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.

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.

Olivia's sister, Rachel, visits; Walter, Peter and Olivia try to solve the murder of an esteemed epidemiologist, which may be linked to Olivia's abduction.

An amnesiac Olivia makes her return from the parallel universe, while Walter, Pete, and Junior Agent Amy Jessup investigate the mysterious death of a man found with puncture holes in his palate. Meanwhile, Broyles defends the Fringe Division from a Senate subcommittee threatening to shut the organization down.