Just one week after Peter Bishop saved the day and was then wiped from existence, the truce between the two worlds remains intact and the two sides are forced to work together. Lincoln Lee joins the Fringe team as they investigate a shapeshifter case that is very personal to him.

The "Over Here" team helps the "Over There" team look into a string of murders in which the victims are frozen from the inside out.

Two bullying boys die and exhibit an alarming state of rapid decay. Their would-be victim, an extremely lonely boy, has a remarkably unusual connection to the killer. Meanwhile, Walter fears for his sanity.

Olivia is haunted by an energy force that attracts metallic objects and Walter recalls his subject 9 that has the ability for astral projection. They chase the patient Cameron Jones but they conclude he is not the responsible for the energy force. However and Cameron faces the force, something happen.

Shapeshifter Nadine hunts down a former Massive Dynamics scientist to help rectify her cellular translucence. Meanwhile, Peter finds conversing with Walter difficult.

The Fringe Division begins to wonder if Peter or his presence is behind a series of time displacements between 2007 and 2011. Walter imposes a self-exile to his bedroom.

A manhunt begins for an invisible killer who steals human pigmentation.

Peter convinces Olivia and Lincoln to help him to go to the parallel universe to ask for help to Walternate to return to his timeline since Walter refuses to help him. They cross using the original device used by Walter and try to reach Walternate; however their plan fails and Lincoln is arrested by the Fringe Division. Peter succeeds to meet Elizabeth and her mother convinces Walternate to help Peter. However Walternate proves to Peter that he is not responsible for the shapeshifters. Further, he asks Peter to help him to convince the other universe that he is facing also problems with shapeshifters. Meanwhile the alternate Olivia and Lincoln decide to investigate Lincoln's information about a mysterious phone call.

The alternate Olivia and Lincoln arrest David Robert Jones and bring him to the Fringe Division headquarters. Peter uses his knowledge about the criminal to help to interrogate him. However David uses his accomplices to create havoc with a terrorist attack that kills everybody in a hospital. They let him go but with a tracking device, but David is warned by Broyles and uses a similar device in dollar bills to escape from his pursuers. Lincoln discloses to the alternate Olivia and Lincoln that it might have a mole within the Fringe Division. Peter and Astrid find that David is searching for a mineral. Capable to open holes between the two universes. Meanwhile Elizabeth decides to help Peter and has a surprising encounter.

A girl delivers a sketch to a man showing him impaled by a girder. A couple of minutes later, there is an accident at a construction site, and the man is indeed impaled by a girder. The Fringe Division investigates the case and Olivia and Lincoln identify the girl. Emily Mallum talks to them but her father Jim does not allow the conversation, afraid to turn her into a Massive Dynamic guinea pig. However, Emily contacts Olivia and meets her in a park. She explains that when her head hums, she can foresee death. Further she is haunted by a vision of a pile of dead bodies. Olivia brings Emily to Walter's laboratory to help the girl and identify where the tragedy will happen. Will they succeed?

Our Astrid gets an unexpected visit from her Alternate, while Peter and Olivia track a killer using a toxin that has yet to be invented. Both universes collide in a case that pushes the boundaries of what is possible.

Peter, Olivia and Walter come face to face with a mysterious and terrifying Fringe event as they get trapped in a town that there's no escaping.

As the Fringe team investigates a mentally ill patient who appears to be connected to a series of murders, frightening clues and connections are uncovered that lead Olivia to some shocking revelations.

Olivia and Nina Sharp are prisoner in an abandoned facility by David Robert Jones. He tortures Nina to force Olivia to use her abilities to activate the lights in a box. However Olivia tells that she is tired and he leaves Nina with her. Olivia confesses to her that only Peter would be emotionally connected to her to activate her ability. However Nina is from the parallel universe and is partner of David. Meanwhile Peter is contacted by September that is wounded on the chest and almost dying. Peter decides to enter in his mind to find the location of Olivia, and he learns who The Observers are. He also tells to Peter to go home and they are coming. When Peter understand the meaning of the message, he is abducted by David's men.

The team hunts a killer who seems to be targeting couples - dehydrating the husbands and smothering the wives - with a very unusual motive. Peter and Olivia try to come to terms with her surfacing memories and emotions from the original time-line and the fact that she's beginning to forget parts of her life from the new time-line. Meanwhile, Walter and Peter try to figure out September's disappearance from the lab the week before.

An incident occurs that bears remarkable similarities to an early case in the original time-line, though there are some notable differences. Olivia's memories of the new time-line continue to fade, and Broyles places her on temporary leave, but her memories of original case assist Peter and Lincoln. Lincoln gets infected with a virus and Walter must figure out a cure.

Lincoln travels to the other side to join forces with Faulivia and his own alternate, as they search for a vigilante with a surprising connection to the shapeshifters.

When both of the two identities of people from the separate worlds experience the same catastrophes from incidents in just one world, the two Fringe teams collaborate. Walter crosses over to find that Jones is behind the phenomena, but to what ends? Also, the investigation into the Fringe-mole continues.

In the future, the Observers rule and humans that survived the purge serve them. There are still a small number of people fighting for the resistance, and one of them has discovered one of the original Fringe team in the form of Walter protected in amber. As the resistance attempts to get rid of the Observers, we get a glimpse into a rather dark dystopian future.

Multiple earthquakes are happening simultaneously around both our world and the alt-world. Walter believes he knows what the end game of David Robert Jones is. And, even though Olivia has a connection to one of the players Jones is using that she thinks she can utilize, in the end it leads to some hard decisions for the Fringe team.

A mysterious Fringe event, causing people to spontaneously combust, forces Walter to revisit his painful past while the Fringe team faces off against David Robert Jones to save the world - or worlds.

In the Season Four finale, the Fringe team is pushed to their breaking point as they desperately attempt to prevent a catastrophic event threatening the lives of everyone.