Episode 1: "Pilot"
An international flight lands in Boston's Logan Airport, its crew and passengers dead from a mysterious flesh-dissolving toxin. When Special Agent Olivia Dunham's partner, John Scott, is infected by the same toxin, she recruits Dr. Walter Bishop, a mentally unstable researcher in fringe science, and his estranged son, Peter, to help her to save John's life. They discover a cure to the man-made toxin, but learn that the mass infection was but an experiment, and part of a larger mystery called "The Pattern." Her partner is found to be responsible for funding the creation of the toxin, but is killed while trying to escape. At the end, John's body is delivered to Massive Dynamic to be revived for questioning.
Episode 2: "The Same Old Story"
Olivia, along with Peter and Walter Bishop, reopens a cold case involving a serial killer who extracted the pituitary glands from his victims after investigating the strange death of a woman who had an even stranger child. The woman was pregnant for a few minutes, yet the baby she birthed was fully developed - then aged eighty years in the span of another few minutes. They discover that the killer is an artificially-aged human, who is using the enzymes extracted from the removed glands to halt his accelerated aging disease. The team is able to track him and his creator down, causing the man to die from being deprived of the enzymes keeping him young.
Episode 3: "The Ghost Network"
A man seems to be having visions of Pattern-related terror attacks before they occur. The team, led by Dr. Bishop, discovers that he is receiving signals from the Ghost Network, an otherwise undetectable frequency range on which the masterminds are communicating. With his help, they are able to intercept a strange crystalline disk, which is given to Nina Sharp for analysis
Episode 4: "The Arrival"
A mysterious cylinder emerges from beneath the Earth in New York City, so Broyles enlists the trio of Olivia, Dr. Bishop and Peter to investigate the significance of the object. However, others also seek it, including a bald man known as the Observer who only watches events as they unfold and another willing to kill to retrieve the cylinder. Dr. Bishop hides the cylinder against the wishes of the rest of the team, owing a debt to the Observer for saving his life and that of his son many years earlier. An unknown man abducts and tortures Peter for information regarding the cylinder's location, and learns its placement through the ideas Peter has absorbed from his father through osmosis. The man takes him to a cemetery where Peter's grandfather is buried and finds the cylinder. Olivia shows up after learning the location from Walter and kills the man. The object burrows back underground before either side can discover its purpose. Peter encounters the Observer, who demonstrates telepathic abilities before shooting Peter with a yet unknown weapon. At the end of the episode, Olivia, who is standing in the kitchen, sees John Scott standing in the kitchen entrance.
Episode 5: "Power Hungry"
The team discovers a man with the uncontrolled ability to affect electrical energy, made the way he is by a scientist performing illegal experiments on humans. With the help of carrier pigeons modified to track the man's electromagnetic signature, the team manages to track him down and arrest the scientist. Meanwhile, Olivia begins seeing visions of John, which she learns are caused by memories transferred to her during their experience in the first episode. Through these memories, she discovers one of John's secret hideouts, where a large number of investigation files relating to the Pattern are found.
Episode 6: "The Cure"
A woman with a rare disease, "Bellini's lymphocemia," is kidnapped and given a nootropic drug that makes her brain emit a microwave burst, killing her and the patrons of a diner she stumbles into. When the team investigates, they find that another woman with the same rare disease has been kidnapped. After talking to the doctor who was treating them, Olivia learns that the chief scientist of a competitor of Massive Dynamic is the one who gave her the drug. Peter makes a deal with Nina Sharp, who tells him where to find the second victim before she can be turned into a radioactive bomb.
Episode 7: "In Which We Meet Mr. Jones"
Agent Mitchell Loeb, a friend of Broyles collapses on assignment, his heart being constricted by an engineered parasite which is slowly working its roots into his circulatory system. To find a cure, Olivia must talk to David Robert Jones, a biochemist held incommunicado in Frankfurt, Germany. Problems arise when David demands to speak to a colleague of his in exchange, who is unfortunately killed in a raid set up by Broyles. Walter, however, devises a way to wire Peter into the dead man's brain, enabling Peter to speak on his behalf. The procedure is successful and the parasite is removed, but the team doesn't realize that the entire incident was set up by Loeb to get the information Peter extracted from the dead man.
