After killing his brother, The Ice Truck Killer, Dexter can't seem to kill again. He wants to, but he can't seem to get past his feelings. Debra returns to work, but is showing signs that she may not be ready to return.
Dexter chases Little Chino, a gangster to try to recover his killer instincts. Meanwhile, Debra returns to work, but loses control on the job. And Agent Lundy, an FBI agent comes to Miami to track down the newly discovered serial killer, the Bay Harbor Butcher.
Dexter goes after his newest victim. Dexter learns that the smooth talking charm and lying are skills that Dexter is having trouble with these days. Rita suspects that Dexter is a drug addict and wants him to go to a 12-step program or she will leave him.
Dexter joins N.A. and gets a sponsor to make Rita happy, but the sponsor doesn't turn out to be a positive addition for Rita. Meanwhile, Dexter tries to throw the FBI agent off his trail.
Dexter learns that the man who killed his mother is still alive and starts a new mission. Gail talks to Dexter telling him to stay away from her daughter, Rita. Rita and her mother fight and then her mother announces that she's going to move in with them and help out.
When a copycat killer goes on a vigilante serial murder streak, Dexter is determined to stop the imposter. While on this mission, he ends up in the arms of Lila, which puts his relationship with Rita in jeopardy.
Dexter sends a manifesto to the task force to throw them off his trail, but Lundy figures out that that's exactly what he wants, and concludes that the killer has a law enforcement background.
The flirtation between Debra and Lundy heats up when they go on their first date. Doakes breaks into Dexter's house and discovers the blood slide souvenirs from his murders.
Dexter tries to distance himself from Lila, but she insinuates that she might let his secrets slip out if he rejects her. Dexter notices that federal agents are following him, which makes returning to dispose of Jiminez's body impossible.
Doakes has tracked Dexter to his latest kill at a remote cabin, but killing Doakes would violate Harry's code, so Dexter finds a murderer (the type who would make a good victim for the serial killer) and brings him to the cabin to kill him and frame Doakes.
Still trapped in the cabin, Doakes tries to convince Dexter to turn himself in, and he seriously considers it. Dexter starts making plans to get his affairs in order before letting Doakes bring him in: he has Deb sign a living trust agreement, and even gives Rita the minivan.Lila frames Angel for rape in an attempt to blackmail Dexter into taking her back.
In the season finale, Lila steals Dexter's GPS and arrives at the cabin where Doakes is imprisoned. Doakes tells her that Dexter is the butcher. She's shocked, but she tells Doakes that she's Dexter's soul mate.