Dexter has been unable to satisfy his killing-urges for over a month, due to the constant surveillance by Sgt. Doakes. When the opportunity to kill arises, he has problems executing his victims after having killed his brother. Dexter struggles with his life as a serial killer thanks to him learning that Harry was sleeping with Dexter's biological mother, Laura Moser, before she died and that Harry took his own life after walking in on Dexter in the middle of a murder, unable to deal with the reality of the monster he had created. With his confidence in the Code of Harry and himself destroyed, Dexter plays out the possible resulting scenarios in his head of turning himself in.
Debra continues to struggle with the trauma of her experience with the Ice Truck Killer. For a sense of safety and comfort, she stays with her brother, another new source of stress in Dexter's life. To further complicate matters, treasure hunters discover Dexter's underwater dumping ground for his victims. As the police extract body parts from the ocean, the media dubs the killer the "Bay Harbor Butcher," and FBI Special Agent Lundy is brought in to catch him. A cult following begins to form behind the "Butcher" when it is discovered that his victims were themselves responsible for deaths.
Rita's relationship with Dexter becomes tense as she and her children deal with the death of her ex-husband Paul, who was killed in a prison fight. Paul's repeated suggestions that Dexter was to blame for his imprisonment cause Rita to finally accuse Dexter of setting up her ex-husband. Dexter admits to setting up Paul, but Rita refuses to believe that Dexter premeditated the crime and assumes that Dexter is a heroin addict. He admits to "having an addiction"; in return, she vows to stay with him while he goes through the Narcotics Anonymous program. There, he meets and becomes involved with his sponsor, Lila, a pyromaniac who starts to obsessively pursue Dexter.
Doakes confronts Dexter leaving an NA meeting. Doakes is temporarily satisfied that Dexter's odd behavior can be explained by traumatic experiences from a career in law enforcement and drug abuse. Doakes' suspicions about Dexter eventually return, and he ultimately discovers Dexter's glass slides. The possibility of matching them with the bodies of the Butcher's victims sets up a climactic showdown in which Doakes confronts Dexter at a remote cabin, ending with Dexter overpowering Doakes and keeping him locked in a cage inside the cabin. Dexter then begins framing Doakes as the Butcher after the police discover Dexter's slides in Doakes's car. Lieutenant LaGuerta, Doakes's former partner, is the only one who believes that Doakes is innocent. She finds evidence of this and takes it to Lundy, who rejects LaGuerta's case files.
In the season finale, Lila finds the cabin where Doakes is imprisoned and causes a propane tank explosion, blowing up both Doakes and the corpse of one of Dexter's victims, preventing Dexter from being caught. Lila then meets with Dexter, expecting him to accept her love now that she knows his "dark secret". She catches him preparing to kill her and seeks revenge by trying to kill Rita's children and Dexter. Dexter manages to save the children and escape, later exacting his own revenge on her after she has fled to Paris. In the closing scenes, Doakes' memorial service goes largely unattended, with the exception of LaGuerta, Dexter, and Doakes's immediate family.