Episode 8: "The Equation"
The abduction of a young musician is highlighted by a sequence of flashing lights which causes the boy's father to be hypnotized into a suggestive state and upon 'waking up' does not have any memory of what happened while hypnotized. Similar cases have ended with the victim being returned, but left insane from the trauma of the incident. As they investigate, they discover that each case dealt with a genius of some sort working on an unfinished equation. To discover the child's whereabouts, Olivia encourages Walter to return to St. Claire's Hospital and speak with his old bunkmate, a former mathematician who disappeared under similar circumstances. The visit does not go well, and Walter is held by the hospital administrator, who remains unconvinced of Walter's sanity. Walter manages to coerce his bunk mate into giving up a vague idea of his whereabouts, which Olivia and Peter use to find the boy once they arrange for Walter's release. However, the kidnapper escapes with the completed formula, which she gives to Mitchell Loeb, who calibrates a frequency generator in such a way to allow him to pass through solid matter.
Episode 9: "The Dreamscape"
A Massive Dynamic employee jumps out of a window when he believes he is being attacked by butterflies. Olivia's connection with John Scott leads her to breaks in the case, but she becomes fed up with his manifestations and decides to return to the sensory deprivation tank to rid herself of them. Meanwhile, Peter's past catches up with him when his enemies find out he's back in Boston. Walter discovers that a hallucinogen produced by frogs is being used to literally scare victims to death, and the frogs are tracked to a suspect with whom John was involved. The suspect points to Massive Dynamic as the real culprit and tries to make a deal to testify, but is himself poisoned by the hallucinogen before this happens.
Episode 10 : "Safe"
Agent Dunham investigates a body trapped inside a wall in a bank. He turns out to be a member of Mitchell Loeb's team, who uses the technology he obtained in "The Equation" to engineer a string of bank robberies, targeting safe deposit boxes Walter used to hide a teleportation device. He succeeds in recovering the device and uses it to teleport David Robert Jones right out of a prison in Germany. Furthermore, Massive Dynamic's plan to resurrect John Scott is halted when they realize a crucial piece of his memories are inside Dunham's mind, after Olivia discovers she is mistaking his memories for hers. Jones instructs his partners to retrieve Olivia, and she is abducted while trying to track Loeb's group.
Episode 11 : "Bound"
Olivia's former adversary, Sanford Harris (Michael Gaston), conducts a formal review of the Fringe division. Olivia manages to free herself from her abductors. She, along with Walter and Peter, investigates the murder of an epidemiologist, who is killed by a chemical which creates a giant, slug-like single cell of acute viral nasopharyngitis in his stomach. Olivia succeeds in connecting the murder to Loeb and obtains the necessary evidence to capture him. Olivia tries to question him about her abduction but he tells her that he was trying to save her. Olivia's sister Rachel (Ari Graynor) pays a visit with daughter Ella.
Episode 12 : "The No-Brainer"
The trio investigates the deaths of a teenager and a car salesman whose brains have been liquefied after watching a video sent to their computers. All of the victims are connected to a computer programmer who has lost his job. The murderer then sends the video to Olivia's laptop, almost killing her niece Ella, before Olivia is able to intervene. In order to catch the suspect, Olivia defies an order from Agent Harris, and Broyles puts his friendship with Harris on the line to defend her.
Episode 13 : "The Transformation"
When a plane crashes after a passenger transforms into a monster, the team suspects a possible smuggling of bioterror weapons, which is linked with John Scott. They also find a crystalline disk, similar to one seen inside the woman killed in "The Ghost Network", in the passenger's and his accomplice's body. While solving the case, Olivia learns that John Scott was working undercover for the National Security Agency and his body is being kept by Massive Dynamic for extracting more information. Following Olivia's successful operation to take down the weapons dealer, she returns to the sensory deprivation tank and bids farewell to John's consciousness, which has finally left her own.
Episode 14 : "Ability"
Following his escape from a German prison, David Robert Jones turns himself in to the FBI, having begun to suffer side effects of the teleportation in "Safe." Walter mentions that the teleportation side effects won't kill Jones but will do something terrible to him. As insurance, Jones has developed a toxin which causes the orifices of those exposed to it to seal up, suffocating them. A bomb containing the toxin is set to go off if Olivia cannot pass his tests. The first test is to shut off a series of lights using only her mind. Jones says this is possible due a nootropic drug present in Olivia, one designed by William Bell and patented by Massive Dynamic. The team discovers a manuscript, which explains the letters ZFT (Zerst�rung durch Fortschritte der Technologie, "Destruction by Advancement of Technology"), which is essentially a Bible to Jones and his followers. According to the manuscript, there is a conflict going on between our world and a parallel universe. Jones wants Olivia as a "recruit" and the tests are the part of the selection process. Initially, Olivia believes Jones is playing mind games with her and refuses to cooperate, but when she is forced to disarm the bomb in the same manner as the test, she succeeds.
