Unable to police a world in which science has advanced beyond our wildest dreams - and nightmares - FBI Special Agent Olivia Dunham seeks help from brilliant but damaged scientist Dr. Walter Bishop and his estranged son with a dark past, Peter. Under the direction of Agent Phillip Broyles, they solve gruesome mysteries and prevent imminent attacks. Season Two of FRINGE continues to explore 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.
Walter wants to make Peter custard for his birthday because it was his favorite as a boy, but Peter explains that he has never liked custards. Walter says he merely cannot remember. They get a call about an accident in Manhattan.
After three weeks, Olivia is finally ready to check out of the hospital. Upon her leaving, "evil Charlie" watches her go (remember that Charlie was killed by a shape shifter that is now pretending to be Charlie) whose assignment is to get Olivia to confide in him about what happened with William Bell. Walter has been investigating her disappearance and still can't explain what happened to her during the time she went missing from her car accident and when she flew through the window. One thing is for sure: she came back with heightened senses that help her to solve the latest fringe case. Olivia jumps right back in -- ready or not.
Police Officer Gillespie receives a phone call telling him "It's time." He is instructed to go to a metro station and take a black briefcase from a man wearing a black trench coat. Gillespie arrives at the station and locates the man. Gillespie grabs the suitcase and his body begins to crystallize before suddenly exploding!
Security guards at Elias Cryonics-Research and Storage Company load cryogenically frozen heads onto a secure truck. A man, Smith, pulls up in a car and asks for directions. The guards order him to leave, but Smith just exits his car and begins to shoot. One guard turns out to be his accomplice and throws Smith a set of keys to the truck. Smith drives off as his accomplice is shot multiple times before being killed-what's this guy made of?! He bleeds silver.
Olivia returns to the bowling alley, with bowling shoes in hand -- her memory has been restored, and says she no longer needs Sam's help. Sam instantly asks, "Who died?" After chatting, Sam tasks Olivia with collecting business cards from every person she meets wearing red.
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.
When a peculiar abduction occurs in Boston, the Fringe team uncovers details of the mysterious man known as The Observer. Is there more than one of him? 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 a milkshake.
A soaking wet Chinese man, Wu Zhe Lan, runs frantically through the streets of Boston searching for Ping-On Street. He finally locates the house he is looking for and urgently presses the intercom button. Another Chinese man, Ming Che, lets him in and tells him that he is the first to arrive. Wu Zhe Lan cries out that everyone else is dead. Ming Che tries to console him when he suddenly begins to cry out in pain. A tentacle begins to emerge from one of his nostrils!! Ming Che is unaffected and suddenly a multitude of thrashing tentacles begins to emerge from Wu Zhe Lan's mouth.
The Fringe team investigates a mental institution after a patient has brain surgery and begins to show an improvement despite having his brain exposed. Agent Dunham makes a discovery of her own after seeing footage from the surveillance tapes.
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 “Unearthed” episode of FRINGE – and here’s another mystery: is it an unaired episode from Season One or is it from an alternate universe?
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.
While investigating a case in an office building where a man's blood literally burst from his arteries and veins, Peter and Olivia are trapped in a CDC quarantine when it's discovered that the blood carries a deadly pathogen.
Unseen killers target a wedding with a toxin that targets specific individuals, and Walter discovers that the case may be tied to a branch on the Bishop family tree.
When the sole survivor of a building demolished by an earthquake in downtown Manhattan proves to be from the other Earth, Walter leads the team to Jacksonville, the source of a related experiment that he and William conducted years ago. Now only Olivia and the secrets of her past can prevent another catastrophe.
After Olivia discovers that Peter is not from this universe, Walter visits her to explain what happened.
After meeting with an ill childhood schoolmate, a woman named Miranda Green develops malignant tumors all over her body and dies. The Fringe team is called in to investigate, and Walter discovers a handprint on Miranda's arm. He hypothesizes that she somehow caught cancer by skin-to-skin contact.
Back at the lab, Walter attempts to retrieve a fingerprint from Miranda's arm. Olivia and Peter visit Miranda's workplace, and discover that the name of the man that she met with on the day she died is Neil Wilson.
After several nights of tossing and turning, Olivia confronts Walter and tells him that she wants to tell Peter the truth about his past. Walter begs her not to say anything, but Olivia is resolute in her decision.
Neil Wilson, now looking a little less sickly, goes to a grocery store to stock up on healthy foods.Â While paying for his items, he becomes violently ill and runs out the door. Neil goes home and begins searching for another childhood schoolmate named Lloyd Becker.
When Becker turns up dead, Walter suggests that Neil may be infecting others with cancer in an effort to slow the progression of his own illness. Astrid finds three more similar cases, and Olivia discovers a commonality among them: all of the victims were Cortexiphan children.
Olivia goes to Massive Dynamic to see if Nina Sharp has a complete list of the Cortexiphan children's names, but she comes up empty handed. She tells Nina of her intention to tell Peter the truth, and Nina calls her bluff.
Meanwhile, Neil Wilson visits Nick Lane's aunt, and she unwittingly mentions that Nick (from the episode "Bad Dreams") was recently in contact with another Jacksonville schoolmate... Olivia.
At her home, Olivia figures out that Neil Wilson's real name is James Heath and that he was a Cortexiphan child as well!Â She calls Broyles and explains that Heath's sister became the first victim to die after visiting Heath in the hospital when they were younger.
Olivia rushes out the door to investigate further, but she is confronted by Heath.Â A fight ensues and Olivia ultimately prevails. Heath breaks down and confesses that the whole ordeal began as an accident when a mysterious man came to his hospital bed and attempted to activate his abilities.
Heath is whisked away to a top secret facility and placed under a drug-induced coma. Broyles and Nina Sharp meet at the facility to decide that they must track down all of the other Cortexiphan subjects before they fall into the wrong hands.
Olivia goes to Walter's house and tells him she has decided not to say anything to Peter about his past. Walter thanks her, but explains that he wants to atone for his previous mistakes and that he will begin doing so by telling Peter the truth.
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 (Joshua Jackson) remains suspicious that something is amiss with Walter (John Noble), who is struggling to keep the unimaginable a secret. When the investigation leads them to Alistair Peck (guest star Weller), 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 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 (Sebastian Roché). Upon discovering a shape-shifting embryo, Walter (John Noble) returns to the lab to conduct further analysis, and Olivia (Anna Torv) and Peter (Joshua Jackson) 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 (John Noble) deals with some upsetting news, he tells Olivia’s niece, Ella (guest star Lily Pilblad), a fairy tale that includes musical performances by Olivia (Anna Torv) and Agent Broyles (Lance Reddick).
Peter (Joshua Jackson) teams up with a local law enforcement official, Sheriff Mathis (guest star Plimpton), on a serial murder investigation with ties to Newton (guest star Roché). Meanwhile, Walter (John Noble) 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 Season Two finale, Walter (John Noble) and Olivia (Anna Torv) travel to the parallel universe, and the anticipated face-off between Walter Bishop and William Bell (Leonard Nimoy) occurs.
Sacrifices will be made and both universes may never be the same again after Walter and Olivia visit the “other side” in Part 2 of the climactic season finale.