After the extraordinary turn of events that shockingly left an imprisoned Olivia "over there," she fights to find her way home. Meanwhile, Peter and Walter try to move on with their lives unknowingly alongside alternate Olivia.

Three men abduct and keep a family tied up and gagged in the living room. Two of them dig the basement while the third one watches the family. The men find a box and decide to take a peek inside. The two men and the family immediately die. The Fringe Division investigate the case and Walter performs an autopsy on the bodies. Soon he finds that they die because they have been exposed to an ultrasound signal. Walter receives an envelope from William Bell's lawyer as inheritance and he discloses to Astrid what William left for him. Meanwhile the alternate Olivia and Newton, who had hired the men to find the box and bring to him, plot a scheme to retrieve the box. Then they set in motion a Machiavellian plan.

In the alternate universe, Olivia and the Fringe Division investigate weird accidents with casualties apparently with no connection except ballpoint pens found on the spots. But when Olivia sees the freak Milo, she suspects that he might be the responsible. Olivia and Charlie investigates and soon they follow a lead to a hospital where they learn what happened to Milo.

When the American Senator James Van Horn has a serious car accident, he immediately goes to surgery; however Newton invades the hospital and abducts him shooting the staff. There is a shootout with Broyles and Newton shoots Van Horn in the eye. The Fringe Division finds that the senator is a shapeshifter and they take his body to Walter's laboratory. He finds that it is possible to revive the shapeshifter and recover his data disc. But the alternate Olivia calls Newton and he sends the shapeshifter Ray to the hospital to retrieve the disc. When he returns home, Newton orders him to kill his family. However Ray is connected to his wife and son and refuses to follow the order. What will happen?

In the parallel universe, a man releases his twin brother from an area in quarantine, removing him from the amber. The Fringe Division investigates the case that is classified since The Secretary does not want that the population learns that the family and friends are alive enclosed in amber. Olivia interviews Matthew, who is the twin brother of Joshua, and suspects that he is lying. Meanwhile The Secretary lures Olivia and convinces her to be submitted to n experiment while she has daydreams with Peter.

The latest broadcast on a numbers station transmits amnesia to its listeners. Walter clashes with Peter over Peter's work on the machine from alternate Earth.

In the parallel universe, a kidnapper called The Candy Man abducts the boy Max. The Fringe Division is assigned to investigate the case and soon Olivia learns that Broyles' son Christopher was also abducted two years ago and returned blind and with physical deficiencies to his family. She asks Broyles to interview Christopher to see any missing information but Broyles does not accept; however his wife agrees that Olivia meets Christopher. Olivia recalls an old case and guess whether The Candy Man would be draining the pituitary gland from the children to use the hormones to stay young. Based on the received information, Olivia and Broyles meet Reverend Marcus, who was a former physician and now is responsible for a church where they believe the abductor is a member. Meanwhile Olivia meets Henry and asks him to help her to go to the Liberty Island to use the deprivation tank to return to her universe.

Peter grapples with the aftermath of recent events as Olivia desperately searches for an ally. Meanwhile, the Fringe Team discovers a critical device that communicates between universes.

Fringe Division seeks a man who has been harvesting transplanted organs, leaving victims with nearly nullified decay rates. Olivia faces the aftermath of Fauxlivia running her life.

The Observer returns, taking an active role in righting an old wrong (which includes - mundane for him - thwarting a bank robbery).

The Fringe Division visits the Massive Dynamic to see the Doomsday Machine and the presence of Peter assembles the device. He is submitted to tests by Dr. James Falcon against Walter's will. Walter asks Nina to find William Bell's research since he wants to restore his brain to increase his IQ and help Peter. Meanwhile Broyles gives access to the main frame where the alternate Olivia's files are to help the investigation and they suspect there is a mole accessing the information. Soon they find that someone is killing the shapeshifters. Who might be the killer?

When a scientist is killed by a blue dust that grinds his bones up, the Fringe Division investigates the case and suspects a biological attack. The investigation leads them to a former marine that flees but is hit by a car. In coma, Walter recalls his Cortexiphan patient Simon Phillips that is capable to read mind. Olivia, Peter and Walter try to convince Simon, who leaves in a desert area, to help them to locate the terrorists, but he is sensitive to other people since he cannot control his ability. Simon agrees to help and also disclose Peter's real feelings for her.

In the parallel universe, the Fringe Division investigates a case where a man was eaten from inside out by an extinct beetle. Meanwhile Broyles is considered missing and Lincoln is the head of the division. Olivia welcomes her boyfriend Frank that has just returned from Texas and wants to propose her. When a second man is also eaten by the insects, the Fringe Division identifies the scientist Dr. Armand Silva that was researching the cure for avian flu using this insect. Lincoln and Olivia goes to his address and split. Lincoln is locked in a refrigerating chamber while Olivia is brought to his laboratory, where she drinks water. Dr. Silva explains that only human beings are capable to host the beetle and a new cycle has just began. Olivia concludes that she has been infected by the insect and despairs.

A series of Fringe events leads the team to the home of a woman grieving over the death of her husband, while Peter and Olivia make an effort to repair the emotional rift between them.

This follow-up to last season's "Peter" flashback episode revisits a poignant period of time for both the Bishops and Olivia.

The Fringe team attempts to find out what process enables people to become lighter than air and float. Peter and Olivia deal with trust issues in their relationship, while Walter becomes increasingly obsessed with retrieving William Bell's consciousness from beyond the grave.

As the Fringe team hopes to alleviate Olivia's possession quickly, Agent Lincoln Lee of the F.B.I. meets them for the first time over the curious case of what he calls "the compassionate soul vampire."

In the parallel universe, Olivia submits to a viral-propagated eclampsia (VPE) test since her sister died while giving birth to her baby. When she returns to her apartment, she is abducted and taken to a facility where she is subjected to a procedure that accelerates her pregnancy. Meanwhile the Fringe Division seeks her out while her mother Marilyn is informed that Olivia's VPE has been confirmed.

With the latest estimate that the team has only one day to save Olivia's consciousness, Walter leads a group on an LSD trip into Olivia's mind.

The beginning of the end is triggered when Walternate finds a way to wreak havoc "over here" - putting both universes in jeopardy.

Olivia joins forces with the mysterious Sam Weiss in a desperate race against time.

Peter successfully enters the machine with Olivia's help, and is transported to the future days where Walternate's universe is the one which has been destroyed. Walter learns about the origins of the machine and its ultimate purpose and sends back Peter to change his choice but gets lost in time warp.