Dexter investigates a crime scene in a comic book store. There he sees a poster of The Dark Defender, a character inspired by Dexter's own crimes under the guise of the "Bay Harbor Butcher." After he dreams that he, as The Dark Defender, saved his mother's life, Dexter's Narcotics Anonymous sponsor, Lila, encourages him to seek closure by confronting one of his mother's killers, Santos Jimenez.
While drinking coffee with his sister Debra, Dexter is called to a murder scene at a comic book store. Talking to a witness about the victim, a shopkeeper who had been bludgeoned to the head with a snow globe, he sees a poster of The Dark Defender, a vigilante killer based on the Bay Harbor Butcher. Later, at a Narcotics Anonymous meeting, Dexter falls asleep and dreams about the death of his mother, Laura Moser. In the dream, he enters the cargo container where she was killed, dressed in The Dark Defender's cloak, and beats his mother's murderers to the ground, saving her. When he tells his sponsor Lila about his dream, she tells him that he must confront them to seek closure.
He and Lila travel to Naples, Florida where one of the three men, Santos Jimenez, is alive and running a tavern. Having been warned by his girlfriend Rita's mother, Gail, to leave Rita and her children alone, Dexter tells Rita that he is going away while Gail is visiting. Leaving Lila in their motel room, he goes to Jimenez's bar and waits until all of the patrons have left. Dexter tries to explain to Jimenez how he feels, but Jimenez takes out a baseball bat and threatens to beat him. In response, Dexter disarms and brutally beats him, revealing his past to Jimenez as one of the boys he left in his mother's blood. Jimenez tells Dexter that his mother was killed because she was not only a narcotics informant to Harry, Dexter's adoptive father and a police officer, but also his lover. Dexter punches Jimenez and is close to killing him when Lila phones and he tells her that he is about to "use." Thinking that he is about to use drugs, she urges him not to go any further. He returns to the motel, leaving Jimenez unconscious in the bar, and falls asleep in Lila's lap. The next morning, Lila reveals that she had burned down a house with her ex-boyfriend inside.
Debra is insecure in her relationship with her new boyfriend, Gabriel, because her ex-fiancé Brian Moser, the "Ice Truck Killer," had kidnapped and tried to kill her. When she looks through Gabriel's e-mail, she sees that he has sent a book titled The Ice Princess to a number of publishers. Debra assumes that Gabriel is using her to write a book about her engagement to the "Ice Truck Killer" and angrily breaks up with him. Discussing the break-up with FBI Special Agent Frank Lundy, he gives her the background check that he had run on Gabriel, revealing that Gabriel is a children's writer, and Debra realizes that The Ice Princess is a children's book.
When Dexter visits Rita the next morning, Gail, who believes that Dexter is drug-addict —announces that she will be staying in Miami and will live with Rita. Dexter realizes that he must protect his true secrets, so he begins by cleaning his boat that night with a black light to detect any blood. He is unaware that Coral Cove Marina is being videotaped by the Miami Metro Police, who believe that the Bay Harbor Butcher may be keeping his boat at that marina.
- The episode's writer Tim Schlattmann made two cameo appearances in the episode.
- "The Dark Defender" was praised by critics and Schlattmann was nominated for Writers Guild of America Award for his script. The episode was also submitted as Dexter's sample episode to determine the nominees for Outstanding Drama Series at the 60th Primetime Emmy Awards; although nominated, the series didn't win.