Strange deaths by a mysterious shadow leads the Fringe Team to the scene where they learn that a Russian astronaut was possessed by an alien and his brother is convincing Dr. Bishop to solve the equation to free him.
Olivia and Peter look into some patients of mental institutions that regain their mental state after having gone through a brain intervention performed by a shape-shifter named Newton. This is directly related to Walter and his brain.
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.