Several months after the second season finale, Dexter hunts down drug dealer Fred "Freebo" Bowman but mistakenly kills an innocent man who happens to be the younger brother of Assistant District Attorney Miguel Prado. Dexter frames Freebo, but begins to question the necessity of his father's code. Meanwhile, Debra has reformed her life and is determined to become a detective, but refuses an Internal Affairs officer request to co-operate in an investigation of Quinn. Also, Rita realizes that she is pregnant.
Several months after the deaths of his colleague Sgt. James Doakes and his Narcotics Anonymous sponsor Lila, Dexter's life has returned to normal. He looks up a drug dealer, Fred "Freebo" Bowman (Mike Erwin), whom he believes to have killed two female college students. Pretending to want to buy heroin, Dexter visits Freebo's house, where he sees Freebo's girlfriend Teegan Campbell (Jelly Howie). He returns to the house at night and finds Freebo fighting with another man (Oscar Prado). When the man attacks Dexter, Dexter stabs and kills him in self-defense. Dexter flees, shocked about breaking his father Harry's "code" and killing an innocent person. He is called to the scene the following day and discovers that the man was Oscar Prado, the brother of well-known assistant district attorney Miguel Prado. Miguel seeks an explanation and consolation from Dexter, and invites him to Oscar's wake. Dexter attends, leaving Debra alone on their dead father's birthday. He begins to question Harry's code and whether his loyalty is necessary.
In the police department, Det. Angel Batista (David Zayas) is promoted to a sergeant. Debra has changed her hairstyle and given up men, alcohol and cigarettes. Det. Joey Quinn (Desmond Harrington), recently transferred to the department, is being investigated by Internal Affairs. Sgt. Yuki Amado (Liza Lapira) asks Debra repeatedly to keep an eye on Quinn, but Debra declines even when she discovers that "snitching" may earn her a detective's shield. She discovers from one of Quinn's informants, Anton Briggs (David Ramsey), that Oscar was a drug addict, but after she accidentally and loudly divulges the information in Miguel's presence, Lt. Maria LaGuerta (Lauren Vélez) asks that Batista remove her from the case. Batista does so and instead puts her on the case of a "Jane Doe", who Dexter recognizes as Teegan.
Dexter's personal life is going well; his relationship with Rita has become more amorous and he is bonding with her children, Astor (Christina Robinson) and Cody (Preston Bailey). Rita craves chocolate pudding and, recalling the last instance of this, realizes that she is pregnant.