An amnesiac Olivia makes her return from the parallel universe, while Walter, Pete, and Junior Agent Amy Jessup investigate the mysterious death of a man found with puncture holes in his palate. Meanwhile, Broyles defends the Fringe Division from a Senate subcommittee threatening to shut the organization down.

A highway construction worker in rural Pennsylvania goes missing when he is mysteriously drawn into an underground tunnel filled with human remains. Meanwhile, back in the lab, Walter is attempting to simulate travel between realities on frogs. When it, 's discovered that the disappearance in Pennsylvania is not an isolated incident, the Fringe team travels to the crime scene to unearth evidence.

Peter, Walter, Olivia, and Broyles pursue a strange and deadly occurrence in Philadelphia where a bomb blew up inside a train station but left no trace of any explosive device. The perplexing and unexplained set of circumstances returns Walter to the lab to closely examine the human remains where he uncovers an unlikely energy source that triggered the explosion. With the explosive threat of more bombs and links to a classified military project, the intense investigation leads Olivia and Peter to Iraq

Recuperating from the traumatic and alarming meeting with Massive Dynamic founder William Bell, Agent Dunham consumes a powerful fringe concoction that Dr. Bishop prescribes to stimulate her memory. Meanwhile, the Fringe Division investigates a series of robbery cases that are tied to shape-shifting. As clues are tracked and memories are jogged, another woman experimented on by Dr. Bishop is introduced and a flashback reveals more about Olivia’s visit to the alternate reality.

The Fringe division tries to decode dreams after going to Seattle to investigate a man’s frightening visions that caused him to attack his boss; Broyles has a meeting with Nina Sharp.

The Fringe team investigates instances of victims being transformed to ash by high-energy discharges, and discover a connection to Broyles’ past...

The Fringe Division investigates an unusual kidnapping with connections to Massive Dynamic...

The Fringe team closes in on the mysterious Observer after they investigate a bizarre abduction case in Boston, MA....

After a cargo ship runs aground, the shoreline becomes littered with bodies hosting a giant squid-like creature. The Fringe team descends upon the scene to examine the bodies and discovers that the mysterious organisms are actually giant parasites. As the investigation unfolds, Walter heads back to the lab while Olivia, Peter and Broyles race against time when they realize the case has ties to a threatening organization.

During the investigation of strange circumstances surrounding brain surgeries at a mental hospital, Olivia finds a reason to believe the leader of the shape-shifters may have something to do with it. Leonard Nimoy guest stars as William Bell

A teenage girl pronounced brain dead wakes up in the middle of the operation to remove her organs... speaking numbers in Russian. When the Navy confirms that the numbers are nuclear launch codes and a missing officer named Rusk knows them, the search is on for the missing man. '

Following an unexplained attack involving disfigured humans, the Fringe team visits Edina City, a small town in upstate New York to uncover leads surrounding the bizarre case. When it's determined that these disfigured people have managed to hide themselves for a while and they'll do just about anything to keep it that way, the investigation takes an unexpected turn.

When a man enters an office in Boston for a meeting, he becomes disoriented and collapses, only to have his veins erupt and spray blood everywhere. Shortly after Olivia and Peter arrive at the scene to investigate the bizarre case, it's discovered that a lethal virus with deep ties to something very valuable is spreading, so the CDC moves in to quarantine the building and eradicate the pathogens. Isolated inside with the rest of the exposed office employees, Peter and Olivia face life-threatening circumstances, sending Walter, Broyles and Astrid on a frantic search for a solution to save them.

When a specific group of guests at a wedding in Brookline, MA, suffocate from the inside out, the upsetting and disconcerting crime scene has the Fringe team investigating how the toxin was delivered and targeted. As evidence is taken into the lab, it's discovered that the wedding ceremony was a testing ground for a weaponized science experiment. Adding to the intense lab investigation, Walter uncovers an alarming formula that reveals a link to a branch on the Bishop family tree. With the escalating threat of more deadly attacks and unexpected familial ties to the case, the Fringe team stops at nothing to prevent further catastrophic events.

The arrival of a building from the alternate Earth causes massive death and destruction to those occupying the site at its arrival. Walter soon realizes that to equalize the balance between universes, another building will have to disappear... along with everyone inside it. The team's only chance is for Walter to activate Olivia's long-buried ability to distinguish objects from the other universe.'

Walter flashes back to 1985 while explaining Peter's otherworldly origins to Olivia. Also, Peter's mother is introduced and details of the neighboring world reaffirm that there is more than one of everything.

When a perfectly healthy woman is found dead from a disease she never had, the Fringe team investigates the origin of this inexplicably fatal condition before it claims more innocent victims. Meanwhile, Olivia struggles to keep Walter's secret from Peter, and her loyalty to Peter is tested as time goes on.

When passengers aboard a commuter train appear to have died a still death, it seems that a switch was flipped because all cell phones, mp3 players, laptops, batteries and bodies have been drained of power. As the Fringe team assembles at the bizarre crime scene, Peter remains suspicious that something is amiss with Walter, who is struggling to keep the unimaginable a secret. When the investigation leads them to Alistair Peck), a very powerful man who has tremendous energy with severe consequences, an ironic set of circumstances surface.

When two teenagers on a date turn up "dead" at an abandoned warehouse with the three puncture wounds to the soft palate - a trademark of the shape-shifters - the Fringe team investigates the evidence as well as the motives of mastermind Newton. Upon discovering a shape-shifting embryo, Walter returns to the lab to conduct further analysis, and Olivia and Peter head to Massive Dynamic for answers. Meanwhile, Peter reveals a family secret to Olivia as Walter struggles to recall what Newton knows about "building a door".

While Walter deals with some very upsetting news, he tells Olivia's niece, Ella a fairy tale that includes musical performances by Olivia and Agent Broyles.

Peter teams up with a local law enforcement official, Sheriff Mathis, on a serial murder investigation with ties to Newton. Meanwhile, Walter copes with the possibility of being sent back to St. Claire's, and someone from the "other side" pays a visit.

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

Sacrifices will be made and both universes may never be the same again after Walter and Olivia visit the "other side."