After killing Miguel and framing The Skinner, Dexter is targeted by Ramon. LaGuerta tries to persuade Dexter to expose Miguel as a murderer when she learns that a highway will be named after Miguel. Angel's recommendation of Debra for promotion to detective is threatened when Angel learns that Debra slept with Anton. Dexter discovers that Rita has been married twice before, once when she was sixteen, which she hides from him. Dexter is captured and held prisoner by The Skinner, who demands to know Freebo's whereabouts, but Dexter escapes (and kills him) in time for his wedding.
Senior staffers clash with newly hired political operative Bruno Gianelli and his aides Connie and Doug. Josh is upset because Leo won't let him "wave off the FDA" on RU-486. C.J. contemplates her future at the White House. President Bartlet makes it clear he values both Bruno's team and his senior staff and gets them focused on running a successful re-election campaign as allies rather than adversaries.
At Zoey Bartlet's birthday party, magicians Penn and Teller appear to burn an American flag in the White House, prompting a publicity nightmare. Aboard Air Force One, Bartlet is stricken by a paralyzing MS episode, while Josh is approached to run the Vice President's presidential campaign. The Bartlet Administration offer Republican California Senator Arnold Vinick the position of the US Ambassador to the UN, but he turns it down and announces his candidacy for the Presidency instead. Governor Baker drops out of the Democratic nomination race, making Russell the clear front-runner.
The transition is speeding ahead, and Matt and Helen Santos are overwhelmed by almost everything about their new lives – including Secret Service protection, choosing a DC school for their kids, and dealing with the White House household staff. Vinick slips back into anonymity with too much time on his hands, and his staffers come to realize he's plotting another run for the presidency. Santos is trying to figure out how to get his vice-presidential choice confirmed, and makes a surprising offer to Vinick: be the new administration's Secretary of State.
A 14-year-old leukemia patient's (Jascha Washington) only hope of survival is a bone marrow transplant from his younger brother (Dabier), but when he gets sick, the team must race against time to save both siblings. Meanwhile, Foreman must deal with the consequences of the previous case.
Vogel reveals to Dexter that she helped Harry create his Code, harboring a perverse interest and admiration for psychopaths. She asks Dexter to track down the Brain Surgeon, whom she believes to be one of her former patients and a grave hazard to her life. While tracking down the stolen jewels, Debra is beaten by El Sapo, but later murders him; Dexter finds traces of her blood at the crime scene, but hides it from the police. Quinn and Jamie argue over Quinn's future and Batista's involvement in their relationship. Dexter tracks down one of Vogel's patients, Lyle Sussman, who he believes is the Brain Surgeon, but discovers he has been murdered. Vogel and Dexter find a DVD from the Brain Surgeon, showing the killer forcing Sussman at gunpoint to do his bidding. Dexter agrees to track down the killer from Vogel's list of suspects.
A college student named Brandon (Kevin Zegers) collapses after having sex with his fiancée. His symptoms seem too numerous to be explained by just one disease. Foreman and House each suggest different diagnoses and argue that his own respective theory better conforms to Occam's Razor. But then Brandon's white blood cell count drops, proving both doctors wrong. At the clinic pharmacy, House theorizes that the pharmacist accidentally gave Brandon colchicine instead of cough medicine, which explains all of his symptoms aside from his cough. House gives Brandon the cure, and he immediately begins to recover, though nobody believes the pharmacist made a mistake. However, when Brandon comments that his old cough medicine did not have letters on it like his current pills, House discovers colchicine pills that look similar to cough medicine, revealing the source and confirming House's diagnosis.
Dexter removes all of the evidence pointing to his relationship with Vogel before calling the police. Elway and Clayton suspect that Debra is harboring Hannah. Saxon offers Dexter a deal that the two will leave each other alone; Dexter agrees, but secretly plans to kill him before leaving. With a hurricane approaching Miami, Hannah goes to the airport to wait for Dexter, but she is followed by Elway. Meanwhile, Dexter captures Saxon, but realizes that he no longer has murderous urges in response to his relationship with Hannah. Instead of killing Saxon, Dexter calls Debra to arrest him, but Clayton tails Debra and unknowingly interferes. Saxon kills Clayton and escapes after shooting Debra.
The Ice Truck Killer strikes again, leaving a real nightmare before Christmas at Santa's Cottage. Sergeant Doakes becomes more suspicious about Dexter after his ambivalence about Batista's survival. Dexter finally finds he is connected to the Ice Truck Killer over a past case involving Harry Morgan and a blood-bath crime scene in 1973 involving Dexter's biological mother. Lieutenant Maria LaGuerta braces herself as Captain Matthews blames her for the department's failure to find the Ice Truck Killer and he has her replaced. Rudy and Debra spend some quality time together, and Rudy proposes marriage to the smitten detective. Rita decides to take her children, Astor and Cody, to visit Paul, who has been sent back to prison.