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.

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.

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.

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.

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.

A teenage girl pronounced brain dead wakes up in the middle of the operation to remove her organs... speaking numbers in Russian. When the Navy confirms that the numbers are nuclear launch codes and a missing officer named Rusk knows them, the search is on for the missing man.

In a follow up to last season’s “Peter” flashback episode, the all-new “Six Months Later” episode revisits a poignant period of time for both the Bishops and Olivia.

The Fringe team faces a case that appears familiar to Peter. Strangely, it takes place in this timeline.