The episode opens with Will hunting the elusive stag in the woods at night. He fires at it. Following a violent blood trail to a stopping point, he briefly glimpses it in its new form -- while it has antlers, the head and body are more human now, the figure shrouded in darkness while the eyes glow red.
Will awakens from the nightmare to find his hands, bare feet and shins are caked in mud. He is once again in a fugue state, the lines between his reality and dreams increasingly blurred.
After forcing down medication, Will vomits into the sink, where he is shocked to see a human ear after stepping back. He huddles on the front porch as Hannibal pulls up in his car. Will tells him he took Abigail to Minnesota but came back without her. Hannibal also finds the ear in the sink while Will mutters about not even remembering coming home to sleep. He asks Will to focus and think of the last time he saw Abigail -- just before he had his episode in the cabin in Minnesota. Will confesses that he hallucinated that he killed her but is certain it wasn't real as Hannibal feigns concern. He tells Will they have to call Jack, that he cannot run from this.
Jack arrives on the scene with the FBI team. He asks Will what they will find in Minnesota before sending him off for processing. He passes a dejected looking Forensics team, everyone eyeing him with suspicion. His dogs whimper as Will gets taken away. Will is in a daze as Agents Zeller and Price go over what Will has on him, taking pictures of cuts and scars on his feet and ankles. Katz finally presses him for answers while she scrapes under his fingernails, asking how it got there. Will is still uncertain of how it happened, and Katz tells him to interpret the evidence. He breaks down, admitting that all evidence suggests he killed Abigail Hobbs.
In his office, Jack meets with Alana to go over what they have found so far. The tissue of the ear as well as the blood under Will's fingernails are a match for Abigail, evidence suggesting that she put up a struggle. Alana can't hear anymore, blaming Jack for pushing Will too far when he knew that he was crumbling under the pressure. He defends himself, saying that the decision to keep Will in the field was made to save lives and was done so under the advisement of Dr. Lecter. Alana says Hannibal must have seen something was wrong. She says the dementia that Will was exhibiting was a symptom, not a disease, but Jack reveals that brain scans turned up nothing. She says that Abigail's blood is on everyone's hands, not just Will's.
After emotionally breaking down in her car, Alana goes to see Will in the FBI interrogation room while Jack observes. He tells her that she must feel like she dodged a bullet in not taking up his romantic overtures. Alana says she feels more wounded. She promises him that she will take care of his dogs until animal services can find homes for each before asking Will if she can run a few psychological tests. Will references drawing a clock face as Hannibal made him, which puzzles her. She asks him to draw one for her and, once again, what appears normal to Will is deformed in reality. Alana sighs, suddenly understanding that Hannibal knew more than he was letting on.
Hannibal visits Dr. Du Maurier, tearfully relaying Will's crimes to her and blaming himself for Abigail's death. Du Maurier talks about the grieving process, that it is only natural to go through it after a life has impacted his as much as Abigail's did. He says he never considered having children, but felt a connection to Abigail. She tells him that Will is a loss to grieve as well, but Hannibal says he has not given up on him. Du Maurier recommends he not take part in rehabilitating Will should he be convicted. He says it is tough to accept failing both Will and Abigail so profoundly.
In the morgue, Agent Price analyzes one of Will's homemade fishing lures, showing the results to Jack and Alana. Katz says analyses revealed that several of the lures had parts of human remains on them -- specifically, the copycat's "victims." Jack sees it as further evidence against Will, but Alana is still in disbelief.
In the interrogation room, Will once again hallucinates of the human/stag, barely visible through the two-way mirror. Jack shakes him out of it, letting him know that they are transferring Will to a secure medical ward. Will is shocked to learn of the human remains found in Will's fishing lures -- he tells Jack he wasn't sick when the first two copycat victims were killed. Jack doesn't want to hear this, as if Will killed the victims while not in a fugue state, it would suggest that he was fully aware of what he was doing the whole time. Will says Jack should be afraid of whoever is framing him, warning him that whoever it is must be close to Jack, perhaps even working alongside him. Jack thinks he is delusional, reading him his Miranda rights before sending him away in handcuffs. In the ambulance, Will mimics Gideon's tactic of pulling his thumb out of the socket in order to remove the handcuffs before attacking his guard.
