When all the passengers and crew on Flight 627 Hamburg-to-Boston die in a hideous manner, FBI agent Olivia Dunham investigates the event. While following up a lead, her partner and lover, John Scott, undergoes life-threatening chemical contamination. A desperate Olivia looks for help and finds Dr. Walter Bishop, who cannot help her because he has been institutionalized. The only way to even question him is with the help of his son Peter.
Olivia continues her investigations and goes to Nina Sharp, a manipulative executive. Olivia, Peter and Dr. Bishop begin to discover what really happened on Flight 627 and start to uncover a larger truth.
Olivia, Peter and Walter Bishop investigate 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 80 years in the span of a few minutes. Olivia asks Nina Sharp of Massive Dynamic for help.
Roy McComb, a man who claims to receive visions from God, sees passengers on a bus caught in a gas attack that solidifies the air around them, asphyxiating them. Now the team must use Roy's visions to find the man responsible.
The team investigates a strange cylinder, found in a deadly explosion at a construction site in New York City. The cylinder was in the middle of the explosion and was completely unharmed. Olivia uncovers a correlation between different disturbing events.
The team investigate the case of a man who can generate electrical phenomena... and is at the center of a series of strange deaths involving electronic devices.
The team investigates a woman that re-appears after weeks of being missing, with a rare disease and she inexplicably causes pain and death to the people she meets. In the investigation dangerous level of radiation are detected. Meanwhile, Walter obsesses about cotton candy, Peter strikes a deal with Nina Sharp and a truth about Olivia is discovered.
A parasite mysteriously latches onto a dying FBI agent's internal organs. Agent Dunham rushes to Germany to meet a prisoner for information about the threat they face.
Walter's former bunkmate at the mental institute is linked to the abduction of a young musical prodigy by a serial kidnapper. Peter is concerned when Walter insists on going back to the mental institute to solve the case.
A Massive Dynamic employee leaps to his death after hallucinating a butterfly attack. Agent Scott proves useful in investigating the case, but a frustrated Olivia wants to remove him from her consciousness once and for all. Meanwhile, Peter deals with some enemies from his past.
The team is called in to investigate a bank robbery when one of the thieves is found embedded in a solid wall. Walter believes they're after something of his, but things take a turn for the worse when the thieves ambush one of them.
The FBI and an increasingly desperate Peter search for the abducted Olivia... unaware that the man heading the investigation is the one responsible for her disappearance.
Olivia, Walter and Peter are brought in to try and stop a hugger with the ability to liquefy the human brain.
Olivia and Peter go undercover to investigate after the discovery of bizarre remains at a jumbo jet's crash site.
The German authorities interrogate Olivia in an attempt to locate Mr. Jones. Meanwhile, the team investigates a bizarre series of incidents where the victims' facial orifices close over, leaving them faceless inactive persons.
Olivia makes a bond with a mysterious child that was living alone underground. Meanwhile, a serial hugger reemerges.
A man-made creature attacks Charlie and Walter's history catches up with him.
A suicide incident occurs at Grand Central Station, which Olivia dreams about. Meanwhile, shocking details emerge about the ZFT manuscript.
Someone is killing people and draining their spinal cord fluid. Olivia, Peter, and Walter go to great lengths to stop the deaths, which are happening more and more frequently.
Olivia has some bad dreams that end up coming true, and then begins seeing visions while awake that aren't really there. She uses these visions to help solve the case of a woman who spontaneously combusted.
Someone close to Fringe Division is attacked, and bioterrorist David Robert Jones returns. Meanwhile, Walter disappears inexplicably.