Olivia has been abducted, and Broyles and the Fringe division must investigate her disappearance - while also undergoing an audit by an agent from Olivia's past who bears a major grudge against her.
A man undergoes a painful and ultimately fatal transformation aboard a plane. Meanwhile, Nina Sharp and Broyles reveal more information about John Scott to Olivia.
The team investigates a number of people who died faceless after their orifices are sealed while German agents investigating David Robert Jones' escape question Olivia.
Walter examines a number of dead bodies that had the spinal fluid removed. Olivia and Charlie go after the scientist who created the person behind the murders.
The Fringe team investigate a case of spontaneous human combustion. Olivia starts experiencing visions of the alternate Universe. She uses this ability to solve the case.
Olivia and Peter investigate a series of strange disappearances. Olivia hears and sees things from the alternate Universe but fails to realize Charlie isn't really Charlie.
Walter analyzes the body of a shapeshifter and then reconnects with an old patient that has the ability to distinguish the people from the other world. Olivia finally recalls her encounter with Belly.
People who once had sleeping problems but were cured by having a biochip inserted in their brain suddenly start to die. Walter suspects the chips were accessed by someone who used mind control.
Strange deaths caused by a mysterious shadow lead the Fringe Team to the scene, where they learn that a Russian cosmonaut was possessed by an alien and his brother is convincing Dr. Bishop to solve the equation to free him.
The Fringe team investigate a child that is supposed to have mind control abilities. Peter is kidnapped and controlled by him. Walter is extremely worried and afraid he might lose Peter again.
Peter and Olivia look into the latest appearance of an observer, other than September, who kidnaps a young woman. August prevents her from getting on a plane that would crash.
Walter examines some bodies that have been infected with unusual worms. Olivia and Peter run an investigation after speaking with a survivor. Meanwhile Walter demands more independence from Peter.
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.