and Bella slaps him across the face. Katz, on Graham’s advice examines the body of James Gray, the mural killer. She finds that the stitches connecting him to the mural were also surgical stitches on an opening through which his kidney was removed. Katz, starting to suspect Dr. Lecter and against Graham’s advice, breaks into Dr. Lecter’s home and discovers his murder dungeon. She removes a package from a freezer but is caught by Dr. Lecter and gunshots are fired.
Episode 5 is called Mukōzuke. An anonymous tip brings Freddie Lounds back to the observatory she and Dr. Chilton was taken to by Abel Gideon. There she finds the body of Beverly Katz, sectioned vertically and displayed in tableau. Graham is brought to the crime scene and convinces Crawford that it is the work of the Chesapeake Ripper and the mural copycat; that they are one and the same. A post-mortem examination of Katz reveals that her kidneys were removed and replaced with the kidneys of James Gray, the mural killer. Graham convinces Chilton to return Abel Gideon to the asylum, to glean information about the Chesapeake Ripper’s identity. Graham uses Lounds to write an article, hoping to inspire contact from the killer of the bailiff and the judge at his trial. A new orderly at the asylum, Matthew Brown, confesses to Graham that he killed Sykes, hoping it would exonerate Graham, but the death of the judge was someone else’s work. Brown asks Graham how he can serve Graham, who tells Brown he could kill Dr. Lecter for him. Gideon overhears this and gives Alana the chance to save Graham from himself. The orderly tranquilizes Dr. Lecter while the latter is swimming laps, slits his wrists and strings him up with a noose, and is about to kick away the bucket on which Dr. Lecter is standing when Crawford arrives. He shoots the orderly, who even while falling dead manages to kick the bucket out, but Crawford saves Dr. Lecter.
Episode 6 is Futamono. Crawford confronts Graham about setting the orderly on Dr. Lecter, and Graham denies it but tries to make Crawford see that Lecter is the Chesapeake Ripper by explaining to him why he only kills in sounders of three or four; he has to eat the meat he takes before it spoils. Graham assures Crawford that if the Ripper is killing again, Dr. Lecter will be throwing a dinner party. Sure enough, Dr. Lecter soon invites Crawford to a gathering he is hosting. Meanwhile, local city councilor Sheldon Isley is found surgically grafted onto a tree in a parking lot (for which Isley brokered the development deal and in the process destroyed the habitat of some rare songbirds), his chest cavity emptied of all organs except his lungs and stuffed with poisonous flowers. The autopsy reveals a number of Ripper tell-tale signs and that Isley was drowned. Price and Zeller determine from the water in his lungs that he was killed within a fifty-mile radius. Chilton records Abel Gideon confessing to Graham that he was in Dr. Lecter’s home, but Gideon denies this when questioned by Crawford. Gideon is beaten by a pair of guards and put in the infirmary. Dr. Lecter throws his dinner party and Crawford takes a few samples of the food to Price and Zeller to be tested. Alana and Dr. Lecter sleep together and Dr. Lecter kidnaps Gideon from the infirmary while she is sleeping (helped by a drugged glass of wine). The infirmary guard is killed and strung up with fishing lines. Dr. Lecter uses Alana as an alibi when confronted by Crawford. Dr. Lecter cooks and serves Gideon’s leg to him as a last meal. Though Price and Zeller do not find any human tissue in the samples of Dr. Lecter’s food, they do find body materials in the fishing lures from such victims as the Judge, James Gray, Miriam Lass, all the way back to Marissa Schur. Crawford and his team finally realize that there was no “Copycat Killer,” responsible for the deaths of Boyle, Schur, Sutcliffe, and Madchen: it was the Chesapeake Ripper all along, toying with them. They also find a piece of rare tree bark, which Crawford traces to an abandoned farmhouse in the initial search area, where he finds Miriam Lass still alive.
