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

Two young bullies are found dead and in just a few hours they rot to an advanced state of decomposition. The Fringe team investigates and uncovers an amorphous figure claiming more victims. Walter becomes increasingly distracted with his mental state.

Olivia uncovers a dangerous force that may be connected to past experiments with Cortexiphan. The investigation forces Walter to leave the lab for the first time in years and travel to Massive Dynamic to examine old case files. Walter struggles with his emotional state as he confronts the demons of his past.

Olivia and the others of Fringe division attempt to determine the origin of Peter Bishop, who purports himself as Walter's son who had died as a young boy in the original time line. The Fringe division is brought to investigate the violent murders of a woman and her live-in boyfriend in her home. They find that she was earlier married to Dr. Malcolm Truss a former Massive Dynamic biochemical researcher, and believe her murder was an attempt to access his aborted research on cell cloning by one of the new shape shifters, Nadine, previously seen in "Neither Here Nor There". While at Massive Dynamic, it is revealed that Nina Sharp raised Olivia and her sister after Olivia killed her stepfather and ran away from Walter's Cortexiphan trials. Walter resents Nina for both this and for her interference that led to young Peter's death. Fringe is unable to locate Truss before Nadine does, and place a manhunt to track him down. Meanwhile, Nadine has tried to convince Truss that she is a patient in need of his cloning research, and coerces him to take her to his unmarked laboratory to synthesis the cure. It's revealed she has a daughter, Haley. As Fringe division attempts to work out Truss' location, Peter, from his cell, uses the intercom electronics to try to convince Olivia and the others that he knows about shape shifter technology. Under guard, Peter is able to use one of the memory discs previously recovered by Fringe to identify a tracking signal allowing Fringe to set off to Truss' laboratory. Truss has come to discover Nadine's truth after she temporarily loses control and takes the form of his former wife, but under threat of death, continues to synthesize the cure. Truss finishes the cure just as the FBI and Fringe division surround the warehouse containing the lab. After being given the cure, Nadine attempts to fight off the agents, but appears to have dived into the water below. On recovering a body from the water, they realize that Nadine had taken the place of a fallen agent and has escaped their grasp. Nadine uses a Hermes 3000 typewriter stored in a locker at a Boston train station to type a report informing them of the success of Truss' cure; moments later, the typewriter, on its own, types out further instructions for her. Walter, after trying to resolve his issues with Peter, returns to Fringe to inform Peter that he had two chances to save his son and let him down both times, he will not try to help again for fear of doing more harm. Meanwhile, Olivia experiences an unexplained time fluctuation.

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.

When a man mysteriously dies by an invisible force, his body rapidly begins turning ghostly white. The Fringe team learns that this is not an isolated incident, and there’s evidence that links the predator to someone who passed away with an unknown genetic disorder. Meanwhile, Olivia suffers from migraines.

Olivia and Lincoln take drastic measures to deal with the looming threat from the translucent shapeshifters, while helping Peter find his way home. Something “over there” occurs that hasn’t happened since the universes were linked at the end of last season.

Peter's visit to the other side intensifies as the alternate FRINGE division faces off against a formidable new foe in a harrowing race against time.

Olivia continues to cope with the ominous warning from the Observers, while Peter and the team track a girl with the mysterious ability to predict death

Over Here 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 from.

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.

Peter and the Fringe team take extraordinary measures in an attempt to stop life-threatening events.

Following the recent shocking revelations and emotional events, Peter weighs his options as the Fringe team investigates a killer targeting love.

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

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

Walter travels to the Alternate Universe to assist in the investigation of a Fringe event with ties to both worlds. Meanwhile, David Robert Jones reveals his next target.

The Fringe team goes back to the future as the story jumps ahead to 2036, when the Observers and the Fringe team engage in a game-changing battle.

The teams on both sides fight on for a common cause, and there are shocking developments tied to the Cortexiphan children.

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.

The Fringe team is pushed to the breaking point as they desperately attempt to prevent a catastrophic event that threatens the lives of everyone.