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 begins to follow Travis in a market place, hoping that he would eventually lead him to Professor James Gellar, however he receives an urgent call from Debra who told him that Brother Sam has been shot and is in critical condition. Dexter immediately rushes to the "Good Shepard" garage, however at the same time Travis meets Gellar and purchases a sheet likely having to do with the "Whore of Babylon" ritual, he begs Gellar to give the woman they kidnapped before to be given some painkillers to ease the pain of her broken arm but Gellar refuses as she is a "whore" and deserved it.
Dexter arrives at the scene seeing the EMT rushing Sam to the hospital, Dexter begins to suspect 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 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 Julio's gang blamed Sam for Julio's disappearance.
Meanwhile, Debra begins to feel under pressure of being avoided by her own friends due to her position as their superior and barely has time to catch up. Dexter visits Sam at the hospital and promises that his Dark Passenger will make amends, Dexter later joins a Candle Light Vigil for Sam held at the garage, he meets Nick and asked him for Leo's current whereabouts.
Batista and Quinn begins to unravel Gellar's plan to sacrifice seven people to bring upon the end of the world in a manner depicted in his journal, they also discovered that three years ago, Gellar did an artistic installation on campus with a female accomplice who Quinn identified as Carissa Porter. Quinn requests Batista to keep his affair with Carissa a secret from Debra.
Meanwhile in Gellar's hideout, as Travis prepares the "mark," he begins to feel resentful as he hears the women he kidnapped in agony due to her broken arm.
Dexter begins to feel remorse for what happened to Brother Sam, considering that to him Sam saw the darkness in him and wanted him to follow the path of light.
Debra reveals to her psychiatrist that she felt that her world has been turned upside down since her promotion to Lieutenant, her psychiatrist suggested that she should live a while by having a party in her new beach house.
Dexter parks by Leo's house to wait for him, however at the same time Detective Anderson also learned of Leo's whereabouts from a junkie and leads a raid at Leo's house which resulted in Leo's death.
They deduced 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 act up, something that the dog only did around Sam and Nick. 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 give her any painkillers or let her go, Travis later visits his sister Lisa at her school where she teaches elementary students.
Dexter begins to investigate Nick, finding the bullet shot from earlier in his apartment (at Brother Sam when he was high) matching it with the bullets shot into Sam.
Batista interrogates Carissa regarding her relation with Gellar, but all goes wrong as Debra orders Quinn to join the interrogation, which resulted in Quinn's affair being exposed and losing Carissa as a key witness that could help solve the Doomsday Case.
Brother Sam regains consciousness but his condition begins to deteriorate, Dexter meets with Sam at his deathbed and is told to put his darkness aside, embrace the light and forgive Nick for both himself and Sam.
Meanwhile, Debra held a party at her beach house but is interrupted by a drunken Quinn. As Travis prepares to give the woman the "mark," Travis shows some mercy by letting her go. Quinn begins to become rude towards the other guest and is beaten by Batista, Quinn stated that Debra never loved him and leaves.
After receiving words of Sam's death, Dexter is hesitant to agree to Sam's dying wish by just letting go, however he does end up meeting with Nick and brings him back to the beach where he says he knew that Nick was the shooter. Nick seems nervous and upset, saying that he needed to shoot Sam to prove himself for the gang but Dexter decides to forgive him along with saying Sam forgives him. Nick, seemingly feeling terrible about it, says that he wants to see Sam only to hear that he passed away that night...and at first he is shown to be very upset, he suddenly replaces this with an intense joy. A joy, that blatantly disrespects Sam's sacrifice for him and disgraces the fact that Dexter chose light over darkness...the rage built up inside of Dexter forces him to tackle Nick into the water and drown him in the same waters that he was baptized.
Shortly after killing Nick, Dexter's darkness as Brian Moser appears, clapping his hands, and Dexter slightly smiles.