Episode 7 is called Yakimono. Miriam Lass is brought in to identify the Ripper, but has no memory of her encounter with Dr. Lecter and only vague recollections of her captivity. When Dr. Lecter himself is brought in, Miriam is positive it is not him. The evidence gathered from the most recent Ripper killings serves to prove that Will’s alleged victims were actually the Ripper’s, exonerating him of all charges. Graham is released from the asylum and urges Dr. Chilton to share what he knows about Dr. Lecter’s unusual psychiatric treatment on him, by confessing his own psychic driving of Abel Gideon. Graham figures out that Alana and Lecter are together and warns her to stay away from him. He visits Miriam and tells her about the flashes of light used to induce his blackouts. Miriam recalls similar experiences with her captor. He drops in on Dr. Lecter confronts him with a gun. He says killing Dr. Lecter would feel right, but ultimately doesn’t. Crawford takes Miriam to Lecter’s office and he performs hypnotic regression therapy on her. The last thing she remembers before being captured is the Wound Man illustration. Price and Zeller find one of Lecter’s fingerprints on a flower from Sheldon Isley’s body, and Crawford repeats what Graham said in the farmhouse, i.e. that whatever evidence is found, it would lead away from the Ripper. Drugs are found in Miriam’s blood which were used in both Graham and Gideon’s treatment, pointing to either Dr. Lecter or Chilton as the suspect. Crawford wants them both brought in, but Dr. Lecter moves first and frames Chilton by placing Gideon’s mutilated body in Chilton’s house and murdering the two FBI Agents who were to bring Chilton in for questioning, dressing one of them as the Wound Man. Chilton goes to Graham for help, intending to flee the country, but Crawford catches up with him first and brings him into custody. While Alana is questioning Chilton, Miriam, watching, “remembers” him performing the treatment on her, identifying him as the Ripper. In a moment of rage and confusion, she takes Crawfords gun and shoots Chilton in the face. Graham visits Lecter again and asks to resume his therapy.
Episode 8 is called Su-zakana. Dr. Lecter begins therapy with a new patient named Margot Verger, who suffers abuse at the hands of her sadistic brother Mason. Will Graham, now cleared of being the Chesapeake Ripper, resumes assisting the FBI, and willingly continues his therapy with Dr. Lecter. Finding a female victim placed inside a dead horse’s uterus, Graham and Crawford interview previous stable employee Peter Bernardone, who denies committing the crime. Performing an autopsy, the horse victim is found to have a live bird trapped in her chest cavity, and soil found inside her throat leads the FBI to a mass burial ground. Graham questions Peter further, who states he placed the soil to lead them to his social worker Clark Ingram who is responsible for the mass grave and the horse victim. Clark is interviewed by Alana, telling her Peter is sick and sometimes violent. Observing, Graham tells Crawford that Peter isn’t guilty and accuses Clark of being the real killer; despite Clark’s counter-accusation of Peter, Graham sympathizes with Peter’s vulnerable state, and believes he is being manipulated, but Crawford lets Clark go. Peter returns to the stables, only to find Clark has used a hammer to kill a horse that had earlier injured Peter further implicating him. Graham and Lecter later arrive at the horse stable as Peter is sewing up the dead horse’s torso, and they learn he placed Clark inside the horse. They take Peter outside, where he clarifies that he did not murder Clark, but instead trapped him alive so he could experience the fate of his victims. Returning to the stable to find Clark emerging from the horse and picking up his hammer, Graham holds him at gunpoint and threatens to kill him for trying to frame Peter. Dr. Lecter warns that killing Clark won’t resolve Graham’s internal conflicts. After Lecter takes Graham’s gun, the pair detain Clark for his crimes. Lecter then confides in Graham that he is fascinated with his unpredictability.
