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.

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.