As Flight 718 reaches cruising height, Marshall Bowman is writing notes to himself about avoiding capture when he notices that his nose is bleeding. He goes to the lavatory and swabs the back of his throat, then does a test on the sample. When it proves positive, he begins to panic and demands to talk to the flight attendants in private. He asks them to get as many tranquilizers from the passengers as they can and administer them to him. Bowman can’t explain but insists they’ll all die if they don’t do what he says. He starts bleeding and tells them he’s going to lock himself in the lavatory, and if he doesn’t answer or he’s something different, they need to keep the door closed.
Bowman goes into the lavatory and his teeth start to fall out. He falls to the floor and his clothing rips open as he transforms. Outside, the attendants try to inform the captain when a grotesquely mutated, beast-like Bowman slams out of the lavatory and starts killing everyone.
In Scarsdale, NY, a mother is taking her children home from soccer when Flight 718 flies overhead and crashes into a nearby hillside.
Olivia finds her niece Ella playing with her makeup and jewelry. As Rachel sends her out of the room, she finds the engagement ring John gave to Olivia. She finally drags out of Olivia the fact that John was a traitor and proposed to her as part of his cover to earn her trust. They’re interrupted when Olivia gets a call summoning the team to Scarsdale to investigate the crash of Flight 718. Among the bodies is Bowman’s mutated animal-like form. Walter confirms that it was a human being that underwent some kind of transformation. Charlie arrives with a passenger manifest and Olivia as goes through it she sees one familiar face: one face that she recognizes: Bowman, which she “remembers” from John’s imbedded memories. Charlie wonders how she knows him and Olivia dismisses it as a hunch.
At the lab, Walter dissects Bowman’s corpse and finds a glass disk in one mutated hand.
At the Federal Building in Boston, Charlie reports that Bowman was a banker in France who managed overseas accounts. Olivia recognizes one of the client photos as belonging to a man with Bowman in her memories from John. Before she can pursue the matter, Broyles plays the black box recording, where the pilot and passengers are savagely attacked. Olivia asks him to follow up on the man she remembers, Daniel Hicks. When he wonders why, she explains that she has some of John Scott’s memories. She thinks John, Bowman, and Hicks were all working on a weapon deal. Charlie agrees to bring Hicks in and hold back his questions, and she thanks him. She calls Peter who informs her that Walter has identified Bowman by the blood tests and that the man was dosed with a designer virus that would have killed him even if the plane crash hadn’t. Peter sends her a photo of the disk which Olivia recognizes from the DEA agent who had one in her hand.
Charlie and Olivia interrogate Hicks and Peter and Walter watch. Hicks claims to be a furniture import/export dealer. He denies any special knowledge of Bowman, and then his nose starts bleeding. Walter sees it and has Peter get him sedatives, while Hicks goes into convulsions. They prepare to administer the sedatives but Olivia refuses the treatment until Hicks gives her a name. He says they must have been dosed and finally gives her the name “Conrad.” Walter administers the sedative and he passes out, suspending the transformation.
Olivia is going through Jon’s files at the Harvard laboratory when Astrid informs her they haven’t come up with any information on someone named Conrad. Walter has put Hicks into a coma and has synthesized a possible antidote. However, he warns that the transformation may finish before he can succeed. Olivia asks Walter to open his hand and see if there’s a disk inside. There is, and Olivia takes it to Broyles. She wants permission to exhume John to see if he has a disk in his hand. Broyles says it isn’t possible and Olivia snaps at him, and he relents to explain why.
Broyles takes Olivia to Massive Dynamic and Nina Sharp explains that they are keeping John’s corpse in stasis, believing that the disk in his hand will self-destruct when the host dies. Massive Dynamic tries to use John’s DNA to gather data from the disk, but all they’ve discovered is that he was part of a bio-terrorist cell. There were also references to Conrad, who they have scattered information on him selling bio-weapons on the black market. Broyles tells Olivia that they have word that a major sale is taking place in Chicago and Conrad is involved, but they have no idea where or when.
