Dexter continues to live his life according to his newly revised code. Deb is asked to help IA by investigating another officer. Batista is promoted to Sergeant ( Doake's old title). While trying to apprehend a new victim, Dex stumbles upon someone not in the plan. After an altercation, Dex is forced to kill the unknown man. Immediately after, the unknown man is recognized as the ADA's brother. The ADA, Miguel Prado (Jimmy Smits), invites Dex to his slain brother's wake. Dex blows off Deb for their annual celebration of Harry's birthday. Rita tells Dex she is pregnant.
Debra and the homicide unit, Dexter and ADA Miguel Prado are all searching for the same serial killer, who is responsible for the death of Prado's younger brother. Meanwhile at home, Dexter is faced with a decision to make concerning Rita and her kids.
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.
Ramon's career may be in jeopardy due to his obsession with Oscar's killer. Meanwhile, Dexter does a great job in keeping Ramon off balance by manipulation. Deb refuses to "be a rat" after Internal Affairs presses her to come up with more dirt on Quinn. Also, Rita and Dexter decide it's time to tell the children about her "condition," and Angel's quest for companionship nearly get's him in deep water.
As Dexter struggles when Rita pushes to move in together before getting married, Miguel tells Dexter that a husband has murdered his two wives for a financial gain and gotten away with it. Dexter finds this to be the perfect candidate to get away and satisfy that dark urge which every man with relationship pressures go through. Dexter tracks the murderer to Bimini. While he is on the hunt, Rita disappears due to a medical emergency. Meanwhile, Debra works with Anton, her confidential informant to track down one of Freebo’s criminal confidants. But Oddly enough Debra finds herself attracted to Anton.
Dexter tests Miguel to see if he is on his dark-side job. Rita questions her career path after being fired from her job. Debra believes she in some way caused another homicide while working on her current case.
Dexter angers Miguel when he says no to his latest offer, who's unsure the next target lives up (or down) to Harry's Code. Meanwhile, an elderly, deathly ill Camilla asks Dexter to kill her, insisting she would never ask a friend to do something against his conscience. Also, Rita discovers that Sylvia believes her husband Miguel has had an affair; and Anton is told he is bait to get at Skinner.
Miguel brings Dexter another “project,” but this time he wants to get his hands dirty. Dexter realizes it’s time to teach Miguel the Code – for his own safety as well as Miguel’s. As Dexter walks Miguel through the process, Dexter both struggles with, and enjoys, letting Miguel into his private world so completely. But Dexter doesn’t realize that this has only whetted Miguel’s appetite. Rita finds herself losing control because of the pregnancy. She becomes worried that Dexter may get fed up with her. Because of her hard work, Debra finds herself one step closer to catching the Skinner. But after she finds out a secret about her new boyfriend, Anton, he disappears on her.
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Miguel and Dexter's friendship is impacted when Rita confronts Miguel about his alleged infidelity. Believing Skinner has abducted Anton, Debra pulls out all the stops to find him.
Dexter feels like he’s making a deal with the devil when he feigns civility around Miguel after his duplicitous ways. Dexter finds himself in a series of chess-like moves against his former friend, all while hoping that Miguel doesn’t get the upper hand on him. Meanwhile, Dexter watches helplessly as Miguel draws Rita closer through a wonderful wedding gift. Debra, now back with Anton after his close call with the Skinner, wonders if her relationship with Anton is worth putting her career in jeopardy. After all, is it smart for everyone to know that she is dating a former confidential informant?
While preparing for his big wedding day, Dexter has to figure out a way to remove Miguel from his life for good. But how does Dexter manage to do this when Miguel is not only a highly placed D.A., but also his Best Man? Rita has troubles of her own, when Syl reveals that Miguel has been seeing one of his old flames. Meanwhile, Debra finds a new clue that brings her even closer to catching the Skinner.
Dexter’s focus shifts to calming his emotionally unstable brother, Ramon, now that Miguel out of the picture. Now that Ramon has calmed down, Dexter feels he can breathe once again. All that is left now is his upcoming marriage to Rita, until another deadly surprise shows it's ugly head. Meanwhile, Batista informs Debra that she is going to received her Detective's shield, but is instantly blindsided when she receives information which may end her promotion.