Episode 9 is called Shiizakana. We start with Will’s revenge dream. He has Hannibal tied up to a tree with the Ravenstag pulling on the ropes. He is trying to get Dr. Lecter confesses, but Lecter only confesses his love. Will then sees Dr. Lecter turn into the Wendigo, and pulls the ropes severing his head as blood spatter’s everywhere. When he wakes up, he is unsatisfied with the result. A truck driver is found horribly mauled, and Crawford believes it is not a simple animal attack, but the work of someone with a large animal trained to kill on command. Later discovering a couple who are similarly mutilated and killed, the BAU team realize that while it appears to be an animal, it is more likely a killer who stalks and kills while wearing a mechanical beast suit. Dr. Lecter informs Crawford that he previously treated Randall Tier, a patient who fits the profile; only a teenager when Lecter treated him, Tier suffers an identity disorder, causing him to believe he is an animal in the body of a human. Meanwhile, Graham is approached by Margot Verger, seeking insight on Lecter’s unusual therapy, and the two discover that they share similar personal problems. Visiting Lecter, Graham informs him that Dr. du Maurier confided her belief in him, and questions if Dr. Lecter has a history of manipulating patients. Lecter approaches Tier and warns him the FBI is investigating him, and asks him to kill Graham. After one of his dogs, Buster, is attacked and injured outside his home, Graham rescues it and locks himself inside, only for Tier to break through a window and attack him. As Dr. Lecter returns home, he enters his dining room and finds Graham has killed Tier, and has laid the corpse on his dining table.
Episode 10 is called Naka-Choko. As Randall Tier smashes into Graham’s house, Graham alternates seeing him as the Ravenstag, the Wendigo, and as Lecter. A struggle ensues and, overpowering Tier, Graham pummels him before snapping his neck. Taking Tier’s body to Lecter, Graham states he and Hannibal are even, having both sent psychopaths to kill each other. Crawford asks Lecter and Graham to analyze Tier’s corpse, parts of which have been combined with a saber-tooth display. Both Graham and Lecter discuss the former’s actions, their conversation disguised as a crime scene analysis. Meeting with Freddie Lounds, Graham learns she still believes Graham’s story of Lecter being the real Chesapeake Ripper. Margot visits her brother, Mason Verger, who shows her that he is training specially bred pigs to eat people alive. After a therapy session where Dr. Lecter subtly suggests that one way for Margot to get revenge on her brother would be for her to get pregnant, Margot returns to Graham’s house again, and after further confiding in each other, they have sex, intercut between Hannibal and Alana having sex and Will also sees the Wendigo. Lounds visits Alana Bloom for an interview, and after noting that Tier is the fourth ex-patient of Lecter’s to have been murdered, states her suspicion that Graham and Lecter are killing together. Mason meets with Hannibal and explains he is suspicious about what Margot may disclose. When Lecter then outlines doctor-patient confidentiality and offers to treat Mason, he accepts, then offers Hannibal one of his hybrid pigs for slaughter. Learning of Lounds’ suspicions from Alana during a dinner with Hannibal, Alana and Will, Lecter waits in her apartment to kill her. Concurrently, Lounds arrives at Graham’s house and investigates his locked barn, where she finds Tier’s bloodied animal suit along with his jawbone. Graham appears, and when Lounds flees and calls Crawford, Graham overpowers her. Crawford shares Lounds’ phone call, only unintelligible screams, with Graham, who mentions he invited her to an interview where she failed to attend. Joining Lecter for dinner, Graham provides the ingredients and meat, and is vague about the meat’s origin. Eating together, Lecter presses Graham on its source, and the latter confirms that it is “long pig”.
Episode 11 is Kō No Mono. Will has a dream of the Wendigo and Ravenstag and turning into the Wendigo himself. Hannibal and Will have dinner over Ortolan birds and discuss Freddie Lounds. At the TattleCrime offices, a burning body in a wheelchair rolls into the parking garage, and a dental analysis confirms it is Lounds. Margot meets with Graham and Lecter, informing them she is pregnant with Graham’s child, but that she is hiding it from Mason. Graham is visited by Alana, who is worried about his relationship with Lecter, and asks if he killed Lounds; Graham responds vaguely, but gives Alana his pistol and tells her to practice using it. Mason attends therapy with Lecter, who implies Mason could have an heir through Margot, hinting at her pregnancy. Graham attends Lounds’ funeral with Alana, and further implies he murdered her. Several hours later, Lounds’ grave is found disturbed, her body posed like Shiva, which Bloom deduces was done by an admirer of Lounds’ killer. Alana starts to suspect Lecter and Graham. Margot, aware Mason knows of her pregnancy, attempts to flee, only for Mason’s assistant Carlo to crash into her car. Waking on an operating table, Margot learns from Mason that he is having her made infertile, leaving him as the only source of any family heir. Alana confronts Crawford, demanding to know what he and Graham are hiding; Crawford reveals Lounds is alive. Learning what Mason did to Margot, Graham breaks into his farm and, when taunted by Mason, hangs him over his pit of pigs. Graham spares Mason, but notes Lecter is manipulating them all, and suggests Mason feed Lecter to his pigs.
