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Dexter is deeply frustrated with Trinity, who had followed him to the Homicide Department, figured out his real name, and told him to leave him alone. In his frustration, Dexter, upon beginning his pursuit of Trinity, shoves Quinn to the ground when Quinn tries to confront him. Along the way, he is distracted by a phone call from Rita, during which he accidentally knocks off the sideview mirror of a car. Regardless, Dexter manages to track Trinity down to a parking garage, where he knocks him out with M99 in Trinity's van. After revelling in his victory, however, Dexter gets arrested when the man whose sideview mirror he accidentally destroyed sics the cops on him, prompting Dexter to initiate a struggle in further frustration. In jail, he reflects on his life and realizes how big of a part Rita plays in his life and how much she affects him. Dexter decides to change his ways and become a new man... after he kills Trinity, of course. He returns to the parking garage, only to find that Trinity is gone. Meanwhile, Quinn lets Dexter off, with a warning, for assaulting him. And, as Dexter continues his manhunt for Trinity, he sends Rita and the kids off to Orlando to keep them safe.
As the police finally figure out Trinity's true identity, Trinity himself returns home and extorts all the valuables and money from his family so he can leave Miami. Later, as Dexter himself returns to Trinity's house, he quickly hides in his garage as the SWAT team raid the home; when he is found, he tells them that he was only investigating the Trinity case. Meanwhile, Debra finds out the truth about Dexter's mother, and she tells him that she knows that Dexter's brother was the Ice Truck Killer. Dexter pretends this news was new to him and acted surprised. He is now concerned that Debra is getting closer to finding the truth about him, which gives him more of a reason to change his life.
Dexter finally catches up with Trinity and kills him; allowing Trinity to enjoy his toy train one last time. Dexter realizes he is not like Trinity. He is good for his family and there is a mutual feeling of love. He returns home with a new outlook on his life and his family, only to discover Rita, who had returned to the house because she forgot something for Harrison, dead in the bathtub with their son facing the crime scene; which is the same position Dexter was put in that turned him into a serial killer. Trinity, Dexter realizes, had killed her before he had abducted him, and with Trinity already dead, there's no way he can avenge Rita's loss.