Season 3
Rita discovers she is pregnant and Dexter finds it hard to choose when she asks whether she should keep the baby or not. After some consideration, Rita informs Dexter that she will keep the baby and raise him either with or without his help. It also takes some time for Dexter himself to cope with the idea of actually having a child (an acceptance helped by the fact that he now sees Astor and Cody as his children and therefore to be protected), and he ends up proposing marriage to Rita, which she happily accepts.
While stalking a murderous drug dealer nicknamed "Freebo", Dexter stumbles upon a fight between Freebo and another man, whom he is forced to kill in self defense. This victim turns out to be Oscar Prado, brother of ADA Miguel Prado (Jimmy Smits) a prominent assistant district attorney and old flame of Lt. LaGuerta. Dexter assists on the case, and Miguel confides in him and grows to trust him. Dexter is able to track down Freebo and kills him, but as he leaves he encounters Miguel, who has followed a lead to the Drug Dealer's location. Dexter tells Miguel he had discovered Freebo and killed him in self defense, but instead of reprimanding him, Miguel thanks him and helps him cover up the crime.
As Dexter and Miguel cooperate to conceal Freebo's true demise from everyone else, the duo end up becoming close friends, as do Rita and Miguel's wife Sylvia. While the Prados assist Rita during a medical emergency, Miguel searches for Dexter, who was on a cruise ship killing a murderer Miguel has complained about. Miguel realizes that Dexter committed the murder and praises Dexter for killing another murderer and offers his aid in the future. Trying to discourage Miguel, Dexter proposes a risky operation to free an infamous Aryan Brotherhood leader, who continues to commit crimes while inside prison, in order to kill him. Miguel agrees with the idea and the plan succeeds (despite the alarm sounding during the escape), and Dexter starts to recognize Miguel as his first and only true friend, to the point of inviting him to be his best man at his wedding.
Throughout Season 3, Debra starts working more seriously in order to earn her detective shield, but due to an untimely commentary on her part she is cut off from the Freebo case. She starts working with a new partner, Joey Quinn, to investigate a serial killer with the habit of skinning his victims while alive (labeled "The Skinner"). She also starts a relationship with Anton, one of Quinn's confidential informants who starts working with her. However, Yuki Amado, a female Internal Affairs officer, starts pressuring Debra to give her information on Quinn, promising to help her become a detective in return, but Debra refuses to cooperate, despite Yuki's claims that Quinn cannot be trusted.
A notable change from previous seasons is the increased use of fantasy scenes with Harry, Dexter's foster father. Harry offers guidance, ideas, and guilt. This differs from the earlier seasons' use of flashbacks to illustrate Dex's past.
Camilla Figg, an old friend of Dexter and his family, is dying of terminal lung cancer and asks him to end her suffering, which he (who had never purposely killed an innocent before) reluctantly agrees to do. On the occasion, Camilla reveals to Dexter that she knew that his brother was the Ice Truck Killer and congratulates him when he confesses to her that it was he who killed Brian. She also indicates that she knows of Dexter's hobby before she dies.
Miguel and Dexter's partnership takes a new step when Miguel offers to be the one to kill their next target, a former football player turned gambler who in order to pay his bookie commits murders on the bookie's behalf. With some reluctance, Dexter accepts, and after preparing the trap and teaching him the basics of his "code", he witnesses Miguel killing the victim without hesitation. However, the next day, Ellen Wolf, a ruthless defense attorney and old courtroom adversary of Miguel's, goes missing, and Dexter, suspicious, discovers that Miguel has killed her. After some investigation, Dexter also discovers that Miguel has been manipulating him since the beginning and never trusted him at all.
While the relationship between Dexter and Miguel begins to unravel, so does Miguel's marriage when Sylvia begins to suspect that Miguel is having an affair and confides her fears to Rita, who in turn confides in Dexter.
Dexter and Miguel then begin to dance around in a game of who has leverage over whom as the police investigate the death of Ellen Wolf. This game of leverage ends with Dexter realizing that Miguel cannot be allowed to run loose any longer (at which point Dexter decides to kill him using the Skinner's Modus Operandi) and with Sylvia, convinced that Miguel is having an affair with Lt. LaGuerta after seeing them leaving LaGuerta's house together, ordering him out of the house. Miguel helps the Skinner escape and evade police custody in return for his agreeing to kill Dexter.
Striving to discover the truth about Ellen Wolf's death, LaGuerta ends up obtaining evidence linking Miguel to the crime, while Miguel himself discovers that LaGuerta was investigating him, and decides to kill her, but Dexter realizes it beforehand and captures him while he was looking for her. Before killing Miguel, Dexter confesses to him that he was the one who murdered his younger brother Oscar.
After Miguel's body is discovered, he is immediately identified as a victim of the Skinner, just as Dexter planned. But Miguel's other brother Ramon is still suspicious of him. After pointing a gun on Dexter during a dinner with Rita he is captured by Angel and Debra. During a visit to him in prison, Dexter helps Ramon put his demons to rest offering advice and personal relation to Ramon's life.
However, on the night before his wedding, Dexter is captured by the Skinner, and manages to break free by taking advantage of a moment of distraction by him, but breaks his hand in the process. After some fighting, Dexter manages to snap the Skinner's neck and make it look like suicide by throwing his body before a running police car. Dexter gets his broken hand put in a cast and attends his wedding. He admits to himself that his wedding vows "to be the best husband and father he could be" were absolutely true. The season ends as a drop of blood from Dexter's cast falls upon Rita's wedding dress as they dance.
Note: This is the first time he used strangling for killing.
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