Olivia's sister, Rachel, visits; Walter, Peter and Olivia try to solve the murder of an esteemed epidemiologist, which may be linked to Olivia's abduction.

Olivia, Walter and Peter are called in to investigate the death of a car salesman who was found in a pool of "goo," exactly like another man across the country. When Walter discovers that the "goo" is brain matter, the trio tries to figure out how the killer can liquefy human brains. As the deaths pile up, the investigation reveals a common thread linking the victims together in an unthinkable manner. Meanwhile, Olivia is horrified when the case places a loved one in harm's way

When the Fringe Division delves into another bizarre occurrence aboard an international jumbo jet, freakish remains are discovered at the crash site. Memories tip the team toward some promising leads, but the bigger picture and mysterious threat eludes them. With limited options and insufficient intelligence, Olivia and Peter go undercover.

Just seconds before a building is demolished, a mysterious mute child that has been living alone underground is discovered. When the FBI's Fringe Division investigates, the boy forms an unspoken connection with Agent Olivia Dunham. Meanwhile, an especially gruesome serial killer resurfaces and showcases his "artistry" by displaying his work publicly. As the boy gradually assimilates into a new environment, Olivia and the team must race against the clock to prevent the mad man from causing further massacre.

As animal rights activists ransack a laboratory, they get more than they bargained for when one of the caged "animals" unleashes a ferocious appetite. Leaving grotesquely mutilated dead bodies in its wake, the scientifically engineered beast with the body of a lion, claws of an eagle, fangs of a viper, skin of a rhinoceros and tail of a serpent attacks Charlie. With Charlie’s life on the line, Walter must come face-to-face with both his past and the beast.

Olivia dreams about a suicide as the event really happens at Grand Central Station; shocking information about the Z.F.T. manuscript is revealed.

The Fringe Division is on the case when severely mutilated bodies drained of spinal cord fluid begin to pile up. After their investigation leads them to a scientist with possible ties to the Z.F.T. bioterrorist cell, they are shocked to discover the identity and motive of the killer. When the kills occur with increasing frequency, Olivia, Peter and Walter go to desperate lengths to stop them.

The Observer chooses to do something other than observe, abducting a college student. However, when the Fringe team investigates, they discover that there is more than one Observer.. in both time and space.

When Peter disappears, Walter seeks solace in marijuana. In that state of mind, he and Astrid babysit Olivia's niece Ella, and Walter tells her a fairy tale of a gentle inventor, a stolen glass heart, a detective looking for true love, and a mysterious group of bald men known as the Watchers.

When Walter discovers that Peter has traveled to the alternate universe, he and Olivia gather three cortexiphan children with the ability to transition safely between the two Earths.

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”.