Season six follows Dexter's and Miami Metro's investigations into a string of bizarre ritualistic killings featuring overtly religious apocalyptic symbolism.
Dexter Morgan attends his 20th high school reunion to hunt a former Prom King. Everything's going perfectly for Dexter until Homicide comes up against a gruesome, faith-inspired murder. It leaves Dexter asking some bigger, spiritual questions about what to pass on to his son.
To solve a mysterious and macabre murder, Homicide brings in Brother Sam, a minister with a criminal past. But when Dexter meets Brother Sam, he doesn't recognize a man of God, but a fellow killer who might have found a cover even better than his own.
Dexter is confronted with a sobering glimpse of his own potential future when a serial killer from his past makes a startling reappearance; Debra is uncomfortable in her new job; Travis struggles to keep his mentor happy, as he and Gellar prepare a new twisted tableau, ensuring Debra's next task will be a daunting one.
Much to his own surprise, an emergency with Harrison and a new tableau from Gellar and Travis has Dexter leaning on Brother Sam and an unexpected winged messenger for support as he questions the idea of faith; with proof of a religiously motivated killer, Homicide hunts for a zealot, with Debra giving her first official press conference.
With the help of his newfound friend Brother Sam, Dexter wonders if there is light within him to counter the darkness, while the search for the Doomsday Killers takes him in a new direction; Batista and Quinn pay a visit to the university where Professor Gellar taught; due to departmental regulations following the shooting, Debra is forced to begin therapy.
Dexter is caught up in a very personal case that 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 case.
Dexter finds himself teamed up with a fellow Dark Passenger when he takes a road trip to Nebraska to tie up some loose ends from the past; Debra deals with the complications of her promotion as she leads the Doomsday investigation.
Dexter uses lessons he learned from Brother Sam to follow up on some new leads in the Doomsday investigation; Debra butts heads with Captain LaGuerta over the case of a dead call girl.
Dexter receives help from an unexpected source while hunting the Doomsday Killers and staying one step ahead of Homicide; Debra discovers something new about herself in therapy.
Dexter tries to figure out the Doomsday Killers' next victim before it's too late; Debra has a strong reaction to a crime scene, which leads her to the realization that she leans too heavily on her brother.
Dexter finds that in order to catch the Doomsday Killers, he must create a macabre tableau of his own; Debra's battle with LaGuerta over the case of the dead call girl boils over, and her therapist makes an unnerving suggestion.
Dexter and the Homicide Division race against a lunar eclipse to catch the Doomsday Killers before their final gruesome act. Debra struggles with, but finally faces up to, a new emotional reality.