Walter analyzes the body of a shapeshifter and then reconnects with an old patient that has the ability to distinguish the people from the other world. Olivia finally recalls her encounter with Belly.

Peter and Olivia look into the latest appearance of an observer, other than September, who kidnaps a young woman. August prevents her from getting on a plane that would crash.

An earthquake from the other side is being felt on our Universe as well. Furthermore, the only survivor seems to be from the alternate Universe. Walter attempts to get Olivia to "recover" her ability to make out things from the other side.

The body of a male teenager is found along with shapeshifter marks. Walter examines the embryo of a shapeshifter, that came from the alternate Universe. The team try to anticipate the shapeshifters' next moves.

Walter has just smoked a drug that he calls "Brown Betty" when Olivia arrives at the laboratory to leave Ella with Astrid. The girl asks Walter to tell a story and he creates a detective story where the Fringe Division are the characters.

Walter and Olivia travel to the parallel universe, and the anticipated face-off between Walter Bishop and William Bell occurs.

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.

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.

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.

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.

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?

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.

The intensity of life "over there" accelerates as Olivia finds herself in mortal danger.

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.

In an effort to find a way home, Peter journeys to the Other Side to confront Walternate. His venture proves more dangerous than expected. Meanwhile, Olivia receives a dire premonition from an Observer.