Using Dexter's satellite navigation system, Lila West arrives at the cabin in the Everglades. She breaks in to find an imprisoned James Doakes, who tells her that Dexter is the Bay Harbor Butcher. She can only sympathize with Dexter, however, for having to hide such an enormous secret, and refuses to unlock Doakes' cage. Convinced that Dexter is her soulmate, Lila tries to help him by setting the cabin on fire with Doakes inside. Meanwhile, Lundy's task force has determined Doakes' location, and Dexter must race his colleagues to reach the cabin first. When he arrives at the cabin, he discovers that it has been destroyed in a fiery explosion and at first believes it to be a miracle. The next morning, the police find Doakes' body in the water, while Dexter embraces his freedom. He visits his girlfriend Rita's house, where they reconcile after having sex.
Lt. LaGuerta, grieving the loss of her former partner, is in denial over Doakes' incrimination and tries to collect donations for his memorial service. Debra remains determined not to let the end of the Bay Harbor Butcher case break up her relationship with Frank Lundy, but their plans for a vacation are crushed when Lundy is called to Oregon to work on another murder case.
With all of the evidence of the Bay Harbor Butcher murders pointing to Doakes as the killer, the case is closed. Forensic investigator Vince Masuka tells Dexter the gas in the cabin was turned on while the stove was lit and, when Dexter sees his own satellite navigation system while cataloging evidence, he realizes that Lila must have found the cabin. He meets with her at the aquarium and tells her that he, like her, has no emotions and lives a life devoid of feeling. They form plans to leave Miami together, Lila not knowing Dexter secretly intends to kill her. When he visits her apartment the next day, though, he finds Debra there, trying to persuade Lila to leave town. Dexter is forced to lie about running away with Lila in front of Debra. A hurt Lila then leaves with what she recognizes as Dexter's bag of murder equipment. She goes to Rita's house and drugs the babysitter so that she can abduct the children, Astor and Cody. When Dexter realizes that Astor and Cody are missing, he goes straight to Lila's apartment, where she lights another fire and locks the three of them inside. Rita calls Debra for her help, and Debra decides to skip her flight to Oregon with Lundy to help with finding the children. Dexter manages to free Astor and Cody through a small window and eventually rams down a thin wall allowing him to escape.
Some time later, Dexter travels to Paris, where Lila has fled to, and kills her in her hotel room. Back in Miami, he attends Doakes' memorial service with LaGuerta. Debra and Detective Batista are awarded for their work on the Bay Harbor Butcher Case.