Resistance Is Futile is the ninth of twelve episodes in Season Two.
In the morning, having spent the night trying to stand watch outside Rita's house, Dexter awakens from a dream about Santos Jimenez's corpse and remembers that he still has to go back to the Everglades and dispose of it. Rita comes outside and is surprised to find Dexter trying to protect her from last night's intruder (Lila). Dexter apologizes to Rita for cheating on her, and tells her that Lila was a huge mistake. Rita is glad to hear it, but still can't fully forgive what he did. Understanding, Dexter leaves.
Dexter's plans to drive to the Everglades are halted when he realizes he's being watched and followed by an undercover FBI car. Fearing that he's attracted Lundy's suspicions, Dexter goes home and then to work.
Deb and Lundy start the day in bed together. Lundy doesn't wish to hide their relationship from their coworkers, but Deb is reluctant to make it public. Lundy then gets a call and learns of a break in the BHB investigation.
At the station, Miami Metro deals with the news that the Bay Harbor Butcher is someone in their department. In his lab, Dexter contends with a team of FBI technicians who look into the forensic database and examine his files.
Having stolen Dexter's blood slides, Doakes takes a plane to Haiti, where he meets his old colleague Leonis. He asks for a discreet laboratory that can analyze the slides, and Leonis agrees to make the arrangements. Doakes doesn't have the slides with him currently, but will have them sent here at a later date.
Dexter is chagrined when Lila comes into the station and invites several of his coworkers, including Batista, out for a drink. Dexter accompanies them to make sure Lila doesn't say anything about Jimenez. In the bar's bathroom, Dexter confronts Lila, who insists that the two of them belong together, that she knows the real Dexter and isn't afraid of him.
At his apartment, Dexter realizes his blood slides are gone, and determines that Lundy has them. FBI agents soon come knocking, with orders to bring him into the station. Accepting that he's been found out, Dexter calmly goes with them. At the station, Lundy and Captain Matthews present Dexter with the blood slide box. Dexter laconically says that the slides are trophies, after which Lundy and Matthews reveal that their prime suspect is James Doakes. They go over how Doakes investigated several BHB victims before their deaths and how he fits the profile of a murderous vigilante. Since Doakes flew out of the country this morning, they got a warrant to search his car at the airport; the slides were found in the trunk. Amazed by how well the story fits together, Dexter goes along with it and says that he's always sensed something off about Doakes, which would explain why Doakes constantly antagonizes him.
Lundy puts a protective FBI detail on Dexter in case Doakes comes after him. To preserve the department's reputation, Matthews enforces an in-house forensic investigation, and makes Dexter the lead technician in analyzing the slides. Dexter wipes the box of fingerprints, and the FBI technicians return to take his orders, much to his satisfaction. He has them stay in the lab and do the blood work, then prepares to go home. On his way out, Dexter tells Batista that Lila's just using him, but Batista doesn't care and ignores Dexter's warnings.
Meanwhile, LaGuerta refuses to believe that Doakes is the Bay Harbor Butcher. Doakes calls her, and she explains the situation. He vows to find proof of the real Butcher's identity, then hangs up and deactivates his phone. LaGuerta later becomes outraged when Lundy plans to release the Doakes story to the press, but he orders her to cooperate with the investigation or risk unemployment.
While being escorted home, Dexter gets a call from Rita. She confirms that his relationship with Lila is over, and reveals that she still has feelings for him. The two arrange to meet tomorrow.
LaGuerta urges Deb to talk to Lundy about the press, but Deb demurs. The two get into an argument, and Deb eventually blurts out that she's sleeping with Lundy, officially putting their relationship in the open.
As the FBI agents stand guard outside his apartment, Dexter sneaks out through a window and takes his boat to the Everglades. He arrives at the cabin and cleans up the murder scene. However, as he later brings Jimenez's body parts to the boat, Doakes suddenly appears and trains his gun on Dexter. He reveals that he put a GPS tracker on the boat, and has now caught Dexter red-handed as the Bay Harbor Butcher.
Doakes attempts to make an arrest, but Dexter sees an opportunity and attacks. Though Doakes manages to shoot him in the thigh, Dexter knocks him out with a sleeper hold. He brings him into the cabin and imprisons him in the large cage where Jimenez was storing his cocaine. As Dexter leaves, Doakes wakes up and yells, "You're going to have to kill me, Morgan!"
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