Lincoln arrives at the lab and discovers that Olivia, Walter, and Peter are taking Gene out for some sunlight. Olivia has an Indian necklace that Lincoln left at her apartment and returns it to him, with Robert Danzig’s name on it, and Lincoln realizes that she doesn’t remember him giving it to her or explaining what it means. He talks about how he never really settled down and that his partner gave him the necklace as a reminder that Lincoln would always have a home with Robert and his family. Gene gets restless and Olivia goes to help, leaving Lincoln alone. Astrid comes in with some file boxes, explaining that they have the files on David Robert Jones that their Other Side counterparts have requested. When she explains that she’s been assigned to deliver them but that she has a prior commitment with her father, Lincoln is glad to help.
At Fringe Headquarters, Broyles is reluctant to let Lincoln goes since the liaison position with the Other Side is merely a courtesy and he’d rather keep one of his better agents on This side. However, Lincoln insists that they can gain some valuable information on Jones and admits that he currently has nothing to do.
On the Other Side in Belford, NY, Paige Randall goes out to her car at the top of a parking garage. A mugger attacks her and she tries to fight back, but her attacker prepares to stab her. However, a shadowy figure emerges, lifts the mugger off of Paige and throws him to the ground. As Paige runs, the mugger stares at his attacker in horror.
When Lincoln comes through the bridge to the Other Side, he’s sent to a briefing room. Fauxlivia comes in and tells him that there’s been a change of plans and that she has a new case. As she drives to the parking garage, Lincoln brings her up to speed on how Jones has been experimenting on her counterpart using cortexiphan. Fauxlivia quickly realizes that’s why they sent Lincoln instead of Olivia. They drive past one of the amber zones and Bolivia explains that since the bridge was established, there world has started to stabilize and they’re able to remove the amber barriers. As they drive, Fauxlivia asks Lincoln to settle a bet and asks what his middle name is.
When the two agents arrive at the parking garage, Fauxlivia can’t help telling Agent Lee that she knows his middle name, Tyrone. He’s dismayed that Lincoln told it to her. They check the body of mugger, which has been warped beyond recognition, and Lee explains that he appears to be the victim of a local vigilante. It’s the first body that the vigilante has left behind and they wonder what happened to the other criminals in the area that have gone missing.
The vigilante, Canaan, now looks like the mugger. He’s removing his belongings from an abandoned church as two hazmat workers, Bill and Ted, remove a nearby amber barrier. They pick up a strong organic reading and follow it to the church, and Canaan hides in a van. They go by him and into the abandoned church, and finds over a dozen bodies in the basement, all hideously twisted and warped.
Fauxlivia and her team get called to the church and she tells Lincoln that the debrief will have to wait until she’s free. She suggests that he go back to his world, but he offers to stay and help. As they arrive at the church, one of the DoD soldiers thanks Lincoln. He thinks that the man has mistaken him for his counterpart until Fauxlivia explains that while Lincoln and his people work in secret on their world, they’re considered heroes on the Other Side for helping to create the bridge and heal the breaches.
Canaan goes to a shelter and the woman in charge, Helen, asks if he has somewhere to stay. The man admits that his home is gone and she offers to help him find a shelter. Canaan settles down to eat but a man notices a bleeding wound on his neck. When he realizes what has happened, Canaan pulls up his collar and quickly leaves before anyone else can notice.
As Lee and Lincoln go over the bodies, Lincoln admits that he isn’t comfortable with the disfigured corpse. Fauxlivia finds some blankets and realizes that someone was living there, and figures that they left when they realized the church would be reopened when the nearby amber was removed. Meanwhile, Lincoln finds a locket on one of the victims and pulls it off. The corpse’s head falls off and he notices a hole in the roof of its mouth. He shows it to Fauxlivia, who says they can use the photo inside to identify the victim. Lincoln has another idea and asks first if they can determine the time of death of the bodies and then check all the surveillance feeds in the area.
At Fringe Division, Agent Farnesworth tells Lincoln that the odds of them spotting who he’s looking or on the feeds is astronomical, but he assures her that it’s necessary. Lee confirms the time of death on the women’s corpse and asks Lincoln why he doesn’t go back. He figures that there’s a problem, but Lincoln insists that there isn’t. He admires his counterpart’s self-confidence and wonders where it comes from, and they compare life stories only to discover that they’re identical. Agent Farnesworth interrupts to tell them that she’s spotted the woman on the feeds, but the time stamps shows that she was walking around two days after she died.
Lincoln goes to Broyles and tells him that he believes that they’re dealing with a shapeshift. He points out that in his reality, the original shapeshifters used a three-pronged device to penetrate the palate of their victims, sample their DNA, and take on their forms. Broyles doesn’t believe it, pointing out that they haven’t been able to confirm holes in any of the other victims’ palates, and points out that Jones would have no reason to kill criminals. He dismisses Lincoln’s theory as obsession with shapeshifters since one killed his partner, and says that it would be best if he went back to his own world.