Episode 15 : "Inner Child"
An enigmatic mute child is found living underground and begins to bond with Olivia when the Fringe Division is brought in to investigate. While the child adapts to his new environment, Olivia and the FBI hunt a bizarre serial killer known as "The Artist", who has resurfaced to publicly display his work. The child leads Olivia to breaks in the case, using a strange ability to sense the emotions of the killer. Once the killer has been captured, Olivia arranges for the child to be secretly put in the care of a foster family, rather than turning him over to the CIA as ordered. As the boy is taken to his new home, he sees the Observer on the sidewalk staring at him.
Episode 16 : "Unleashed"
When animal rights activists ransack a laboratory, they accidentally release a man-made chimera with a ferocious appetite. Walter suspects that his research helped to create it. The creature leaves a trail of grotesquely mutilated bodies in its wake, some of which it injects with its larvae. Charlie survives such an encounter with the creature, and the Fringe Division must race to capture it for a sample of its blood before the larvae eat their way out of Charlie. Olivia discovers the source of the creature, and that it was created based on work by one of Walter's peers, not Walter himself. Walter risks his life to capture the creature and succeeds, allowing them to save Charlie.
Episode 17 : "Bad Dreams"
Olivia dreams of herself committing murders halfway across the country, and the team discovers that, while no one is actually causing the incidents, they are happening as Olivia has seen them. The team discovers that another person treated with the nootropic drug Cortexiphan, Olivia's "buddy" in the drug trials, is unwittingly transmitting his intense emotions and causing others to act on them. While Olivia does not remember him, he remembers her, having nicknamed her "Olive." Olivia non-fatally wounds him so he does not commit suicide with a large group, and he is placed in a medically-induced coma to contain his emotions. Walter watches a video of Olivia as a child, apparently taken during the time she was being administered the drug. Walter's voice is heard on the tape, as is William Bell's. Both are trying to calm Olivia down and there appears to be damage to the equipment in the room.
Episode 18 : "Midnight"
The investigation into the deaths of people whose bodies are drained of their spinal fluid leads the Fringe Division to a scientist named Nicholas Boone with ties to the bioterrorist cell ZFT. Boone's wife Valerie is the killer, having been infected with an extinct syphilis strain that drives her to consume her victims' spinal fluid. Her first victim onscreen is a suave clubgoer, Bob Dunn (Richard Short). In exchange for information on ZFT, Walter aids Boone in creating an antidote to cure Valerie. Boone has to use some of his already low amount of spinal fluid to formulate the antidote, costing him his life. Olivia and Peter successfully capture Valerie and cure her. A video made by Boone prior his death reveals that William Bell has been funding ZFT.
Episode 19 : "The Road Not Taken"<
The Fringe Division investigates the case of a woman who "spontaneously combusts" in the middle of a busy New York street. The team discovers that the victim is the subject of a ZFT experiment to cultivate pyrokinesis. As they investigate, Olivia experiences "visions" while awake. Walter suggests she is seeing a parallel universe which has branched off from our own. Olivia and Peter visit an agoraphobic website designer who is apparently aware of William Bell, the drug trials, and the coming war, although his credibility comes into question when he believes himself to be a character in the plot of Star Trek. Using information from her visions, Olivia tracks down the victim's twin sister, who only moments before was kidnapped for more ZFT experimentation. Harris is revealed to be responsible for the crimes, and while closing in on him, Olivia gets locked in a room with the twin sister, whose unstable pyrokinetic abilities threaten both their lives.
Episode 20 : "There's More Than One of Everything"
Nina Sharp recovers from her attack and reveals to the Fringe division that an energy cell was stolen from her mechanical arm by Jones, which he intends to use to open a doorway into a parallel universe to confront William Bell. Meanwhile, Peter finds Walter at a beach house where they retrieve a device that can seal such an opening. Walter explains to Peter that he once lost something very dear to him and that he had to go and bring it back from another reality, the device being meant to prevent something from following him. Olivia, Peter and Walter intercept Jones opening another window, and Peter triggers Walter's device, killing Jones by sealing the doorway while only half of him is through it. At the end of the episode, Walter goes alone to visit a graveyard in which he tearfully observes a gravestone marked "Peter Bishop 1978-1985", suggesting that Walter's son died and that Peter is actually from the other universe. Nina Sharp later calls Olivia and implies to her that she can meet William Bell in Manhattan. Olivia is taken to the parallel universe while riding the elevator and is directed to an office. She is greeted by William Bell (Leonard Nimoy). The final shot pans out the window revealing that they are standing inside the South Tower of the World Trade Center.
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