Episode 12 is called Tome-Wan. Meeting for therapy, Graham claims that Lecter wants Mason dead, and that he informs Verger of it; despite agreeing with the doctor, Graham still fantasizes about feeding Lecter to Mason’s pigs. Learning Mason compares maiming Margot to “playing chicken”, Lecter informs Graham and Margot, who suggest she seek revenge by surviving her brother rather than kill him. Speaking with Crawford, Graham is told to tread carefully, as his mutilating Tier’s corpse contradicts his self-defense claim. Crawford reveals he has located Dr. du Maurier. Graham interviews her and says the FBI will give her complete immunity. She admits she killed the patient who attacked her. She says it was self-defense, but she was also under Hannibal’s “influence”. She says Hannibal never uses coercion, only persuasion. She warns Graham be cautious lest he be “persuaded”. Meeting with Lecter, Graham boasts awareness of his manipulative ways; concurrently, du Maurier warns Crawford that if they think they will catch Lecter, it’s because that’s what he wants them to think. Three of Verger’s employees capture Lecter and take him to Verger’s farm, where he is to be fed to the pigs with Graham brought in to witness. Asked to cut Lecter’s throat to encourage the pigs, Graham instead cuts him free before being knocked out. Captured by Lecter, Verger is forced to inhale several psychedelic drugs, after which Lecter is able to convince Verger to mutilate his own face. Regaining consciousness, Graham returns home to find Verger removing and feeding pieces of his face to the dogs. Lecter asks Graham what they should do with Verger, Graham replies “he’s your patient”. Lecter breaks Verger’s neck, leaving him alive but paralyzed. Mason, now bedridden and in Margot’s care, lies to Crawford and tells him that his mutilation was due to an accident involving his pigs. Speaking with Lecter about their relationship, Graham warns they will soon be caught, and suggests Lecter reveal himself to Crawford.
Episode 13 is called Mizumono. Speaking with both Lecter and Crawford, Graham reflects on his relationship with both and, when both ask if he can be trusted, he confirms. Graham requests Lounds respect Abigail Hobbs’ memory and write only on him and Lecter, and when Lounds questions if Graham expects to survive, he does not answer. Helping Lecter destroy his patients' records, Graham brushes off Lecter’s suggestion they escape without confessing, and when they pass each other, Lecter (who has an extremely heightened sense of smell) recognizes Lounds’ scent on him. Alana, accepting Lecter is the Chesapeake Ripper, warns Graham of trapping Lecter, as he could be caught by Lecter instead. Sharing a final meal, Lecter questions Graham’s loyalty and, when asked if he would take Crawford’s forgiveness, Graham notes it isn’t an option as Crawford wants justice. Crawford is confronted by Prunell, and forced to take a work absence; as he allowed Graham to mutilate Tier and is plotting to entrap Lecter, she finds him unfit to work. Warned by Alana that the FBI is attempting to arrest him, Graham attempts to further earn Lecter’s trust, and phones to warn him. A fight breaks out between Crawford and Lecter; Crawford, wounded, hides from Lecter in the pantry, only for Lecter to be held at gunpoint by Alana. Lecter tells Alana to walk away or he will kill her; she tries to shoot Lecter, who reveals he emptied her gun earlier. Escaping upstairs and reloading, Alana suddenly finds she isn’t alone; turning around, she finds Abigail Hobbs alive, who apologizes and pushes her out the window. Graham, arriving to find Alana seriously injured, phones for help and enters to find Jack. Graham finds Abigail, who again apologizes, stating she obeyed Lecter as she didn’t know what else she could do. Lecter appears, embracing Graham and stabbing him with a linoleum knife, while explaining that he spared Abigail as a surprise. Lecter forgives Graham for repaying his trust with betrayal, but questions if Graham will ever do the same as he cuts Abigail’s throat and leaves the others to bleed. He is next seen aboard a plane to France with Dr. Bedelia du Maurier.