Canaan goes to a park and watches one boy, Daniel, playing soccer with the others. When Daniel kicks the ball over, Canaan throws it back to him and says that he’s a good player.
Two petty crooks, Dawes and Mikey, are taking drugs in an abandoned building. When Mikey goes to the bathroom, Canaan breaks in, grabs Dawes, and pins him to the floor. Mikey arrives but the shapeshifter doesn’t notice him as he extends a tendril from his mouth into Dawes’, penetrating the roof of his mouth.
Agent Farnesworth receives a report from the NYPD about Dawes’ death and brings up his file. They confirm he’s a criminal, fitting a profile of the vigilante shapeshifter’s other victims. Broyles orders his people to lock down the area while Lincoln tells Agent Farnesworth to start circulating photos of Dawes’ mugshots. She soon spots “Dawes” on camera and Lee, Lincoln, and Fauxlivia take a tac team into the neighborhood. While they move into position, Lee tells Lincoln that Broyles was out of line earlier for dismissing his theory, and assures his counterpart that he’s a good agent. Lincoln still wonders why the two of them are so different and Lee suggests that he simply decided to be a better man.
Lincoln spots Canaan first and chases. The agent gets separate from the others and Canaan doubles back to attack him and then take his gun. However, rather than shoot Lincoln, Canaan runs away. The tac team quickly surround him and Lincoln yells to them not to kill his attacker. After a moment, Canaan drops the gun and willingly surrenders.
When Broyles gets word that the suspect is being secured at the warehouse, he tells Farnesworth to relay congratulations. However, he then goes off privately and contacts his world’s Nina Sharp. He warns her that they’re moving the shapeshifter and she assures the colonel that her people will take care of them.
Lincoln asks Fauxlivia for a few minutes alone with the shapeshifter so he can talk to him before the DoD take him into custody. When he reminds Fauxlivia that she would do the same thing if she had lots her partner, she gives him five minutes.
A sniper enters an adjoining building, goes to the rooftop, and puts together his rifle.
Lincoln asks Canaan why he didn’t kill him when he had the chance, and asks who he was when he was a human. When he still gets no response, he finds the photo of Daniel in the man’s wallet and the shapeshifter says that Daniel was someone in his life once, but his mother left Canaan and took Daniel with her. Since then, they’ve lived their lives as if Canaan never existed. All he ever wanted was to be needed, or even missed, and Lincoln says that he understands. Jones found Canaan and claimed to understand how he felt, and offered him the chance to be the first of a new breed. However, when the experiment failed, Jones abandoned him. Lincoln realizes that Canaan has been killing criminals to take their DNA and stay alive, but warns the shapeshifter that Jones has always considered him nothing but an experiment to be disposed of. Canaan doesn’t believe it and insists that Jones will find him and cure his condition like he promised.
The tac team takes Canaan out to the transfer van and the sniper opens fire. Fauxlivia spots him and grabs rifle, aims, and fires a single shot, taking out the sniper on the roof. Meanwhile, Lee discovers that one of the stray bullets hit Lee in the chest. As he lies against the van, Lee tells them to figure out who knew that the prisoner was being transferred. Fauxlivia comes over and Lee tells her that he’ll be okay. Angry and shocked, Lincoln grabs Canaan, slams him against the wall, and tells him that Jones is the one who ordered his death. He tells the shapeshifter to choose between being his own man or a puppet.
At a base at Fort Lee, the Other Side’s Nina is monitoring the vats containing the shapeshifters. The sniper arrives and tells her that he’s taken care of Canaan and managed to avoid Fauxlivia’s shot. However, when Nina turns her back, the “sniper” accesses the computer systems and Nina realizes that Canaan has taken his place. She tries to escape but is quickly cut off outside and captured.
At Fringe Headquarters, Broyles gets word of Nina’s capture. Agent Farnesworth comes in and tells him that she has some bad news.
At Fort Lee, Lincoln goes over Nina’s computer systems and discovers that she has a system to monitor all of the tracker implants in the shapeshifters. A soldier calls Fauxlivia over and Lincoln watches as dismay sweeps her feature. A soldier informs him that Lee didn’t make it.
The next day, Lincoln takes Canaan across the bridge and introduces him to Walter and Peter. He assures the shapeshifter that he’ll be able to make his own life and gives him Danzig’s necklace as a gift, and Canaan thanks him for everything.
Fauxlivia goes to Lee’s locker and looks at the photos he had of the two of them. As she studies them, Lincoln comes in and realizes that she probably doesn’t want to see his face. She assures him that she’s okay and admits that it would be nice if he stayed around.