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.
As the victims of a highly intelligent serial killer "Over There" stack up, the Fringe Division "Over Here" is asked to assist. As the two sides tangle and innocent people remain at risk, the suspect's doppelganger "Over Here," a professor who teaches Forensic Psychology, is brought into the fold and forces the team to consider the notion of sending civilians to the other side.
When two 12-year-old kids bully another boy, they are found dead and in just hours after dying their bodies are shockingly in an advanced state of decomposition. As the Fringe team investigates the mysterious case, they uncover an amorphous figure claiming more victims. Meanwhile, Walter becomes increasingly distracted by his hallucinations.
Olivia uncovers a dangerous force that may be connected to Walter's past experiments with the drug Cortexiphan. Their investigation forces Walter to leave the lab for the first time in years as he and Olivia head to Massive Dynamic in New York to examine old case files. Walter struggles with life outside the lab as he comes face-to-face with the demons of his past.
In the aftermath of recent shocking events, things really escalate when the translucent shapeshifters return. As the threat and circumstances intensify, former Massive Dynamic scientist Malcolm Truss enters the fold. Meanwhile, Nina Sharp pays Walter a visit in the lab.
The Fringe team must find the pattern between tragic time loop anomalies. As the investigation unfolds, Raymond, an electrical engineer, and his wife Kate, a professor of theoretical physics, enter the picture.
Murders occur in which the victims are initially thought to be albinos, but when the body count reaches four, it seems evident something else is happening and gets the attention of Fringe Division. Blood at one such scene is traced to a strange, pale baby hypersensitive to light who supposedly died 4 days after his birth in 1989. But U-gene (for Unknown) Bryant almost certainly survived and came to the attention of the body that later became Massive Dynamic, where he became the subject of intensive experiments. Walter demonstrates that UV light can reveal an otherwise...
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.
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.
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.
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, feeling out of place on the team now that Peter is back and Olivia is beginning to forget him, volunteers to take liaison duty for the day, and joins the alternate Fringe team in the search for a vigilante killer with some unusual abilities. He bonds with Fauxlivia and Alt-Astrid, and he and Alt-Lincoln compare life stories to figure out the way in which their two lives diverged, only to find that they're not so different as they initially seem to be. Alt-Lincoln still suspects that there may be a mole in his team working for David Robert Jones.
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.
In the first of a two part season finale, 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.