Dexter attends his high school reunion to investitage an old class mate. He also discovers that he is well remembered and cool now. He is also looking for schools for Harrison and worrying about the kind of religion he should be exposed to. Quinn is planning on proposing to Deb. Batista and LaGuerta are divorced and getting promoted. Two new killers with a religious zeal appear and sow snakes into the belly of their victim.
Deb is promoted to Lieutenant above Batista. Quinn proposes and she says no. Dexter investigates an ex-con who claims to be rehabilitating other former inmates at his garage. The mysterious religious killers strike again.
A dead prostitute makes Dexter think that a decade dormant serial killer called the tooth fairy might be responsible. Deb struggles with her new job as she has to hire another detective, deal with politics and an angry Quinn. Masuka asks Ryan out and is surprised that she says yes. She seems even more interested in the Ice Truck Killer case.
Dexter and Mike begin to decipher the clues left by the Revelation killers. Travis is more interested in a waitress than the next part of Gellar's plans. Deb has to give her first press conference and LaGuerta suggests she be herself. Batista and Quinn get high. Masuka discovers that Ryan has put evidence on an online auction site. Harrison becomes ill and Dexter waits nervously in the hospital. Brother Sam comes to see him and discusses his own path to God.
Dexter captures Travis and gets him to admit that Gellar is the one doing the killing. Gellar pushes Travis to capture a woman to play the role of the Whore of Babylon. Quinn and Batista trek out to interview one of Gellar's old students and Quinn sleeps with her. Deb is feeling increasingly stressed and a murder-suicide suddenly opens up a nice beachside apartment. Masuka's new intern helps him cover up the missing evidence.
Suspicion falls on Leo Hernandez for the shooting of Brother Sam. Dexter prepares to kill him but Mike gets there first having independently tracked him down. Dexter works out that it was actually Nick who did it and Brother Sam regains consciousness in time to ask Dexter to forgive him. Batista and Quinn have to bring Carrisa Porter in for questioning and Deb finds out that Quinn slept with her. Deb throws a house warming party and Quinn shows up drunk with another woman. Travis has an attack of conscience and frees the woman he was holding captive.
Debra tells Dexter that the Trinity killer is back and killed his wife and daughter. Brian is sure that Jonah did it and encourages Dexter to go to Nebraska to kill him. Dexter takes some time off and heads off in his car. He checks into a motel after an initial talk with Jonah. The motel owner tries to extort him and with Brain cheering on he kills him. Then Jonah calls Dexter wanting to talk.
Dexter apologises to Deb about his unexplained absence. She is increasingly frustrated by his refusal to communicate. Dexter visits Travis and tries to convince him to turn Gellar in. Gellar kills Travis' sister and dresses her up as the whore of Babylon. Batista has to get used to his sister dating while Quinn drowns his sorrows at a strip club.
Dexter puts Travis in a hotel and they track down Gellar's next target - an atheist college professor. Deb's therapy continues to dig into her issues. Batista takes Quinn to find his phone and gun which he left at a woman's house. Louis decides to not let Batista stop him dating Jamie. Dexter and Travis trap Gellar in the church and prepare to kill him.
Dexter hides Gellar's body to keep Travis for himself. Travis recruits new disciples to help him bring about the end times. Dexter figures out that Travis will try to kill Holly Benson. Quinn continues to drink at night and sleep by day. Deb continues to uncover her feelings about Dexter in therapy. She also uncovers Matthews' connection to the Jessica Morris case.
Dexter prevents Wormwood from going off but inhales some of the poisonous gas leading to nose bleeds. Deb sees him as a hero and her shrink suggests that maybe she loves him as more than a brother. Matthews asks Deb to ignore the call girl case. She does but LaGuerta doesn't. Quinn saves Batista from Travis. Dexter sets a trap for him but then gets a nose bleed at the wrong time and Travis tries to set him on fire.
Travis heads out to find a sacrificial lamb and settles on Harrison. Dexter is rescued and brought ashore by a boat of immigrants. Deb is very relieved to see him alive and tells him that she loves him. He takes Harrison to his school performance of Noah's Ark but when he turns his back Travis kidnaps him. The Miami police are patrolling all the skyscrapers in the city trying to find where Travis will greet the eclipse. Dexter captures him and takes him to the abandoned church to kill him. Louis asks if he can stay working for Masuka and Batista tries to get Quinn to transfer to another city.