Dexter frantically searches for clues to Debra's whereabouts when Rudy, finally revealing himself as the Ice Truck Killer, abducts her and forces Dexter into a series of mind games to find her. Dexter returns to his apartment in hopes of finding clues left there by Rudy, and then sees his "new" screen saver playing the song "Born Free." He suspects that Rudy might be keeping Debra at the cargo container where his mother was butchered and where Harry found him. At the hospital, LaGuerta and Doakes pay a visit to Batista who is being treated for the stab wound he endured earlier in hopes of finding leads to the Ice Truck Killer. They suspect that Rudy Cooper might indeed be the killer and could have kidnapped Debra, as well.
As Dexter frantically searches for the container, he is unexpectedly visited by LaGuerta and Doakes, Doakes accuses Dexter knowing something as he was skulking in the lab ordering secret blood tests from Batista's collar which he is forced to reveal to be Rudy's. Rita is contacted by the imprisoned Paul who tells her that Dexter framed him for his drug possession charge. Meanwhile, LaGuerta locks horns against her replacement Lt. Esmee Pascal, who's even MORE officious and pompous than her or Captain Matthews, and who hampers the case by ignoring key evidence to further advance her own personal career.
Dexter sneaks into the shipping yard to find the container "CBAN-348 9" and has a brief flashback of Harry finding him as a child, as Dexter nervously opens the container, but finds nothing but bananas inside it. Doakes catches Dexter by surprise and the two engage in a brief brawl until security arrives. Meanwhile, as Rudy is driving Debra to an unknown location, Dexter enters Rudy's apartment where the police have been finding evidence linking him as the Ice Truck Killer, including his Kill Room. Rita is visited by Paul's Narcotics sponsor Bob Hicks who tries to convince Rita that Paul had been framed. Dexter searches the apartment and finds a record player playing "Born Free" and a Barbie doll with "Home Sweet Home" written on it. In an, as yet unknown, location, Debra struggles to escape. Rudy kicks her to the ground and sedates her.
Dexter suspects that Rudy might be at his mother's house and searched through the database for her address, Rita makes an unexpected visit, but it was brief as Dexter explains that Debra might be in trouble. At the hospital, Batista watches the news regarding Rudy who's true identity is still left a mystery as his prints weren't present at the criminal database. After hearing the nurse talk about how dangerous psych patients can be, Batista calls the department to run a test on Rudy's prints on the psych mental institution database as he suspects that Rudy might indeed be a psych patient.
Dexter arrives at his mother's house. He suddenly has a flashback of his childhood, and Rudy appears revealing himself to be his biological brother, Brian, Dexter marches straight into the house in search for Debra but is sedated by Brian. Batista returns to the station handing LaGuerta the file revealing Rudy to be Brian Moser who was institutionalized for anti-social personality disorder. Brian was released at the age of 21 after it was believed that he had been cured of his mental disorder. Lt. Pascal believes that Brian might be 20 miles off the coast by boat, which this leads to LaGuerta and Pascal in having a brief confrontation with each other.
Brian tries to reconnect with Dexter by revealing his past to him and tries to convince Dexter to kill Debra who he had wrapped in plastic in a similar manner to Dexter's victims. Dexter refuses and tackles Brian, Doakes and several officers arrived at the scene but Brian escapes before they could capture him. Dexter tries to convince Doakes that Brian had called him, Doakes threatens to give Dexter a suspension, but Debra steps in and yells at Doakes to leave her brother alone. While on the way to the hospital, Debra worries because Brian is still out there and he might try to kill her again. She hugs Dexter and thanks him for saving her life. Paul contacts Rita one more time to warn her that Dexter was actually the one who set him up. Paul begs Rita to find his missing shoe that might have slipped from his foot when Dexter dragged him, Rita doesn't believe Paul's warning and hangs up.
At the hospital, Dexter is beginning to wonder if Harry betrayed him because he had kept his brother's existence from him all these years. Brian later goes to Dexter's apartment, where he believes Debra is staying, and tries to kill her. However, it turns out to be a trap set by Dexter. He strangles Brian until he passes out and transports him to Brian's apartment, where he suspends him in the air, just as Brian did to his victims as the Ice Truck Killer. Brian tries to convince Dexter to set him free, telling his brother that he can be free to be his true self with him. A frustrated Dexter loudly dismisses this, causing a single tear to run out of Brian's eyes. Dexter says he can't let Brian live because he knows he will always want to kill Debra. Brian continues to lecture Dexter on how he's choosing to live a lie for people who will never really know or care about the real him, instead of embracing his real brother who accepts him. Dexter is tempted, but ultimately slices Brian's throat, telling him he can't hear anymore, while admitting Brian is right.
Dexter is able to convince the police that Brian committed suicide by using the same method with which Brian had killed his victims. The next day, Dexter returns to Rita's house to make up for the previous visit. When he leaves there for work, he notices Doakes tailing him and worries that he might find out what he really is, as Rita waves good bye to Dexter, she notices the shoe that Paul mentioned and worries that what Paul said might be true. Dexter mourns his brother's death and still wonders if what he is doing is worth it. As he and Debra walk to the crime scene, he fantasizes about a crowd of people cheering for him for what he does. Dexter embraces his shadow self and considers himself one of them -- in their darkest dreams.
- According to the original script, the title of the episode used to be "Black Heart Optional". The relation to the episode is the choice between Dexter choosing to kill Debra or spare her, then ultimately killing his brother Brian while expressing his true emotions for the first time after his death.