Season Two opens with Olivia's shocking return to this perplexing alternate reality, while Peter, unknowingly in a race against time with an ominous mobile force, pursues information about Olivia’s visit. Walter reenters the lab to cook up a bit of fringe science, and of course, some custard for Peter’s birthday.
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, Olivia, and Walter race against time to investigate the bombing of a train station. Walter discovers something unusual about the human remains.
Agent Dunham, still recovering from her traumatic visit to the alternate reality, is given a concoction by Walter to help her remember. Another woman being experimented on by Walter is introduced. Meanwhile the Fringe team look into a series of robberies that are linked to shapeshifting.
A man attacks his boss after a disturbing dream and the team travels to Seattle to investigate. Meanwhile, Broyles needs to meet with Nina Sharp.
The Fringe Division takes on a puzzling investigation of victims who inexplicably disintegrate into ash. The shadowy case casts light on Special Agent Phillip Broyles past and leads the team to the possibility of foreign fringe science.
When a kidnapping rapidly escalates into a hostage situation in New York, local authorities close in on the suspects only to discover that an unknowable force has mind-blowing consequences. The investigation intensifies and the mystery and threat deepen to unimaginable proportions when the Fringe Division identifies a link between the kidnapping and Massive Dynamic.
A peculiar abduction occurs in Boston, leading the Fringe team to uncover details of the mysterious man known as The Observer. While the bizarre case takes center stage, Walter, Peter, and Astrid hit the lab to analyze unusual evidence and deal with Walter's insatiable appetite for milkshakes.
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.
A Fringe investigation is triggered when a patient at a mental institution undergoes an impromptu brain surgery that unexpectedly leaves his brain exposed. Despite the unthinkable circumstances, the patient's condition and sanity miraculously improves before the Fringe team arrives. While Agent Dunham and Peter scan surveillance tapes (and Walter enjoys his pudding), Olivia recognizes a familiar face as Thomas Jerome Newton, the leader of the shape-shifters. As similar cases stack up, the Fringe team heads back to the lab to determine exactly how patients are being cured. Walter's brains are put to the test and William Bell resurfaces.
After a teenage girl is pronounced brain dead, her mother takes her off life support, but when doctors operate quickly to remove her organs, the deceased girl shockingly awakens screaming an alphanumeric code. Equally as perplexing as her resurrection is that she is now somehow able to speak Russian and possesses classified information only a high-ranking soldier would know. While the girl's mind-bending condition intensifies, Walter dusts off some old lab videos and hypothesizes the unthinkable, sending Olivia and Peter to investigate the bewildering case.
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.
After a unhappy tremor shakes a Manhattan office building to its core, leaving only one survivor who leads the Fringe Team to believe he is not from this reality. Walter surmises that what shook the building was not geologic, but rather something discovered by him and William Bell many years ago. With another catastrophe imminent, the team races to Jacksonville, the site of Walter and William's experiments, forcing Olivia to face her mysterious past in an effort to save hundreds of people from certain death.
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 hugging 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".