A commercial airliner: As MARSHALL BOWMAN sits writing in his notebook, his nose begins to bleed. He goes to the bathroom where he checks his teeth, tongue, and eyes. He swabs his mouth, dabs the swab into a vial filled with liquid, then panics as the liquid turns red. In the cabin, he grabs a flight attendant and tells her he's in trouble, that he needs to be sedated. As the flight crew tries to calm him, his nose begins to bleed again. He makes one final plea: keep him in the bathroom no matter what. Inside the bathroom, Bowman shudders in pain. His teeth begin falling out. He screams in agony as quills pierce the back of his shirt and he doubles over in pain. Outside, the flight crew are considering their options when the bathroom door splinters and a hideous, inhuman beast bursts into the cabin.
A soccer field in Scarsdale, NY. A mom packs her son's equipment into the back of her minivan after soccer practice, then turns to see an airliner plummeting from the sky and crashing in the distance.
Meanwhile, at Olivia's apartment, Ella plays dress-up with her aunt's clothes and jewelry. Rachel tells her to go wash up and pulls an engagement ring off of Ella's finger; it's Olivia's. Rachel pries, and Olivia comes clean about John Scott - how he betrayed both her and his country. As the two discuss their failed relationships, Olivia gets the call about the plane crash.
Crash zone. The team surveys the wreckage. Broyles leads them to what look like the charred remains of one of the passengers. But the charred corpse looks more like beast than man. Charlie gives Olivia the passenger manifest, and something in it catches her eye: the name Marshall Bowman.
Olivia has a flash: she is sitting in an undisclosed location with Marshall Bowman and another man. They speak vaguely about a product that's a "horror show." And then Marshall calls her John.
As Olivia returns to reality, she tells Charlie that Marshall Bowman is their guy. Knowing this is a hunch, Charlie reluctantly goes to investigate further.
The Harvard lab. Walter performs an autopsy on the beast. He suggests that whatever caused the transformation altered his internal organs. He also finds a small glass disk imbedded in the beast's palm.
At the FBI Office, Olivia goes through Bowman's file and sees a familiar face: DANIEL HICKS, the other man Olivia was sitting during her memory flash earlier. Broyles arrives and plays the last 60 seconds of the black box recorder and the beast attack. Afterwards, Olivia tells Charlie that Daniel Hicks was the man Marshall Bowman was flying to meet. Charlie, uncomfortable with Olivia asking him to bring Hicks in for questioning on another hunch, presses her for answers. She explains that she and John Scott shared consciousness through a procedure performed in Walter's lab, and she believes she is experiencing John's memories. Charlie agrees to bring Hicks in for questioning.
Back in the lab, Peter receives a call from Olivia and verifies that Marshall Bowman's DNA in the beast. He tells her that a "designer virus" rewrote Bowman's genetic code and that he wouldn't have survived the transformation even if the plane hadn't crashed. Peter also streams her a video of the glass disk they found in Bowman's hand. Olivia recalls that they found a similar disk in a DEA agent's hand a few months before ("The Ghost Network").
At the FBI, Charlie and Olivia interrogate Daniel Hicks. Daniel says Marshall Bowman was his banker, but Olivia and Charlie don't buy it. They show Hicks a photo of Bowman's remains, saying they believe he and Bowman were planning on buying and distributing a deadly virus. Hicks denies it, but not before his nose starts to bleed. Walter and Peter look on from the observation room. Walter tells Peter they need to get sedatives immediately, as Hicks is undergoing the same transformation Bowman did. Hicks begins to experience crippling pain. Walter and Peter arrive in the interrogation room with a med-kit, as Walter believes he can suspend the transformation process. But Olivia stops him short and tells Hicks he needs to talk before they will help him. Hicks chokes out the name "Conrad," and Walter doses him with the sedative.
Olivia digs through some files looking for anything John may have had to a Conrad. Walter runs tests on a sedated Hicks and tells Olivia that he's slowed the process and has already synthesized an antidote. Olivia takes Hicks' hand and tells Walter to cut it open. Lodged inside is a familiar glass disk.
Broyles's Office. Olivia shows Broyles the disks and asks permission to exhume John Scott's body. She believes John was working with Bowman and Hicks and that John may have a glass disk on his body too. Broyles tells her that's not possible, because he hasn't been totally forthright with Olivia about John. He was never buried.
Massive Dynamic. Nina Sharp leads Broyles and Olivia into a secret room, where John Scott's body lies in a cryogenic chamber. Nina informs Olivia that they did, in fact, find a disk in John's hand. It appears to be a data storage device, and they've been trying to analyze it. But apparently the information degrades when the host dies. Using John's body and DNA, they retrieved a small amount of data that seems to implicate John as part of a bio-terrorist cell. It also contained information on Conrad, a scientist they believe develops chemical and biological weapons for sale on the black market. Broyles says they have new intelligence that a major weapons sale is going down later that day in Chicago, but the exact location is unknown. He does know the man behind the sale's name is Conrad.
