John Scott was a Special Agent for the FBI with questionable allegiance. His activities before his death, and his retrieved memories, indicated intimate knowledge of persons and events associated with the Pattern. It was for this reason that his body was taken to Massive Dynamic, where technicians worked to retrieve his memories. He was also romantically involved with his law enforcement partner, Agent Olivia Dunham. It was discovered that John was a part of a secret NSA task force with the mission of infiltrating a bio-terrorist organization run by a man named Conrad Moreau.
Prior to joining the FBI, John Scott served in the Marines alongside Raul Lugo, who became a very close friend. John celebrated Raul's promotion to First Lieutenant with him and wife at their home, where the three had dinner. ("Safe")
During an unspecified time leading up until his death, John was a part of a secret NSA task force whose goal was to infiltrate a bio-terrorist cell run by a man named Conrad Moreau. It is unknown whether or not Moreau was involved with ZFT. John's investigations led him to several Pattern related crimes, suggesting that Moreau's bioterrorist organization has a connection to the Pattern. Scott's case files were held in a secret cellar in Boston. This cellar was filled with documents related to the Pattern. During one specific stakeout, John Scott had Moreau lined up in his sights, but did not pull the trigger because he wasn't sure. He claimed later that he could have taken Moreau out right there and then. ("The Transformation")
John Scott began a relationship with FBI colleague Olivia Dunham. He took her out to eat at a restaurant for their first date, beginning a relationship that would progress to become very serious. Many of their outings culminated in romantic nights at the motel. ("The Dreamscape") John also purchased an engagement ring with the engraved word "Always" on it in hopes of marrying Olivia. He died before he could propose, leaving the ring hidden amongst his personal effects in the underground cellar. ("Power Hungry")
While having a late-night rendezvous with lover Olivia Dunham , Scott was called in to investigate Flight 627. Following up leads back at FBI headquarters, Scott and Olivia Dunham were sent to U-Case Storage to investigate some suspicious activity. Agent Scott discovered a secret laboratory in one of the storage rooms, and its owner Richard Steig. After a chase through the storage facility, Steig detonated some explosives, injuring Scott and knocking Olivia unconscious. The explosion also exposed Scott to synthetic chemicals that were in the labs, afflicting him with the same symptoms as the Flight 627 passengers; albeit with a much slower rate of tissue decay.
Scott was taken to a medical facility and monitored in the Kennedy Wing Isolation Unit, where he was put into a drug induced coma in an attempt to slow down his dissolving tissue.Olivia searches for a cure, involving Peter Bishop and Walter Bishop along the way, and sets up a Synaptic Transfer to talk to Scott. Scott is able to share his memories with her and shows her Steig's face. After Olivia identifies Steig and tracks him down in South Boston, Steig cooperates and provides them with a full inventory of the chemicals Scott was exposed to, allowing Walter Bishop to synthesize a cure.
Once cured, Scott recovers almost as rapidly as he degenerated. At the point Olivia discovers that Scott has threatened Steig and knew about the Flight 627 contagion already, Scott gains entry to Steig's room in the hospital and suffocates him with a pillow. He then leaves the hospital and drives away but is spotted by Olivia, who gives chase. When he sees Olivia following him, he panics and attempts to drive her off the road, but he drives up a ramp, flipping his car and suffering fatal injuries to his head. He crawls from the car and, in his last moments, tells Olivia to question why Phillip Broyles sent them to the U-Case facility. After this he succumbs to his head injuries and dies.("Pilot")
A glass disk is discovered implanted in Scott's hand, but the technology exceeds that of the US Government, leading Phillip Broyles to enlist in Massive Dynamic , whose technology is far superior to the governments, to try to read the data and discover what connection Scott had to the Pattern. ("The Transformation")Scott's corpse is brought to Massive Dynamic, where Nina Sharp orders an attendant to "question him".
Scott is given a hero's funeral at Mount Briar Cemetery. ("The Ghost Network")
Olivia Dunham receives a phone call, and as a man's voice says "Hello, Olivia", she reluctantly asks "John?". The connection is broken, and when she calls the Bureau attempting to trace the call, she is informed that there hasn't been any call at all.
A couple of days later as she enters her home, she sees John. Dunham later describes the incident to Charlie Francis, adding that when she reached for her weapon, the figure disappeared. ("The Arrival")
Scott speaks to Dunham twice. On the first occasion, after Dunham accuses him of trying to kill her, he responds that it was not him. On the second occasion, he kisses her. While they are kissing Peter walks up
behinds Olivia, but can not see John. Walter explains that it's possible that a portion of agent Scott's consciousness remained as a result of the Synaptic Transfer. Scott leads Dunham to a basement filled with files of investigations he was conducting on his own of Pattern-related incidents. It was here that the FBI discovered John's personal effects, which Broyles gave to Dunham. Among these personal effects was the engagement ring, which was given to Olivia at last. ("Power Hungry")
Olivia sees Scott at the scene of Mark Young 's death. She later receives an e-mail from him containing a basement address, this leads to a major break in the case. However, Olivia has been frustrated with these appearances by Scott and demands to Walter that she be put back in the sensory deprivation tank to rid her consciousness of Scott's. Once inside, she witnesses their first date, and John seems to notice Olivia, even though Walter said such a thing is impossible. Olivia uses John's memories to find a suspect, George Morales. Later on, George Morales hallucinates John Scott slitting his throat, which manifests as a real event, killing him. At the end of the episode, Olivia receives another email from John, reading "I SAW YOU. IN THE RESTAURANT." ("The Dreamscape")
Olivia once again returns to the sensory deprivation tank, so she can talk with John, in order to gain critical information about a case. John reveals that he, along with Marshall Bowman and Daniel Hicks, were all working undercover for the NSA, in order to infiltrate the bio-terrorist cell run by Conrad Moreau. After the case was closed, Olivia returned to the dreamscape for one final time, where she and John stood on the pier. John finally gave her the engagement ring that he never had the chance to give to her, explaining "I know we can't ever be together. Not really. Maybe I won't know the difference." With John's name cleared, Olivia accepts the ring as the two enjoy one last moment together. ("The Transformation")
John Scott was affected by the flesh-melting toxin in 2008. He was cured. Soon after that he was chased down by Olivia. Seeing as she thought he was a traitor and he ends up dying in a fatal car crash.
- John Scott has O-Positive blood type.
- Although he stopped appearing in episodes after The Transformation, John had a cameo in Brown Betty in Walter's story, in the form of a photograph on the desk of Detective Olivia Dunham. Walter's narration implies that John Scott's fictional counterpart had broken Detective Dunham's heart.
- Actor Mark Valley, who played John Scott, was actually married to Anna Torv (who plays the character of Olivia Dunham) between 2008 and 2010.
"You do that and we will come after you -- I will come after you."
- - John (Pilot)
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