The episode begins at the scene of the fifth arson attack in five weeks, this time a six-year old and his mother. Witnesses claim the suspect was enormous. The same accelerant was used and the word "Bobby" was again scrawled into a wall. Dexter is suspicious of the arson investigator, Phil Bosso. Dexter tells Hannah about "The Phantom," and admits being frustrated he's promised Debra he wouldn't take any cases from the police. He tells her about feeling like the Dark Passenger doesn't give him a choice. Hannah doesn't seem to understand. Her father, Clint, shows up unexpectedly. Hannah hasn't seen him since he went to prison for writing bad checks.
After sessions with the prison psychiatrist he feels the need to apologize to Hannah and tell that he always loved her. He has brought her a dollhouse from her childhood. Hannah doesn't look happy and after he leaves she tells Dexter he couldn't have brought a worse gift. She says he bought her the dollhouse after leaving her along for three days to play in a poker tournament. Bosso briefs Miami Metro about the likely suspect. Dexter thinks it sounds a lot like Bosso. It doesn't seem like there are any leads. Hannah sends Dexter a text that she's meeting her father. The rest of the department is finding out about Dexter's relationship with Hannah. Debra asks Dexter whether it's safe for him to be dating somebody so notorious when he needs to lay low. She tells him she's not going to stop investigating Hannah. It is shown that Debra is taking medication for anxiety.
Dexter looks into Bosso and grows even more suspicious. He follows him from the station to a Civil War reenactment and learns that he has an alibi for the most recent fire. Boss isn't the Phantom. Hannah asks Dexter to join him for dinner with Clint. At dinner Hannah and Clint seems to be getting along splendidly. They are planning to spend the night together, with Dexter saying he'll bring them breakfast the next morning. A shady-looking character is seen on a public bus. He puts on a fire retardant suit and begins spraying people down with an accelerant. Then a huge fire is in the bus. The next morning, Clint and Hannah still seem to be doing fantastically well. He talks about needing to raise $20,000 for a fishing business. When she says no he gets very angry.
He goes for a drive and Dexter tells her she's doing the right thing. Hannah isn't sure and this leads to an argument about the Dark Passenger. Dexter gets a text about the Phantom's latest crime scene. This time the Phantom has written "It's Bobby" on a bus window. Dexter tells a suspicious Debra about vetting Boss and she's upset he put himself in a dangerous situation. A very upset Hannah calls Dexter. Dexter arrives at Hannah's store to find that a drunken Clint drove his truck through her green house. He begins to yell at her, saying she is responsible for the death of her mother. Dexter demands that he leave as Hannah sobs. Dexter doesn't know how to help Hannah emotionally. Maria meets with Matthews. The only suspicious Miami employee left in her opinion is Dexter.
Matthews thinks she should look into Doakes' final days, as the real BHB probably killed him. Hannah tells Dexter she feels like Clint suckered her into thinking he was a good person. She says she hopes he's gone for good and remarks how scary Dexter sounded when he told Clint to get lost. Masuka has analyzed security footage from the bus. They can't see his face, but notice that he grabs a pole with his bare hand. Quinn gets a call from Nadia that she's being sent to a sex club in Dubai. Angel joins him on a trip to the club. In the back room George starts slapping Nadia around and Quinn shoots him. Quinn has Nadia help him pretend that George shot him in the arm beforehand. Quinn tells her to grab money from the safe and leave.
There is no match for the Phantom's print. Debra and Dexter focus on the meaning of "Bobby". Dexter takes a copy of the Phantom's fingerprint to the juvenile records office. He breaks into an office and runs the print. He finds the name Joseph Jensen, who burned down his school's gym at age 12 and was just released from a psychiatric hospital a month ago. Dexter tells Harry he doesn't think he can control himself. Harry and Dexter talk about the possibility that the Dark Passenger isn't real. Maria and Matthews visit the man who owned the property where Doakes was staying. He tells them he never knowingly rented to Doakes instead to a man named Santos Jimenez he later found out was connected to Columbian drug dealers.
Matthews recognizes the name Jimenez. Matthews tells Maria that Jimenez was one of the three men responsible for killing Dexter's mother. He also tells her that the Ice Truck killer was Dexter's brother. They wonder if perhaps Doakes was onto Dexter; which would give him motive. Matthews thinks he's the one who should talk to Dexter. Clint drops by Dexter's place unannounced. He says that he has evidence Hannah killed a counselor at a halfway house. Clint knows of a roommate who witnessed her poison him. If Dexter doesn't give him money, he'll turn in Hannah. It also turns out that Clint was selling Price information about Hannah for his books. The real reason he needs the money is that he has significant gambling debt.
Dexter tells him to leave, with Clint dropping the name Arlene on his way out. Based on the timeline of the two shots, Angel demands the truth from Quinn. Quinn sticks to his lie. Dexter tells Hannah about the conversation with Clint. She confirms that Arlene is the only person who can put her in jail. Hannah says she can't kill her own father and goes to call her bank. Dexter tells Harry that Clint doesn't meet the code. Dexter pays Joseph a visit at his home. After knocking Joseph out, he tapes him to the slab. Joseph tells him Bobby was his best friend when he was young. He took the blame for a fire Bobby set and he blames him for getting send to the "nut house". He says Bobby is the reason he's been killing people.
Dexter positions the knife above Joseph's chest, then pauses. Maria and Angel arrive at Joseph's place because of an anonymous tip. He's lying unconscious, but still alive. Dexter meets Clint in an underground parking garage. He knocks him out and takes him on his boat. Dexter tells Clint that even thought he doesn't meet his code he "wants to" kill him. Dexter stabs him in the chest and throws him overboard. Debra calls Dexter about finding Joseph. She knows it was him. He wants her to lay off Hannah, but she refuses.
Dexter tells Hannah he had "a talk" with Clint and he won't be bothering her again. She hugs him and thanks him. He tells her his Dark Passenger doesn't exist and thinks she might understand him better than he understands himself. She says she loves him and he reciprocates. Debra tells Angel they need to look for a woman named Arlene. Apparently Clint left Debra a message the night before saying she was a witness to a murder. The episode ends at this point.