The third season of Dexter premiered on September 28, 2008, and ended on December 14, 2008. "Our Father", the season premiere, attracted 1.22 million viewers in the United States, making it Showtime's highest-rated drama season premiere since Nielsen Media Research began compiling ratings in 2004. The season's finale, "Do You Take Dexter Morgan?" attracted 1.5 million viewers. Season three was watched by an average of 1.1 million viewers a week. It received largely positive reviews from critics, which ranged from being praised as "truly and incredibly exciting television" in the San Francisco Chronicle, to "lack[ing] the crackling tension the drama had supplied in previous years" by the Chicago Tribune; the aggregate site Metacritic scored the season at 78 out of 100 based on 13 reviews. Smits and Hall received Emmy nominations for their roles as Miguel Prado and Dexter Morgan respectively, while the show as a whole also received a Best Drama Emmy nomination.
In this season, Dexter kills a man in self-defense and initiates a friendship with the man's brother, Assistant District Attorney Miguel Prado. In the meantime, Rita discovers that she is pregnant, and Debra investigates the murders of a new serial killer, called "The Skinner", hoping to gain a promotion to detective. In addition to Smits, Dexter's third season introduces two recurring characters: Desmond Harrington as Det. Joey Quinn, who becomes Debra's partner when he is transferred from the narcotics department to homicide, and Anne Ramsay as Ellen Wolf, a defense attorney whom Miguel detests.
Dexter has put his life back together but things may fall apart soon. His new victim is also being targeted by Assistant District Attorney Miguel Prado. Deb has to decide how to handle Internal Affairs, as they want her to turn on her new partner.
Dexter continues the hunt for Freebo, knowing he is still in town after finding Teegan's body. Dexter and Rita must make a decision about her pregnancy. Dexter isn't sure whether he can raise a child. Deb searches for the identity of her body, not knowing the link to the Freebo case. Dexter races to beat the rest of the police to Freebo.
Dexter and a pedophile have a run-in; Dexter is unable to restore Freebo's good name after he is accused of a murder he didn't commit. Also, Dexter's friendship with Miguel weighs on his mind.
After a failed marriage proposal, Dexter attempts to convince Rita that he wants more than a financial merger and fatherhood. He wants a family with Rita. Deb lands a new case. Miguel's brother, Ramon, is dead set on finding Oscar's murderer, which worries Dexter and Miguel.
While Dexter struggles with how to handle Rita’s desire for them to move in together before they get married, Miguel tells Dexter about a husband who has gotten away with killing two of his wives for financial gain. Meanwhile, Debra works with Anton, her confidential informant, to track down one of Freebo’s criminal confidants.
Miguel is put on test by Dexter. Meanwhile, Rita is forced to reconsider her choices. The Skinner strikes again, this time killing the young boy who worked as Freebo's doorman and Debra begins to feel like she had some part in it.
Dexter begins working with Miguel but they quickly have differences in selecting a potential new victim. Meanwhile Rita discovers that Miguel's wife suspects him of an affair. And an old friend of Dexter's asks for help in ending her life.
Dexter undertakes to teach Miguel the Code, but doesn't realize he's whetting his partner's thirst for blood. Meanwhile, Debra is one step closer to finding the Skinner but a secret revealed about Anton sends him packing.
The friendship between Dexter and Miguel become strained even as Rita resolves to confront Miguel about his suspected infidelity. Meanwhile, Debra searches furiously for Anton when it's revealed that he was abducted by the Skinner.
A series of chess-like moves ensues when Dexter and Miguel vie for the upper hand, with Miguel winning Rita's affection by presenting her with a lavish wedding gift. Elsewhere, Debra wonders if her relationship with Anton is worth the trouble.
While preparing for his big wedding day, Dexter has to figure out a way to remove Miguel from his life for good. In the meantime, Rita has troubles of her own, when Syl reveals that Miguel has been seeing one of his old flames. Debra finds a new clue that brings her even closer to catching the Skinner.
It is the day before Dexter's wedding and Dexter must deal with two people targeting him, while preparing for his special occasion. Meanwhile, Angel tells Deb he's put her in for a promotion, but after he finds out some information her shield may be gone before she gets it.