Olivia drives back to the lab and asks Walter to place her back in the sensory deprivation tank so she can access John’s memories. Walter goes ahead with the procedure and Olivia finds herself in a memory of the hotel room where she and John went for their trysts. Walter transmits his memory to guide her through as she watches herself and John enter the hotel room. When the memory Olivia leaves the room, John sees the real Olivia and approaches her. She grabs a gun and demands to know who Conrad is. When he keeps coming, she shoots him. Her readings spike and Walter loses contact with her. He warns Peter they need to reconnect before they pull her out.
Olivia finds herself in an alleyway and John waits for her on the street outside. He points out Conrad and says that he’s a monster who creates weapons because he can, then sells them to the highest bidder. John then points out himself on a nearby balcony and explains he failed in his mission because he didn’t know who Conrad was. Olivia asks who his mission was for and John explains that he was part of a black ops NSA task force with Hicks and Bowman. Olivia asks for proof but John insists it was off the books and he could never tell her. She asks him where the sale of the virus is going down, but Johns says that Hicks would know. John starts to fade out and tells her to trust Hicks. Walter reestablishes contact and they pull her out of the tank.
Olivia has no luck confirming John’s story with NSA. They don’t know if the antidote is working on Hicks yet but Olivia wants them to wake him up. Peter wonders if John is still lying to her to tip off Conrad, and says it’s a bad idea. Astrid, overhearing, says that Olivia should trust her instincts. She considers then tells Walter to wake up Hicks.
Once Hicks is awake, they come up with a plan. They’ve arrested Conrad’s intermediary Ernesto when he arrived in the U.S., then put a radio transmitter in Olivia’s left ear. Hicks will transmit all the information Olivia needs to take the intermediary’s place and go through with the deal and purchase the virus. When she’s ready to make the arrest, she’ll give the signal, “Christmas.” They head to Chicago and Olivia waits in the hotel lobby with Peter while Charlie and his men set up nearby. Peter insists on going with her, while Astrid puts Hicks on the speaker. Hicks tells Olivia the necessary information to assure the seller she’s a suitable replacement. Olivia wonders if Hicks is setting her up and he tells her to trust him like he would John. Olivia makes contact with the seller, Gavin, who wants to know who Peter is. Olivia dismisses Peter as a lackey and they go to the designated hotel room. The transmitter doesn’t show up on a scan and Peter turns over the money. As his men count it, Gavin asks Peter questions about his background. When Gavin asks Peter a question Hicks doesn’t know, Peter successfully bluffs his way through on his own.
The money checks out and Gavin wonders why they came after the situation in France. Again, Hicks provides the right answer for Olivia to respond with. Gavin’s man brings in the bio-weapon while Gavin gets a call. He tells them that Conrad is coming to see them. Charlie figures that Olivia isn’t calling them in yet because she wants to get Conrad. Gavin points out that he’s also selling the antidote in case of accidental exposure. He then asks why Ernesto didn’t call himself. Before Hicks can give an answer, he starts to transform and Walter and Astrid are forced to render him unconscious again. As Gavin’s men go for their guns, Peter fakes an outburst and claims that Ernesto is sick and doesn’t want anyone to know. They’re interrupted when Conrad arrives and says he has no idea who Olivia and Peter are. Olivia responds by giving the code word, but Conrad orders Gavin to kill them. The FBI agents break in and takes Conrad, Gavin, and his men into custody.
Later back in Boston, Broyles congratulates Olivia on arresting Conrad, who they’ve tied to over a dozen black market bio-weapon sales. He tells her that John’s status remains unchanged and he’s still considered a traitor, but Olivia is satisfied that she knows the truth.
Olivia returns to the lab where Walter explains that the antidote worked and Peter and Astrid took Hicks to the hospital. She asks him to help her access John’s memories again and he explains that John’s embedded memories are disappearing as her brain waves return to normal. Olivia insists they need to do it now and Walter agrees.
Inside of John’s memories, Olivia finds herself on a dock by a lake. John appears and Olivia tells him they caught Conrad. She apologizes for doubting him and he admits it was his fault because he ran out of time before he could decide to let her know. He tells her there’s one other thing: he gives her an engagement ring. They kiss and John says he loves her… then disappears.
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