Agent Lincoln Lee (Seth Gabel), following both the death of his long-time partner by a shapeshifter, and the recent changes in Olivia Dunham’s (Anna Torv) memories that have made her forget her romantic meetings with him, struggles to find his place in the Fringe division. With the main Fringe team preparing to take Gene, Walter Bishop’s (John Noble) cow, for “grazing day”, Agent Lee offers to take case dockets through the dimensional bridge to the parallel universe to allow Astrid Farnsworth (Jasika Nicole) time to spend with her father. Once through, however, Olivia’s doppelganger, Fauxlivia (Torv), states that the dockets will have to wait as there is a new Fringe case on their side; Agent Lee offers to help.
They arrive at a parking garage, where the night before, a woman had been attacked by a man, but an unknown figure arrived and attacked the man, killing him before disappearing. The deceased man is recognized as a petty criminal, his profile fitting nearly two dozen other criminals that have gone missing in the last month, but this is the first time a body, horribly disfigured, had been left behind. The Fringe team suspects some type of vigilante justice. During the investigation of the scene, Agent Lee meets his doppelganger, Captain Lincoln Lee (Gabel) of Fringe division, finding him to be more outgoing and brash compared to his own mild-mannerisms. Agent Lee also recognizes the close, romantic connection between Fauxlivia and Captain Lee. On further talks with Captain Lee, Agent Lee is surprised to find their backgrounds were exactly the same, deviating only when Captain Lee decided to become more assertive in more recent years.
As the investigation continues, Agent Lee learns of how amber was used to quarantine areas of the parallel universe to protect it from singularities, but with the introduction of the bridge through The Machine, these areas are healing themselves, allowing the amber to be removed. In one such region, two workers discover nearly two dozen bodies in various states of decay in a church, and these are quickly identified as the missing criminals. The Fringe division discover telltale signs of shapeshifter extraction marks, though more advanced than the means used by the initial models created by Walternate (Walter’s doppelganger). Fringe division hears of another attack on a criminal; Colonel Broyles (Lance Reddick) initially denies Agent Lee’s suggestion of a manhunt but eventually relents when both Captain Lee and Fauxlivia agree. The team finds and captures the shapeshifter. They learn he calls himself Canaan, and was the first prototype of the new type of shapeshifter created by David Robert Jones, though ultimately cast aside. Canaan struggles with an identity crisis, feeling alone and rejected, having been promised by Jones to be fixed, but refuses to divulge any information on Jones’ location or plans.
Unknown to the rest of Fringe, Broyles contacts the Nina Sharp (Blair Brown) of the parallel universe, who arranges for a sniper near the building where Canaan is being held. As the Fringe team prepares to escort Canaan to headquarters, the sniper attempts to kill him. Fauxlivia is able to kill the shooter while keeping Canaan safe, but Captain Lee has taken a bullet and is rushed to a hospital. Once secured, Agent Lee implores Canaan to help Fringe, noting how his life is not safe even from Jones. Canaan agrees, and takes on the appearance of the sniper, allowing him to enter the secured facility that Nina had hidden herself in. Believing that Canaan is the sniper, Nina lets down her guard, allowing Canaan to override the facility’s security controls for Fringe to raid the site. Nina and several others are captured, and Agent Lee finds that the equipment in the facility can allow them to track down all the other shapeshifters in the area. As they are clearing out the building, they come to learn that Captain Lee’s wound was fatal and he has died, shattering Fauxlivia’s emotions.
Agent Lee takes Canaan across the bridge back to the prime universe, where Walter and Peter Bishop (Joshua Jackson) promise to help study and fix him. Lee then returns to help the emotionally distraught Fauxlivia to recover from her loss and to sort through the data collected from Nina’s facility.