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.
After a man spreads a pathogen on the grounds of a company, the Fringe team start an investigation. While stuck inside the quarantine zone, Peter and Olivia try to identify the origin of the pathogen. Outside, Walter tries to find a cure.
An earthquake from the other side is being felt on our Universe as well. Furthermore, the only survivor seems to be from the alternate Universe. Walter attempts to get Olivia "recover" her ability to make out things from the other side.
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.
The Fringe team investigate a series of mysterious deaths caused by cancer that seems to have been transmitted by touch. Olivia realizes the perpetrator is after the kids who were part of the Coretexiphan trials.
The body of a female teenager is found along with shapeshifter marks. Walter examines the embryo of a shapeshifter, that came from the alternate Universe. The team try to anticipate the shapeshifters' next moves.
Walter tells Ella and Astrid a story. It's a detective story in which Olivia, who's a detective, is hired to investigate the disappearance of Peter Bishop. Helped by Astrid aka Esther, Olivia fights both Nina Sharp and September aka Gemini to get to the truth. Olivia teams up with Peter to reach a happy ending.
After the extraordinary turn of events that shockingly left an imprisoned Olivia "over there," she fights to find her way home. Meanwhile, Peter and Walter try to move on with their lives unknowingly alongside alternate Olivia.
The story alternates to the Fringe Team "over here" where they investigate a mystifying case that people are discovered in a trance-like state that ultimately leads to their death. The unlikely suspect: a mysterious box. As Peter and Walter collaborate to study its properties, alternate Olivia presses on and turns up the heat on an unsuspecting Peter. Meanwhile, key information about the future is revealed when Walter and Nina meet at Massive Dynamic for the emotional reading of the last will and testament of William Bell.
In this case, timing is everything as a series of anomalous events lead the Fringe Division to investigate deadly incidents with unimaginable coincidences. As the freaky crimes continue to occur, the team is in a race against time to protect potential victims. Meanwhile, Secretary Bishop shares his strategic plan with Colonel Broyles as Olivia grapples with a heart-stopping vision.
Newton, concerned about the consequences of a distressing development involving a high-ranking official, is forced to call to action a sleeping shapeshifter. As Walter and the rest of the team gather evidence, they move the investigation to Massive Dynamic, where Olivia goes on high alert and Walter finds himself in a perilous situation.
The alternate universe Fringe Division investigates a shocking breach of security when a twin frees his brother from a quarantined Amber area. As the team sets out to crack this sophisticated case, Walternate experiments over there more with Olivia as she reenters the tank. Meanwhile, visions of Peter continue to haunt Olivia about returning to the "other side."
When a serial kidnapper "over there" strikes again, the emotional and familiar case hits home for Colonel Broyles, sending a determined Olivia to uncover additional details about the abductions. In the meantime, Olivia fights on and reunites with Henry to enlist his services on an intense and covert mission to return home.