Dexter went home to become a family man, and Rita has given birth to a baby boy named Harrison. The family has moved to the suburbs, where Dexter struggles to reconcile his new life with his killing urges. Special Agent Frank Lundy returns to hunt down the "Trinity Killer" (John Lithgow) who he believes always murders three people in a very specific sequence: a young woman in a bathtub, an older mother of two falling to her death, and a father of two bludgeoned to death.
Lundy begins working with Debra and shortly after, an unseen assailant shoots them both, killing Lundy. Afterwards, Debra is barred from working the Trinity case because the shooting is suspected to be the work of Trinity, making Debra an investigator who was also a victim, creating a conflict of interest. Debra eventually discovers that Trinity was not the shooter, and she is put in charge of the case. Meanwhile, LaGuerta and Batista have renewed their relationship and, in danger of losing their jobs, decide to marry. They call Dexter in to have him be their witness.
While investigating Lundy's data about Trinity, Dexter determines Lundy was killed because he had determined when and where Trinity would claim his third victim. Dexter stakes out the building, and witnesses Trinity bludgeoning a man on a security camera. Dexter follows Trinity to his home, where he is surprised to discover that Trinity is a family man named Arthur Mitchell. Using the alias Kyle Butler, Dexter attends the same church as Arthur and eventually befriends him by helping him at the "Four Walls, One Heart" charity organization. While investigating the reasons behind Trinity's crimes, Dexter learns how he manages to reconcile his family life with his killing urges and utilizes that knowledge to deal with his own issues.
Dexter visits Arthur at his home and discovers that he will be traveling to Tampa on another building project, which could be the start of another three-pronged killing cycle. Dexter decides to make the trip with Trinity to ensure this does not happen. On the way, Arthur takes Dexter to his childhood home and reveals that at the age of ten, he spied on his older sister in the shower out of innocent curiosity. Startled by his presence, she slipped, shattering the glass shower door and cutting open her femoral artery, causing her to bleed to death. His mother committed suicide and his father died soon after. Dexter realizes that Trinity compulsively murders groups of people that bear resemblance to those in his family, recreating their deaths each time.
During Thanksgiving at Trinity's home, Dexter learns that Arthur has been terrorizing his family, locking his daughter away in her bedroom and physically abusing his son. After Arthur attacks his son, Dexter is forced to restrain him. Arthur then goes to see a reporter who has been snooping around the Miami Metro Police Department, Christine Hill, who is revealed to be his illegitimate daughter.
Later Trinity kidnaps a boy while being pursued by Dexter. Dexter does some research and finds out that Trinity's pattern begins with the abduction and murder of a ten year old boy; revealing Trinity's pattern actually cycles in groups of four with the boys always disappearing five days before the first bathtub death. Dexter locates the place where Trinity is holding the boy and arrives just in time to save him, as Arthur escapes.
Debra begins to investigate and eventually arrests Hill after finding out that she is Trinity’s daughter. However, Hill is released due to a lack of evidence. Hill secretly contacts Arthur, but he refuses to help her and instead forbids further contact. Arthur also reveals his disdain for her having killed Lundy, which she did to protect her father. Realizing the error of her ways, Hill confesses to Debra. Distraught, Hill seeks forgiveness from Debra, which the latter refuses to provide. Hill then pulls out a gun and commits suicide in front of Debra.
One of Harry's old informants takes Deb to the house of Laura Moser. Debra immediately recognizes the house as the home of Brian Moser, the Ice Truck Killer. After piecing together Dexter's connection to Brian and Laura, Deb reveals this information to Dexter, explaining that Laura was his mother and Brian his brother. Dexter feigns surprise, stating that Brian must have tried to get to him through Deb.
Dexter decides that he must draw police attention away from Trinity so that he can kill Trinity himself. He finds a man whom he can kill and pin the blame on. He then plants evidence and kills the man. Arthur lures Dexter to an arcade where he previously stalked victims and follows Dexter back to the police station, where he learns Dexter's true identity. Soon after, Dexter tails Trinity, but sideswipes a car on the way. Dexter captures and drugs Trinity, but the driver of the damaged car has found Dexter's car, called the police, and in the ensuing confrontation, Dexter is taken in by the police for leaving the scene of an accident and fighting with the driver in the presence of the police. By the time Dexter is released due to cell overcrowding, Trinity is gone from where Dexter had left his unconscious body.
Dexter eventually tracks down Arthur, capturing and bringing him to the bomb shelter where he held the missing boy. Dexter kills him with a hammer and dumps the body. At the beginning of this episode, Dexter arranges a vacation for Rita, Harrison, and himself in order to get Rita out of harm's way. They're to meet in the Keys at the end of the work day. Rita and Harrison leave in the morning and Dexter promises them that he'll see them after work. When Dexter returns home after dealing with Trinity, he picks up a message from Rita. After listening to the message, he calls her back. He hears Rita's phone ring from within the house and soon after, he hears Harrison crying. He rushes to the bathroom, where he finds Harrison sitting on the tile floor in a pool of blood while Rita lies dead in the bathtub, having been murdered in the same fashion as each of the other Trinity bathtub killings.