The season starts a week after the Fringe divisions in both the universes have started working together in order to solve the imminent collapse. When Lincoln Lee from the prime universe witnesses the murder of Robert by a man with a translucent skin, Olivia comes in to investigate the case. Lincoln then insists on following Olivia to division to further help with the investigation. However, on reaching there, it is discovered that there are multiple cases and bodies that have not been disclosed by the Fringe division. Eventually, two killers with translucent skin are tracked down, and killed in their hideout. However, a third suspect flees the scene. The killers are later identified as shape shifters, who originated from the human race. Peter appears and disappears again, which shocks Walter.

The Fringe division in the parallel universe requests the one in the prime universe to help them capture John McClellan. John kills his victims by freezing their brains in their happiest moments. Olivia of the parallel universe wants the prime universe Olivia to escort the John of the prime universe to track down the killer’s movements. However, upon realizing that he is in the parallel universe, John flees from the Fringe team. Eventually, he meets up with his parallel universe’s version and discovers that the presence of a woman called Marjorie in his life helped him to soothe his killer tendencies. Upon using his equipment to experience the joy of Majorie, the parallel universe John ends up committing suicide, which traumatizes the prime universe John and wipes away his memories of Marjorie. When two young bullies are found dead, their bodies decompose to an advanced stage in a few hours. Upon investigation by the Fringe team, it is found that an amorphous figure is behind the murders.