Olivia is in a car accident, an unusual person is looking for a member of the team, and Walter makes plans for celebrating Peter's birthday.

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.

The Fringe division investigates the explosion of a police officer. Olivia starts having visions about her experience on the other side.

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 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.

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.

A teenager comes back from the dead possessed by a soldier who's gone missing. Walter does an experiment so that the Fringe team can find the soldier's murderer.

When the sheriff of a small town nearby Edina City gives a ride to a boy that is fleeing home, he finds at the police station that the boy has changed to a deformed child. Out of the blue, a group of deformed man slaughter the sheriff and two marshals and bring the boy with them. The Fringe Division is assigned to investigate the case and they head to Edina, here they are received by the local sheriff. They overhear a humming and the sheriff explains that it comes from a military base. Soon Olivia and Peter are attacked by a local in a truck but Peter succeeds to kill him. They bring the corpse to Dr. Bishop that catches a rare butterfly to Astrid that collects the insect. But when he deliver the pot with the butterfly to her, she has turned into a moth. Astrid and Dr. Bishop drive to Edina City and when the moth becomes a butterfly again, Dr. Bishop discovers the secret of Alina City.

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.

A man uses a toxin to target specific groups of people. Walter finds out that the toxin was created by his father in Berlin, long before DNA was even discovered.

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 to "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 Fringe team investigate a train full of people who died in a mysterious way. Olivia and the others then meet the astrophysicist who was responsible for the "experiment" and who can reset the time.

The body of a male 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 has just smoked a drug that he calls "Brown Betty" when Olivia arrives at the laboratory to leave Ella with Astrid. The girl asks Walter to tell a story and he creates a detective story where the Fringe Division are the characters.

Peter stumbles across Newton and his people while running away from Walter and the FBI. He teams up with the local sheriff to try and find Newton.

Walter and Olivia travel to the parallel universe, and the anticipated face-off between Walter Bishop and William Bell occurs.

Sacrifices will be made and both universes may never be the same again after Walter and Olivia visit the "other side."