Weymouth, Mass. An FBI SWAT team speeds across the water at night on zodiac boats, on their way to a sting. The target arrives, a cargo truck. The team swarms the truck and opens the back -- where they find only oversized carnival bears. The team's been had.
At the Boston FBI office, Broyles receives a briefing from AGENT MITCHELL LOEB, who led the sting. Loeb was recently transferred to the Boston office after working abroad in Europe. He explains that the smugglers knew they were coming. He hands Broyles a dossier on JOSEPH SMITH, who has a science background and has been traveling back and forth to Budapest. He also worked for the shipping company that handled the cargo container that Loeb was tracking; he must have switched the contents of the containers. Suddenly, Loeb begins to grab his chest and falls to the floor. It looks like he has gone into cardiac arrest. Moments later, Loeb is rushed into the emergency room, where Broyles does his best to comfort Loeb's wife, SAMANTHA.
In the emergency room, the doctor tries to shock Loeb's heart back into rhythm, but it doesn't work. He cracks Loeb's chest, but once he gets a glimpse of the heart, he steps back in fear. Wrapped around Loeb's heart is a wicked-looking PARASITE that pulses with every heart beat.
Broyles briefs Olivia, Peter, and Walter on the situation. The parasite is not communicable, but otherwise the doctors are clueless. Broyles asks Walter to help, because Loeb is more then just a colleague -- he is also a friend.
Walter, in between requests for breath mints, is amazed by the parasite. He admires the intricate design; he's never seen anything like it. Loeb is removed to the laboratory so Walter can find a means of removing the thing from Loeb's heart. After some examination, Walter suggests that the organism could be something as simple as a common waterborne parasite... only much, much larger.
Samantha Loeb arrives and wants to know why her husband has been moved to the lab. Olivia tells Samantha that a member of her team is "uniquely qualified" to save her husband's life. Samantha hands Olivia a document that Loeb brought back with him from Frankfurt, Germany: a sheet of paper filled with numbers. Samantha thinks it might have something to do with what Loeb was investigating.
Walter tries to remove the parasite, but it reacts by further constricting Loeb's heart. Peter quickly gives Loeb an injection to bring his heart back into normal rhythm, as Walter takes a tissue sample of the parasite for DNA analysis.
A short time later, Walter shows Olivia the results of a DNA analysis. A specific line of the DNA sequence repeats over and over, in a fashion that is much too organized to be random. Walter posits that it could be a code or message of some kind. Astrid thinks it might be a Caesar Shift -- a kind of cipher Julius Caesar used to send covert messages. Astrid has narrowed down the possibilities to a three-letter combination. Olivia realizes it spells out ZFT: an organization that was mentioned in John Scott's case files ("Power Hungry").
Olivia goes to Broyles and explains her theory: since ZFT was working out of Budapest, where the shipping container that Loeb was tracking originated, they must be behind what happened to Loeb. Broyles tells her that a man named DAVID ROBERT JONES was arrested in Germany a month ago. Jones has a background in biotechnology and is known to traffic in genetic weaponry. He was arrested by Interpol for trying to steal state secrets. Broyles doesn't know if Jones is part of ZFT, but Loeb was investigating him in Frankfurt, and the heart parasite might be a form of retribution. Broyles explains that ZFT is a mysterious group that apparently traffics in highly advanced scientific knowledge, such as the kind used in the attack on Flight 627 ("Pilot"). Olivia says she might be able to use a contact she has in Frankfurt to get access to Jones; maybe he can help remove the parasite.
Peter notices that the parasite is growing throughout Loeb's body and is slowly killing him. When Olivia calls to say she's going to Germany, Peter tells her to hurry, there's not much time left.
Frankfurt, Germany. Olivia is picked up at the airport by an old flame, LUCAS VOGEL, now working in the German government. Lucas knows the warden at the prison where Jones is being held. Olivia persuades the warden to give Jones a message in the hope that he will talk with her.
Back in the lab, Broyles checks on Walter's progress and thanks him for his help. Walter responds by describing a fruit cocktail he had in Atlantic City once. The surreal conversation is interrupted when Broyles receives a call from Charlie Francis, who has a lead on Joseph Smith's location in Boston. Broyles immediately sets up a raid on the location to grab Smith.
