As the first season begins, FBI Special Agent Olivia Dunham is called in to investigate a mysterious outbreak that nearly kills her partner. The only person with any answers is an institutionalized scientist, Dr. Walter Bishop who can only be released under the care of his estranged son. Together, the three discover that the answer to this mystery is only a small piece of a much larger, more shocking truth.
When all the passengers on a plane die, FBI agent Olivia Dunham investigates the events and her partner almost dies. A desperate Olivia looks for help from Dr. Walter Bishop who has been institutionalized. Olivia, Dr. Bishop and his son Peter begin to discover what really happened on Flight 627 and begin to uncover a larger truth.
Olivia, along with Peter and Walter Bishop, investigates the strange death of a woman who had an even stranger child. The woman was pregnant for only hours, yet the baby she birthed was fully developed - and also aged eighty years in the span of a few minutes. Olivia asks Nina Sharp of Massive Dynamic for help.
The team investigates a bus full of dead commuters that appear to be fossilized and uncover a man who has visions of pattern-related disturbances before they happen; Dr. Bishop requests a piano in the lab to help him process data.
Broyles calls in the team to investigate a deadly explosion and its source: a strange cylinder unharmed despite the destruction. Olivia determines that the same cylinder, or a similar one, is responsible for similar events in widely diverse locations.
The team investigate the case of a man who can project electricity... and is at the center of a series of strange deaths involving electricity.
The team investigates a woman that re-appears after weeks of being missing with a rare disease. She also inexplicably causes pain and death to the people she meets. During the investigation, dangerous level of radiation are detected. Walter obsesses about cotton candy; Peter strikes a deal with Nina Sharp; and a truth about Olivia is discovered.
When a strange parasite attaches itself to the internal organs of a dying FBI agent, Olivia suspects a connection to the Pattern; Peter and Walter tap into a dead man's brain waves.
Walter thinks the abduction of a young music prodigy is linked back to his old bunkmate at St. Claire's Hospital. When he kidnaps the child he see's a sequence of flashing lights. Olivia wants Walter to return to the mental institution much to Peter's outcry, but Walter's determination to help ends up having chilling ramifications.
The team is called in to investigate why a man jumps out a window because he thinks he's being attacked by butterflies. Olivia gets some breaks in solving the case from her former partner and that she is so desperate to rid herself of him that she demands to go back into the tank. Meanwhile, some former friends and current foes of Peter find out that he's back in Boston.
The team is called in on a bank robbery similar to other robberies in the area but this particular bank has the thief embedded inside the steel wall of the bank. Somehow the thieves have found a way to defy the law of physics. Walter thinks they're after something of his. As the investigation deepens it all comes to a head when the thieves ambush one of the team.
Olivia's sister, Rachel (Ari Graynor), visits; Walter, Peter and Olivia try to solve the murder of an esteemed epidemiologist, which may be linked to Olivia's abduction.
Olivia, Walter and Peter are called in to investigate the death of a car salesman who was found in a pool of "goo," exactly like another man across the country. When Walter discovers that the "goo" is brain matter, the trio tries to figure out how the killer can liquefy human brains. As the deaths pile up, the investigation reveals a common thread linking the victims together in an unthinkable manner. Meanwhile, Olivia is horrified when the case places a loved one in harm's way
When the Fringe Division delves into another bizarre occurrence aboard an international jumbo jet, freakish remains are discovered at the crash site. Memories tip the team toward some promising leads, but the bigger picture and mysterious threat eludes them. With limited options and insufficient intelligence, Olivia and Peter go undercover.
German agents question Olivia about her “relationship” with David Robert Jones, an escaped prisoner questioned months earlier now living in the U.S. The Fringe Division investigates a threatening case where victims die faceless from their orifices suddenly sealing.
Just seconds before a building is demolished, a mysterious mute child that has been living alone underground is discovered. When the FBI’s Fringe Division investigates, the boy forms an unspoken connection with Agent Olivia Dunham. Meanwhile, an especially gruesome serial killer resurfaces and showcases his “artistry” by displaying his work publicly. As the boy gradually assimilates into a new environment, Olivia and the team must race against the clock to prevent the mad man from causing further massacre.
As animal rights activists ransack a laboratory, they get more than they bargained for when one of the caged “animals” unleashes a ferocious appetite. Leaving grotesquely mutilated dead bodies in its wake, the scientifically engineered beast with the body of a lion, claws of an eagle, fangs of a viper, skin of a rhinoceros and tail of a serpent attacks Charlie. With Charlie’s life on the line, Walter must come face-to-face with both his past and the beast.
Olivia dreams about a suicide as the event really happens at Grand Central Station; shocking information about the Z.F.T. manuscript is revealed.
The Fringe Division is on the case when severely mutilated bodies drained of spinal cord fluid begin to pile up. After their investigation leads them to a scientist (guest star Jefferson Mays) with possible ties to the Z.F.T. bioterrorist cell, they are shocked to discover the identity and motive of the killer. When the kills occur with increasing frequency, Olivia, Peter and Walter go to desperate lengths to stop them.
Olivia experiences "awake dreams," seeing elaborate visions of things not really there. While investigating a disturbing case of a woman who apparently spontaneously combusted, Olivia throws caution to the wind and explores her unexplained visions further. Meanwhile, Walter discusses key information about the Z.F.T. manifesto, and Peter reveals a secret that yields unexpected results in the case.
Setting the stage for the dramatic and revealing first season finale are a sudden and unexpected attack on someone with close ties to Fringe Division, the return of bioterrorist David Robert Jones and the inexplicable disappearance of Walter. Find out more about the mysterious events surrounding our trio when questions are answered, observations made, loyalties are tested and the elusive William Bell is finally introduced.