Still at the cabin, Dexter treats the bullet graze wound on his leg. He argues with the captive Doakes, tauntingly accusing him of being a killer at heart, much like himself. This would explain why Doakes has more officer-related shootings than anyone else at Miami Metro and why he has always sensed that Dexter was hiding something. Doakes says that he only kills while on the job, but Dexter claims that his Code is better than the criminal justice system. Done bandaging his leg, Dexter leaves.
In the morning, after disposing of Jimenez's remains, Dexter sneaks back into his apartment. Deliberating whether to kill Doakes or set him free, he lies in bed and flashes back to a murder investigation that Harry worked on:
Dexter is awoken by a visit from Rita. She's heard on the news that Doakes is the Bay Harbor Butcher, but the conversation turns to Astor and Cody. With all that the kids have been through recently, Dexter's presence might be good for them. Though this doesn't mean he and Rita are officially back together, Dexter is happy to start seeing the family again, and agrees to accompany them to the beach on Saturday.
At the station, Deb checks Doakes' phone records and learns that he called LaGuerta shortly after the manhunt was launched. Lundy tells Deb to confront LaGuerta; Deb is reluctant, but Lundy argues that she knows LaGuerta better than he does, and that this could be good practice for her, since he'll leave Miami once the BHB case ends—a reminder that leaves Deb disconcerted.
Deb goes into LaGuerta's office and admonishes her for not reporting the call. LaGuerta, stubbornly convinced of Doakes' innocence, challenges Deb to take the matter to Captain Matthews, asserting that protecting Doakes is worth the punishment.
Lundy goes over Doakes' known fake IDs, while Dexter's analysis of the blood slides yields twelve new BHB victims. LaGuerta quietly approaches Batista and gets a list of the twelve names.
Dexter asks Lundy to pull the protective FBI detail off him, and Lundy agrees. Deb objects, but Dexter insists that a trained killer like Doakes wouldn't be dumb enough to come out of hiding just because of a grudge. Deb criticizes Lundy, and it becomes clear that she's upset about his imminent departure from Miami.
Realizing how devastated Deb, Rita, Astor, and Cody would be if they learned the truth about him, Dexter decides that he must kill Doakes. Meanwhile, Doakes finds Jimenez's cell phone on the table and tries to reach it, but Dexter arrives with a bottle of water and a set of killing tools. Doakes drinks the water, which turns out to be laced with a sedative in order to make the kill easier. Dexter also finds and takes the phone.
Losing consciousness, Doakes brings up Harry. Dexter reveals that Harry knew about his homicidal urges and defends him as a legend on the police force, but Doakes snidely replies, "They never told you..." and passes out. His interest piqued, Dexter drops the idea of killing him.
As Doakes sleeps, Dexter comes up with a third option: plant evidence framing Doakes and let the FBI arrest him; anything Doakes says regarding Dexter would be dismissed as insane rambling. After putting Doakes' fingerprints on his tools, Dexter returns to Miami. He tosses the tools into the ocean, where a diving class will discover them. However, Dexter is troubled by Doakes' words about Harry, and has another flashback:
Sometime after Harry has caught Juan Rinez, Matthews visits the Morgans and informs Harry that, thanks to a faulty warrant, Rinez is being released. Furious, Harry gives Dexter his implicit permission to go after Rinez.
Batista tells Dexter that he has custody of Auri this Saturday, and Dexter invites him along to the beach. Dexter is wary of Lila, but Batista clarifies that she won't be coming, since he's only seeing her "after-hours."
At the cabin, Dexter asks Doakes about Harry. Doakes toys with him, surmising that Dexter can't kill him because he actually has a conscience. Dexter begins to display genuine anger, which Doakes enjoys seeing for the first time. Doakes eventually discloses that, while looking into Dexter's past, he learned something about Harry's death that the higher-ups didn't want anyone to know. However, Doakes refuses to reveal anything more unless Dexter lets him go.
Dexter later approaches Matthews and inquires about Harry's death. After some tiptoeing around the issue, Matthews explains that the number of criminals benefiting from the flawed justice system became too much for Harry—it wasn't heart disease that killed him, but suicide. Shortly before his death, he cryptically asked Matthews to watch over Dexter and Deb, and the official autopsy showed that he had overdosed on his heart medication. Matthews buried the autopsy report to protect Dexter and Deb. Reeling, Dexter can't make sense out of Harry, determined policeman and creator of the Code, suddenly killing himself.
LaGuerta approaches Lundy with an alibi for Doakes: during the time that one of the twelve new BHB victims went missing, she and Doakes were on a constant stakeout. She presents a log of personal notes that she took during the stakeout, but Lundy can't accept them as evidence, since LaGuerta's credibility has been undermined by her keeping the phone call a secret. He then berates her for trying to protect Doakes and thus ruining this chance at exonerating him.
At the beach, Batista plays with the kids while Dexter sits with Rita. He confides to her that Harry committed suicide, and that he doesn't understand why. A sympathetic Rita comforts Dexter.
Dexter gets several texts on Jimenez's phone, sent by wanted drug trafficker and murderer Jose Garza, who's waiting for the cocaine delivery. He eventually sets up a meeting with Garza, planning to kill him at the cabin to further solidify the case against Doakes.
Deb finally confronts Lundy about his leaving Miami. The two talk things out, and Lundy reveals that he thought Deb would get tired of him when the BHB case ended, which Deb finds endearing. Lundy then gets a call and learns that one of Doakes' fake IDs was recently used to rent a car.
After learning from Batista that Dexter and Rita are trying to patch things up, Lila purchases Rohypnol pills from a drug dealer. That night, at her loft, Lila enjoys some wine with Batista and eventually seduces him, encouraging him to be rough with her. After they have sex, Lila secretly takes the roofies and passes out. Batista calls an ambulance, unaware that Lila is framing him for rape.
Dexter brings an unconscious Garza to the cabin. Horrified at what's about to happen, Doakes pleads with him not to do this, but Dexter arranges his plastic wrap around the cabin and murders Garza. Afterward, a shaken Doakes tells Dexter to "stay away" from him. These words unexpectedly trigger a final flashback:
Three days before his death, Harry walks in on Dexter and becomes shocked to find him chopping up Rinez' corpse. Dexter happily shows Harry what he did, hoping for approval. Instead, upon taking in the grisly sight, Harry vomits and tells Dexter, "Stay away."
Dexter now realizes the truth: despite glorifying the idea of the Code, Harry couldn't live with it when he actually saw what he had created—he killed himself because of Dexter.