In the prison in Frankfurt, the warden informs Olivia that Jones will talk with her, but not until the next morning, and she will only have fourteen minutes. But Jones has one condition: he wants to talk with Joseph Smith. Olivia calls Peter to tell Broyles to find Smith, but Peter cuts her off: Broyles is already about to apprehend Smith in a raid.
Peter jumps in the Vista Cruiser and screeches to the raid, hoping to make sure the FBI takes Jones alive. But the SWAT team is on radio silence, and by the time Peter arrives Smith is already fleeing the scene. When Smith pulls a gun on an agent, he is shot and killed.
Peter explains to Broyles that Jones would cooperate only if he could talk to Mr. Smith -- the same Mr. Smith that Broyles's team just killed. Walter calls to tell Peter that Loeb's condition is continuing to deteriorate; they need to get Jones talking fast. When Peter says Jones is dead, Walter asks if Mr. Smith still has his head. He does? Then Walter needs the body; "his death might just be an inconvenience."
In the lab, Walter realizes Smith has been shot in the head, which of course is a problem. It means that Walter's procedure for questioning the dead won't work as planned, because the dead man's brain cannot communicate with his mouth. They will need someone else -- Peter -- to be the dead man's mouthpiece. Walter then reveals that he tried this same procedure for the government back in the 1970s, on a man who (Peter realizes) must have been Jimmy Hoffa. The process was unsuccessful, because when Walter turned on the brain-questioning machine it fried Jimmy's brain.
Walter tests the device by running a current through Smith's brain to a receiving machine with a light bulb, which is standing in for Peter's brain. To Peter's dismay, the first attempt explodes the light bulb.
In Germany, Lucas and Olivia share a romantic dinner. Lucas sees through Olivia's cold shell. He admits that he screwed up with Olivia. He thinks they should try to make it work again. And just as they share a kiss and it looks like things might progress further, Olivia's phone rings. Peter has good news: Walter might just get the dead Smith to answer some questions. The moment is over, and Olivia leaves.
The next morning, Peter's and Smith's brains are connected by a plethora of wires and sensors in a 21st Century Frankenstein lab scene. Astrid feeds questions to a computer that inputs them directly into Smith's brain, while Walter administers an electric shock. The outcome is a feed to Peter, who acts as the dead man's voice. Before they start, Walter apologies to Peter for the pain he is about to endure. As the first question is asked, Peter cries out in pain. He is not getting answers yet, only extreme discomfort.
Olivia finally meets Jones in a bare interrogation room. She explains to Jones that he will ask her one question, and then she will relay that to an agent back in Boston who will ask Smith. Jones finds her attempt at control amusing but plays along. This intrigues Olivia. Why doesn't Jones ask for his freedom? Jones replies, in a condescending tone, that Olivia is terribly native; there are things more important then freedom. Jones further suggests that someone might be playing both of them.
Back in the lab, Walter realizes the process is failing because Peter is thinking too much -- a family curse. Walter drugs Peter to block his higher brain functions, so he can "hear" Jones's answers. Once Peter is stoned, Walter says they're ready and they call Olivia.
Jones asks his one question: "Where does the gentleman live?" Each time Astrid poses the question, Walter ups the voltage, and Peter goes through even more excruciating pain but is still unable to hear the answer.
Back in the cell, the guard tells Olivia her time is up. Just as she is being dragged away, Peter asks for paper and frantically draws a number of vertical lines. He can't hear the answer, but he sees something. Walter realizes that Smith's brain damage is interfering with his perception of horizontal lines. Peter draws in the necessary horizontals and comes up with the answer: "Little Hill!" Olivia tells Jones the answer just as she is being dragged from the interrogation room. Jones divulges the antidote to inject directly into the parasite. Walter performs the injection, and Loeb is saved.
Loeb, recuperating in the hospital, talks to Broyles, who asks Loeb why he would be targeted. He doesn't know. Then Loeb's wife Samantha comes in. She is plainly relieved to see him awake and recovering. Once Broyles is out of earshot, Loeb asks if their plan worked. Did they get the answer? "Yes," she says. "Little Hill." And they both smile in victory.