FBI agent Lincoln Lee insists on helping Olivia investigate a series of killings by a translucent man who left his victims in the same condition. Meanwhile, the two worlds exchange information and Walter is haunted by visions of a mysterious man in his mirrors.
A serial killer on the Other Side has killed 23 victims and Fauxlivia comes to This Side to ask for the loan of the serial killer's duplicate, a mild-mannered Forensics Psychologist. Meanwhile, Walter deals increasingly vivid hallucinations.
Songs: composed by Berlin Philharmoniker -- "Kyrie from Requiem" composed by Mozart, Mozart -- "Requiem In D Minor"
A 12-year-old boy makes an unusual friend, a friend who causes the death of two bullies. While the Fringe team attempts to deal with a growing field of contagion, Walter takes drastic measures to deal with his hallucinations.
When a bizarre energy mass attacks Olivia, she turns to Walter for help. When they realize the attack is related to Walter's Cortexiphan experiments on Olivia, they track down another test subject who had the ability to project his astral self.
While Olivia and Walter attempt to deal with the appearance of the man from their dreams, Fringe Division deals with a shapeshifter who is tracking down a former Massive Dynamic scientist in the hopes of getting him to stabilize her metabolism.
Songs: Violet Sedan Chair -- Seven Suns (Rising), Up Down Up -- Wild Eyes
Time anomalies apparently connected to Peter's arrival start manifesting in the Boston area, but the Fringe team soon discovers that they are caused by a husband desperate to be reunited with his ailing wife.
The Fringe team investigates a man with a broken neck who was drained of his pigmentation. Meanwhile, Olivia suffers from headaches and Peter begins trying to recreate the Machine.
Songs: Mazzy Star
-- Fade into You, Violet Sedan Chair. -- Long List Of Lovers, Bryan Ferry
-- Me oh My, Fillmore Slim -- Thunder And Lightning
Peter asks Olivia to help him go to the Other Side and ask Walternate for help when Walter refuses to help him employ the Machine to return to his own timeline. Meanwhile, the threat of the prototype shapeshifters grows and an old enemy returns.
Songs: The Airborne Toxic Event -- Changing, Tommy James & The Shondells -- Crystal Blue Persuasion
Peter reaches an uneasy alliance with the Other Side's Fringe Division, and helps them once they capture the mastermind behind the shapeshifters. Meanwhile, the Other Side's Elizabeth Bishop comes to see This Side's Walter Bishop to ask for his help.
The Fringe team discovers a girl who can see the future, and she warns that her vision always come true. Now, Olivia and the others must find the source of her newest vision, which shows a courthouse collapsing and killing hundreds of people.
Songs: Mayer Hawthorne -- The Walk
While the Fringe Division on This Side deals with a murderer who uses a poison that can't possibly exist, Agents Farnsworth and Dunham from the Other Side come to pay the team a visit.
Songs: Little Feat -- Dixie Chicken, Mozart -- Violin Concerto No. 1 in B-Flat Major, K. 207: II
While investigating a plane crash near the small Vermont town of Westfield, Peter, Olivia, and Walter discover that they are trapped in the town and surrounded by people who are going insane.
Songs: Billy Bragg & Wilco -- California Stars, Conway Twitty -- Crazy Dreams, John Coltrane & Thelonious Monk -- Epistrophy, The Shirelles -- Will You Still Love Me Tomorrow
Olivia and the team investigate a mental patient who heard voices that describes a real-life murder. While she conducts the investigation, Olivia begins to be overwhelmed by the memories of Peter's Olivia, and they must decide if they wish to give in and accept Olivia's new persona.
Songs: Karen Elson -- The Ghost Who Walks
As David Robert Jones tortures a captive Nina in an effort to activate Olivia's cortexiphan-enhanced abilities, the dying Observer visits Peter and Walter at their lab and Peter must merge minds with him to learn his secrets.
While Olivia deals with the ramifications of the memories of Peter's "Olivia" subsuming her, the Fringe team investigates the deaths of two couples and discovers that a twisted killer is trying to capture love in a bottle.
When a passenger on a Paris-to-New York flight transforms at the NY terminal and kills two TSA agents before dying himself, Peter realizes that the case is the same as one that he dealt with in the original timeline four years earlier. Meanwhile, Olivia is put on leave when Broyles discovers that 40% of her memories as an agent for him are now missing.
Songs: Peter Noone
-- I'm Into Something Good, Dawes -- Time Spent In Los Angeles
Feeling left out on This Side, Lincoln travels to the Other Side to help Fringe Division investigate a vigilante who genetically damages his victims as he kills them.
When three men die under mysterious circumstances on This Side, Walter travels to the Other Side to determine how the same three men died over there and what the connection is.
In the year 2036, the Observers have conquered mankind and taken the planet for themselves. Only two brave Fringe agents stand between the Observers and the total subservience of Man... but to triumph, they'll need the help of a legendary figure from the past.
Walter realizes what David Robert Jones' end game is, and how it involves the cortexiphan subjects. The two Fringe teams work together to stop the pending crisis and realize that one world will have to make a sacrifice to stop Jones.
While dealing with multiple cases of spontaneous combustion, Walter realizes who is responsible for Jones' plan and sets out to get proof. Meanwhile, Jones launches a series of new attacks after the bridge is shut down, in his bid to create a new universe for himself and his superior.
Peter and Olivia attempt to stop William Bell from destroying the world, while Water is forced to watch. However, to save two universes, one of them will have to die.