Olivia tells Peter she believes John knew the location where the deal is going to go down, and that information may have been preserved in her own mind. She wants Walter prep the tank.
The Harvard lab. Walter guides Olivia through a dreamscape, in an attempt to access John's memories. She finds herself in the cheap hotel where she and John used to meet. She sees herself and John Scott enter the room in the midst of one of their secret encounters. When the other Olivia goes to the bathroom, leaving John alone. And in spite of Walter insistence that it's impossible for her to communicate with because this is only a memory, John does exactly that. Olivia gets spooked, pulls a gun and shoots John. Walter's voice leads Olivia to an outdoor location, where she sees John and follows him down an alley. He points to a balcony, where another John Scott holds a sniper rifle. He says he was trying to kill Conrad, but he failed. John explains he was working with Bowman and Hicks on a secret NSA task force. Olivia doesn't believe him, she needs proof. John tells her it was top secret and cannot be confirmed, but that she can trust Hicks. John disappears as Olivia's vitals spike and Walter and Peter pull her out of the tank.
Later, Walter doses Hicks with his antidote, and Olivia decides they need to wake him up. Peter disagrees, suggesting that maybe John and Hicks were working with Conrad, and that dreamscape-John may be using Olivia as a way to tip Conrad off. But Astrid encourages Olivia to trust her instincts: does she think John really was a good guy? Olivia decides to go through with her plan. Walter wakes Hicks up and Astrid tells him they need his help.
At the FBI, Broyles briefs the office. A large weapons exchange will go down later today in Chicago. Olivia has been fitted with an untraceable two-way radio implanted in her ear so that she can talk to Daniel Hicks, who will tell her how to communicate with the sellers. The transaction will take place at the Fairchild Hotel and Conrad will not be present, but his intermediaries will. Teams of agents will be standing by to raid the premises, but not until Olivia says the code word: "Christmas."
Charlie and a surveillance team watch the sellers on surveillance cam as they arrive in a van. Meanwhile, Olivia sits with Peter in the lobby of the hotel. Olivia talks via earbud with Astrid, Walter and Hicks back in the lab. Hicks says Conrad's men will be suspicious, but she should tell them that she used to work with Anderson, and that Ernesto got called back to the basement and couldn't come.
The dealers arrive and interrogate Olivia; they sweep her and Peter for wires, but find nothing. Olivia shows them the money. One of the men, GAVIN, asks Peter where he met Anderson. Hicks tells Olivia to say he met Anderson at Oxford. She does, but Gavin presses further, wondering if they met on campus? Peter surprises Olivia with unexpected knowledge of the Oxford area.
A thug brings in a case and reveals the biological weapon. Gavin gets a call, and he informs Olivia that Conrad's on his way and would like to meet them. He then reveals a reverse-mutator for the virus, a cure included as a bonus with the sale. As Walter listens in the lab, he realizes that his own antidote isn't actually reversing the process, only delaying it. Gavin wants to know why Ernesto didn't call to say he wouldn't be able to make it. Hicks is having convulsions and unable to tell her the right answer. Walter sedates Hicks while Olivia stalls. Then Gavin demands to know whom Ernesto was meeting. Peter and Olivia exchange nervous glances.
Peter tries a desperate gambit, saying he doesn't want to die to protect "Ernesto's secret." He tells Gavin that Ernesto is dying, just as Conrad arrives. Conrad wants to know who they are, so Gavin updates him, but Conrad knows they're lying. Olivia tries to explain and drops the code word. Conrad orders Peter and Olivia killed. But before his thugs can execute the comman, FBI agents storm the room and arrest all of them.
At the FBI, Broyles tells Olivia that Conrad was wanted in connection with at least half a dozen attacks. Broyles tells her that even in spite of the success of the case, John Scott will still be viewed as a traitor by the department, because the truth of his story cannot be proven. Olivia says she knows the truth and that's enough for her.
Later, Olivia returns to the lab. Walter says the others took Hicks to the hospital to recover. The reverse-mutator they recovered during the raid worked. Olivia asks Walter for a favor: she wants to go back in the tank one more time. In the dreamscape, she finds John on the dock by a lake. Olivia apologizes for doubting him, and he brushes it off and says it's all right. And then he gives her a ring, which he wants to have despite knowing they can never be together. The two embrace and kiss as John tells her that he loves her. When she opens her eyes, he's gone, and she is standing by herself alone on the dock.