Season two follows the continuation of a war between two universes, the prime and the parallel, exploring the ever-blurring line between science fiction and reality, where hybrid monsters tear through sewers, thieves walk through walls, and portals open to worlds unknown.
Season two opens with Olivia's shocking return from the perplexing alternate reality, while Peter is unknowingly in a race against time with an ominous mobile force pursuing information about Olivia's visit.
Walter reenters the lab to cook up some fringe science and of course, some custard for Peter's Birthday.
A series of strange disappearances in Pennsylvania attracts the attention of the Fringe team and leads them underground.
Walter also tries to recreate Olivia's accident using frogs and Charlie tries to find out how much she remembers.
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 team travels cross-country to Seattle after learning of a mysterious incident involving a man who attacked his boss because he believed he was an evil ram-horned creature. As these puzzling occurrences continue, the team tirelessly explores strange and creepy links to dreams. In pursuit of additional information, Agent Broyles has a disconcerting meeting with enigmatic Massive Dynamic executive Nina Sharp that leads the investigation in an unthinkable direction.
Human beings are reduced to ash statues and Broyles realizes that the same person responsible murdered five other persons four years ago... a case that he never solved.
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 patient at a mental hospital undergoes impromptu surgery that leaves his brain exposed. William Bell resurfaces during the investigation of the strange circumstances and Olivia finds reason that the leader of the shape-shifters may have something to do with it.
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 in an original.
(This is a season 1 un-aired episode)
Following an unexplained attack involving hideously deformed humans, the Fringe team visits the small town in upstate New York to uncover leads surrounding the bizarre case. When it's determined that these deformed people have managed to hide themselves for a while and they'll do just about anything to keep it that way.
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 violent 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 reaffirms 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.
In part one of the two-part, two-night second season finale, Walter and Olivia travel to the parallel universe, and the anticipated face-off between Walter Bishop and William Bell occurs.