At Hannibal's office, Alana and Jack meet with Dr. Lecter to inform him of Will's escape, though the driver and the guard were not killed. Alana shows him the drawing of the distorted clock face, prompting Lecter to reveal a normal looking clock face which Will drew for him two weeks prior. They go over the symptoms and Alana deduces encephalitis, something that would not show up on a brain scan unless doctors were specifically looking for it. Jack is less and less convinced that Will is suffering from dementia, convinced that an intelligent psychopath could have faked the clock test. Hannibal lies, saying that Will was alone in the office before they left to get Garrett Jacob Hobbs, possibly enough time to alert him that the FBI were on their way.
After Jack and Alana leave, Hannibal realizes that Will is hiding in his library. Hannibal tells him that all signs point to Will's guilt. Will says that if it were just Abigail, he would almost be convinced of his own guilt, but the other victims have him believing that he was being manipulated. He tells Will they should discuss how he could have killed all the copycat victims in order to disprove that he did.
Will hallucinates sculptures of each of the victims, starting with Cassie Boyle, saying he was not even in Minnesota when she was killed. He again sees the human/stag out of the corner of his eye as Hannibal tells him that since Cassie vanished on Saturday and was found on Monday this does not disprove his guilt. They move on to Marissa Schurr, then Dr. Sutcliffe, each of the bodies appearing before Will like one of Hannibal's sculptures as Hannibal continues to suggest motives behind Will killing each of them. He tells Will that he catches killers by getting into their heads, but they also get into his own. Will tells him if he really wants to help, Hannibal should take him to Minnesota where Abigail supposedly died.
That night, Hannibal drives while Will sleeps in the passenger seat. The next morning, Jack and Alana visit Dr. Du Maurier to see if she has heard from Lecter, worried that Will has abducted him and taken him to Minnesota. Will and Hannibal pull up to the Hobbs family home, and Will puts himself in Garrett Jacob Hobbs' position on the day he died. Will hears Hannibal's voice on the other end of the phone line. Hannibal wakes Will -- he had been dreaming. They are at the Hobbs house, but it is now evening. Will and Hannibal look at the crime scene in the kitchen, a massive blood stain still remaining. Hannibal remarks that if Will was in Garrett Jacob Hobbs' frame of mind when he killed her, the police will never find Abigail's body since none of it would have gone to waste.
Hannibal continues to push Will into believing his own guilt, Will quietly and defiantly insisting he knows who he is. He isn't sure who Hannibal is anymore. He knows one of the two of them killed Abigail, and Hannibal replies that one of them is about to kill the other as Will slowly raises his gun. He tells Hannibal he can see who he truly is now, reciting Hannibal's plan to hold Abigail's secrets until she was of no use to him anymore. Hannibal asks if it would feel good for Will to kill him now, as he admitted it did when he killed Garrett Jacob Hobbs. Will replies that Hobbs was a murderer, asking if Dr. Lecter is a murderer as well, just as Jack comes in the front entrance. Jack tells him to put the gun down, but he raises to fire on Lecter and Jack clips in his right shoulder. Will crumples to the floor, asking Jack if he sees now -- Hannibal turns into the stag/human figure, standing side by side with Jack.
In the hospital, Hannibal sits with an unconscious Will and explains to Jack that doctors are keeping him under to treat his encephalitis. He had apparently told Jack that Will forced him to go to Minnesota at gunpoint, but admits he would have wanted to go with him regardless to help him. Jack feels a pang of guilt, shaken at how broken Will seemingly has become from his work. Hannibal remarks that no one in the room will ever be the same again.
At Dr. Du Maurier's home, Hannibal pays a visit with homemade dinner of veal. She asks what is on his mind, and Hannibal reveals that he is paying Will a final visit tomorrow to bid him farewell once and for all. Du Maurier comments on the controversial nature of veal, before warning Hannibal that they are starting to see his pattern: that he develops relationships with patients prone to violence. She tells him that Jack's beliefs about Hannibal could begin to unravel if examined under scrutiny.
At Baltimore State Hospital the next day, Hannibal visits with Will in his cell, similar to the one Gideon occupied. Will slowly gets up and greets Hannibal at the bars. Hannibal smiles as the episode ends.