Dexter must deal with Rita's menacing husband. Debra goes on a date with the prosthetics expert who made prosthetic legs for an Ice Truck Killer survivor. Debra and Angel are investigating the Ice Truck Killer and discover a familiar name with speeding violations near the scene of the Ice Truck Killer's third murder. Dexter investigates Sergeant Doakes's knife victim; he already knows the killer's identity but needs time to locate him. The Ice Truck Killer is finally apprehended, but Dexter doubts that they have caught the correct man.

Under constant surveillance by federal agents, Dexter is unable to dispose of his latest victim's remains. He apologizes to Rita, admitting that his affair with Lila was a mistake, but she is still hesitant to forgive him, as Lila retaliates by pursuing Angel. After finding Dexter's collection of blood slides, Doakes seeks the advice of an old friend in Haiti to analyze them. The department begins to suspect Doakes' involvement in the Bay Harbor Butcher case, but cannot find him for questions. Debra and Lundy spend the night together and contemplate making their relationship public.

Doakes and LaGuerta begin to suspect that Rudy is the Ice Truck Killer, while Dexter finds a suspicious picture of the shipping container where his mother was killed. Doakes begins tailing Dexter, convinced that he is somehow connected to the Ice Truck Killer. A call from her ex-husband makes Rita suspicious of Dexter and his behavior. LaGuerta's replacement, Lt. Esme Pascal (Judith Scott) arrives and takes over the Ice Truck Killer investigation. Dexter recalls that Rudy is in fact his biological brother, whose real name is Brian Moser. Brian intends to kill Debra with Dexter in a reunion with his true family, but Dexter stops him. As the police close in, Brian escapes and Dexter is left with Debra, appearing to have saved her. The same night, Brian breaks into Dexter's apartment and attempts to stab Debra, but Dexter captures him. After an emotionally charged conversation, Dexter slices his brother's throat and leaves him upside down to drain, staging it as a suicide, while wondering what would happen if everyone knew the truth about him.

Dexter removes all of the evidence pointing to his relationship with Vogel before calling the police. Elway and Clayton suspect that Debra is harboring Hannah. Saxon offers Dexter a deal that the two will leave each other alone; Dexter agrees, but secretly plans to kill him before leaving. With a hurricane approaching Miami, Hannah goes to the airport to wait for Dexter, but she is followed by Elway. Meanwhile, Dexter captures Saxon, but realizes that he no longer has murderous urges in response to his relationship with Hannah. Instead of killing Saxon, Dexter calls Debra to arrest him, but Clayton tails Debra and unknowingly interferes. Saxon kills Clayton and escapes after shooting Debra.