Will is determined to fight for his innocence as Hannibal and Jack try to wrap their heads around the fact he's behind bars. Meanwhile, Alana faces a strained relationship with Will while Kade Purnell with the FBI pays him a visit.
The case of the human soup becomes clearer when a victim that has escaped from the killer's clutches washes downstream after a deadly fall, leaving valuable evidence for the BAU team to uncover. Hannibal Lecter assists on the case, sniffing out clues of his own from of the victim's body.
Meanwhile, Will Graham begins a plan of manipulation from within the asylum, set on proving his own innocence. Hannibal is able to put the clues together before the BAU team, arriving at the killer's silo and helping him to carry out his fascinating, yet deadly tableau... just not in the way the killer intended. Jack tries to deal with his guilt over not protecting Will and submits to mandated therapy after Alana Bloom's scathing report. To Jack's surprise the counseling turns out to be beneficial. The BAU team independently arrives at the silo, finding a human tapestry of forty-seven bodies patched together, the killer hidden in plain sight. Awaiting his upcoming trial, Will is surprised by an unexpected guest - Bedelia du Maurier - who gives him a much-needed boost to his psyche.
Will Graham's trial begins and he must watch as those closest to him are forced to take sides. Jack Crawford scathing report about his conduct with Will, is pulled in conflicting directions. He acknowledges that he may be partially to blame for pushing his star pupil over the edge. To add confusion to an already suspenseful trial, a court bailiff is killed in a Copycat-like manner and those closest to Will start to wonder if they were wrong about him. The outcome of the entire trial hangs in the balance as one last key victim is served up.
A killer murders their victim and converts the cranial cavity into a beehive, leaving the corpse for the authorities. Meanwhile, Beverly secretly consults with Will to figure out who the mural killer is, and Will insists that Hannibal is both the Chesapeake Ripper and the Copycat Killer.
When one of the team's own is found in a grotesque tableau, Will volunteers to assist with the profile and informs Jack that it's the work of the Chesapeake Ripper and the Copycat Killer, the two are one and the same. Dr. Able Gideon is brought back to the asylum to help confirm Will's claims of the Ripper's true identity, but instead suggests to Will the idea of putting an end to the Ripper once and for all. Confined behind bars, Will enlists the help of Freddie Lounds to contact his murderous admirer through her website. Once he has the killer's attention, Will asks for help dealing with Hannibal. Alana becomes suspicious of Will's intentions after reading Freddie's article, and Gideon confirms her suspicions, sending Alana and Jack rushing to find Hannibal before it's too late.
When a city councilman's body is found in a parking lot, intertwined with a tree, the artistry and missing organs suggest the work of the Chesapeake Ripper. Jack and the team race against time to catch the Ripper while he's still on his killing spree. When Will suggests the possibility that the Ripper is filling his pantry with the victims' organs, Jack crashes Hannibal Lecter's dinner party to collect evidence and test the meat for human DNA. Jack's growing suspicions drive Alana even closer to Hannibal, believing he is the victim of a witch hunt. Meanwhile, clues from the tree man help the BAU zero in on a location they believe the Ripper used. There they discover the most shocking revelation of Jack Crawford's career Miriam Lass alive.
When Jack Crawford's star pupil Miriam Lass is found alive, she becomes the FBI's best hope to identifying the Chesapeake Ripper, but her foggy memory complicates the search. Evidence found at the site of Miriam's rescue exonerates Will Graham of any involvement in the Ripper and Copycat cases, and he is released from the asylum. Will warns Dr. Chilton that he could be in danger due to his intimate knowledge of the Ripper case, but when Chilton tries to confide in Jack that he shares Will's fears about Hannibal, he is rebuffed no evidence has been found against Hannibal, despite the FBI's efforts.
Meanwhile, Jack wastes no time in reinstating Will on the BAU team as they hunt for the Ripper. After introducing Will and Miriam to compare notes, Jack's suspicions of Hannibal's involvement continue to build. Only Miriam's memory holds the key to unlocking the Ripper's true identity, but can it be trusted?
When a young woman's body is discovered inside of a horse, Hannibal suggests to Jack that Will be brought in to help crack this peculiar case. Will has seemingly cast aside his suspicions of Hannibal, resuming their doctor-patient relationship, but Alana remains skeptical regarding Will's true intentions and worries that Hannibal may still be in danger. The FBI questions the man they suspect to be the killer in their case, but lack of evidence forces them to let him go. Will and Hannibal race to guard the safety of a witness they believe is in jeopardy, but it might be Will's own judgment that is in peril.
The FBI is called in to investigate the discovery of a truck driver's body, seemingly torn apart by two separate species of animal working in tandem, neither of which consumed their kill. After one of his therapy sessions, Will meets Hannibal's strange new patient, Margot Verger. Will and Margot compare notes on Hannibal and his unconventional advice. Continually encouraging his patients to revel in what they are, Hannibal aims to determine Will's true self by sending him a test, the results of which surprise even Hannibal.
Hannibal and Will grow closer as Will undergoes a transformation. The team takes a look at a disturbing tableaux.
Jack and his team work over new evidence in the Freddie Lounds disappearance. Alana's search for clarity regarding Will and Hannibal only gets more confusing when Will urges her to protect herself. Mason Verger decides what to do with his sister, when he hears about a loophole in his father's will. And Hannibal explains more of his relationship with Abigail to Will.
Will honestly shares his vision of killing Hannibal during a therapy session. In his session with Mason Verger, Hannibal discusses Margot's "accident". They have a very veiled and dangerous discussion leading to a very awkward position for Will, who is under pressure from Jack.
When Hannibal prepares for his departure, he is convinced that Will, will come with him. However Will's having issues tying up loose ends to depart somewhere else entirely.