The main character, Dexter Morgan, leads a double life. He is a vigilante serial killer by night and a blood spatter analyst with the Miami Police Department by day.
Now married to the unsuspecting Rita and on honeymoon in Paris, Dexter is eager to return to hunting criminals after the events described in Dexter in the Dark.
While visiting an art gallery, Dexter and Rita are introduced to the concept of body parts being used as art by an avant-garde performance piece called "Jennifer's Leg" in which the artist amputates her own limb.
Upon returning home, Dexter finds his relationship with his sister, Deborah Morgan, has become strained since she learned of his murderous pastime at the end of the first book. Deborah is a Sergeant detective in the Miami Police Department's Homicide Unit and is torn between loyalty to her brother and father (who trained Dexter to confine his murderous impulses to other killers, and taught him how to escape detection) and her duty as a policewoman to arrest him.
At work, Dexter is called to investigate a gruesome tableau on a local beach, where a pair of bodies have been mutilated and arranged in a display that parodies the state's tourist trade.
At home, Rita is concerned for her children, Cody and Astor, who appear withdrawn and different from normal children. Dexter, on the other hand, knows that the two are sociopaths and has promised to train them to kill those who "deserve it" as his adoptive father, Harry, trained him. Cody is enrolled as a cub scout, which Rita believes will help him to bond with normal children. Dexter believes it will help him learn how to pretend to be normal. 
- Dexter Morgan
- Deborah Morgan
- Captain Matthews
- Detective Coulter
- Brandon Weiss
- Officer Meltzer
- Camilla Figg
- Randy Schwartz
- Mr. O'Brien
- Rita Morgan
- Jo Anne
- Alex Doncevic
- In the novels, there is an inconsistency regarding Dexter's use of a firearm. In Dexter in the Dark, he has no second thoughts about stealing a gun and using it to kill two members of the Cult of Moloch, while in Dexter by Design, he states that he does not know how to handle a gun.
- Dexter by Design briefly mentions internet fame, and includes several references to YouTube.