Dexter is caught up in a very personal case that once again awakens the needs of his Dark Passenger; Debra feels overwhelmed by her new lieutenant duties, made all the more complicated when she finds out Quinn slept with a witness in the Doomsday Killer Case.
Dexter follows Travis in a market place, hoping that he will eventually lead him to Professor James Gellar. However, he receives an urgent call from Debra who tells him that Brother Sam has been shot and is in critical condition. Dexter immediately rushes to the Good Shepherd garage as Travis meets Gellar and purchases a fabric for the "Whore of Babylon" tableau. Travis begs Gellar to give the woman they kidnapped some painkillers to ease the pain of her broken arm but Gellar refuses, saying that she is a "whore" and deserves it.
Dexter arrives at the scene as the EMTs are rushing Sam to the hospital. Dexter suspects that the shooting was an act of revenge for Julio Benes and one of Julio's men that he attacked before was the culprit. Dexter scrapes some blood from Sam's bat and identifies the man as Leo Hernandez. Dexter contacts Leo's last known address hoping to find a lead to Leo's whereabouts but no such luck. Dexter blames himself for what happened to Sam as he was the one who killed Julio and the Locos gang blamed Sam for Julio's disappearance.
Meanwhile, Debra feels the pressure of being avoided by her friends due to her position as their superior and she barely has time to catch up on the work.
Batista and Quinn unravel Gellar's plan to sacrifice seven people to bring on the end of the world in a manner depicted in his journal. They also discover that three years ago, Gellar did an artistic installation on campus with a female accomplice whom Quinn recognizes as Carissa Porter. Quinn requests Batista to keep his one night stand with Carissa a secret from Debra. Angel is in "I-told-you-so" mode.
Meanwhile in Gellar's hideout, Travis heats up a branding iron with the Alpha Omega symbol to "mark" Holly Benson, the kidnapped woman. However, he begins to feel sympathy for her as she screams in agony due to her broken arm and terror.
Angel tells Debra that he and Quinn will be traveling to Tallahassee to interview Carissa Porter, but Debra insists that she come to Miami.
After dark, Dexter parks down the street from Leo's house, but there is a party going on so he returns home.
Dexter misses his friendship with Brother Sam, since Sam saw his darkness and wanted him to follow the path of light.
Debra reveals to her psychiatrist that she feels that her world has been turned upside down since her promotion to Lieutenant. Her psychiatrist suggests that she should have a party in her new beach house.
Dexter parks by Leo's house to wait for him. However, at the same time, Detective Anderson, having learned of Leo's whereabouts from a junkie, leads a raid at Leo's house which results in Leo's death.
The police deduce that Leo was the culprit. However, Dexter reviews the security footage from Sam's garage found in Leo's house and notices that Eli, Sam's guard dog doesn't bark or act up. Since the dog only behaved that way around Sam and Nick, Dexter suspects that Nick was the shooter.
Elsewhere, Travis begins storing his blood in several jars for an unknown purpose. He brings the woman some food and apologizes to her that he can't let her go or give her any painkillers. Travis later visits his sister Lisa at her school where she teaches elementary students.
Dexter breaks into Nick's place and finds the bullet that he shot at Brother Sam when he was high. It matches the bullets shot into Sam at the garage.
Batista interrogates Carissa regarding her relation with Gellar, but all goes wrong as Debra orders Quinn to join the interrogation. This results in Quinn's affair being exposed and losing Carissa as a key witness that could help solve the Doomsday Killer Case.
Brother Sam regains consciousness but his condition begins to deteriorate. Dexter meets with Sam at his deathbed and is told by him to put his darkness aside, embrace the light, and forgive Nick.
Meanwhile, Debra holds a housewarming party at her beach house but it's interrupted by a drunken Quinn, who brings a date.
As Travis prepares to give the woman the "mark," he instead shows mercy by letting her go.
At the party, Quinn becomes rude towards Jamie and is punched by Batista. Quinn states that Debra never loved him and leaves in a cab.
After receiving word of Sam's death, Dexter is hesitant to agree to Sam's dying wish by just letting Nick go. While thinking it over, he takes Nick to the beach, and reveals that he knows Nick was the shooter. Nick appears nervous and remorseful, admitting that he needed to shoot Sam to prove himself to the gang. Dexter decides to forgive him and tells Nick that Sam forgives him. Nick insists on seeing Sam only to be told that he passed away that night. At first, Nick seems to be very upset, but he suddenly replaces this with intense joy. This blatantly disrespects Sam's sacrifice for him and disgraces the fact that Dexter chose light over darkness. The rage builds up inside of Dexter and he tackles Nick, drowning him in the same waters where he was baptized.
Immediately after killing Nick, Dexter's darkness represented as Brian Moser appears, clapping his hands, Dexter slightly smiles.
- Most people believe we have freewill. That we all choose our path. Sometimes the path is clear, sometimes not so much. Every twist, every turn, can challenge our sense of direction. But it's the choices we make when we reach a fork in the road that define who we are. -Dexter [voice over]
- There's no light in you. There's no light in me. -Dexter after drowning Nick
- Biscayne Bay
- Community Charter School
- Debra's Beach House
- Doomsday Killer Case
- Eli (dog)
- Good Shepherd Auto Repair
- Santa Maria de Loreto