Olivia and Bolivia from the alternate dimension exchanging boxes of their own world's Fringe division's classified notes for comparison and study to solve the impending crisis. Olivia briefs Bolivia on her own dimension's fundamental traits about honesty and trust, however Bolivia thinks it's not her problem, but Olivia's. As Bolivia had taken up her identity before, she had observed how lonely Olivia's life is. Olivia retorts that just because Bolivia has walked in her shoes before doesn't mean she knows her entirely. After the two leave the room, a brief glimpse of Peter Bishop is seen and fizzles out.
Meanwhile the Observer September meets with another Observer, August, in a diner. September expresses surprise that the timeline has been rewritten and Peter's existence has been erased, but traces of him continue to bleed through. August reminds September that it has always been their responsibility to ensure that events play out as they were intended. But now because of September's intervention, the older Observer passes him a pen-shaped object to him and says, "This started with you. It must be you who ends it." He tells September that the others can never know that the boy lived to be a man. September says he will take care of it.
Lincoln Lee from the prime dimension comes over to his friend and FBI partner Robert Danzig's house to visit his family as well as preparing to head out with Robert on an assignment. They pursue a suspect across rooftops, eventually following him into an abandoned warehouse. They split up and Lincoln goes upstairs. Robert sees a glimpse of someone moving and goes after him. Lincoln ends up entering a room only to be held at gunpoint by the suspect, but he immediately grabs him and throws him onto the floor. He then handcuffs the suspect and calls out to Robert, but his partner does not respond. Following the way he went, Lincoln is stunned to see a man that looks somewhat inhuman on top of Robert's body. Lincoln calls out a warning and the man immediately gets up and jumps out the window to another warehouse. Lincoln looks over Robert, who dies and his face turns a deep red and becomes translucent.
Later, the authorities arrive including the Fringe division. Astrid observes Robert's body in the ambulance while Olivia goes to question Lincoln. As they talk, September and a tall Observer watches them. The tall Observer tells September that Lincoln used to know her, but as September says, he no longer remembers her due to the changed timeline. Lincoln tells Olivia that he and Robert were tracking a sale of illegal weapons. He says that the man he saw who attacked Robert seemed to have translucent skin. When Olivia tells Lincoln that her department would be handling the investigation from here and Robert's body would be brought back to their facility, Lincoln becomes indignant. He doesn't understand why Olivia's department would be handling the case if they have no idea who their suspect is and Olivia wouldn't tell him who she works for or discuss the case further. He wants to talk to another person about the case but Olivia tells Lincoln that she is the only one handling it, and she expresses her sympathies for his loss.
Back in the lab at Harvard, Walter and Astrid discuss their cooperation between the prime universe and the alternate universe to solve the impending collapse of both dimensions. Astrid says it has been a week since then while Walter remains distrustful of "Walternate," the other Walter who is U.S. Secretary of Defense on the other side. Astrid reminds Walter that the other Walter also has plenty of reasons to hate him too. Lincoln visits the lab and is forced to help Walter perform a little experiment on a quite dead bird, which is successful in bringing it back to life for a few moments before dropping dead entirely.
Olivia is not pleased to see Lincoln at the lab and tells him that he is not part of their investigation and tells him to leave. Lincoln is not willing to leave without any explanations and asks Olivia what her division is. He has already checked some basic details on their division's location at Harvard. Olivia receives a call from Broyles about another body turning up and Lincoln requests to go with her, stating that he was the first person at the crime scene.
Olivia allows him to come with her and Astrid to their latest crime scene. They are informed by an agent that there was a car crash and the victim, a woman in her 30s, was found dead in the same manner as Robert Danzig. Walter, via his latest surveillance device which Astrid wears on her ear, observes that the victim's eyes are dilated and there is hematoma on her right jaw. He then asks to check the victim's anus, much to Astrid's embarrassment. Olivia tells Lincoln that the victim was driving home and thinks the suspect was hiding in her back seat and attacked her. This caused her to struggle and her car hit a lamp post. Lincoln observes that although there are several witnesses to the car crash, he sees one of them, a woman, seems to be deeply unsettled.
The woman tells Olivia that she heard the crash but seen nothing. Olivia tells her that her friends were in the field and she was beside the street when the crash happened, and hopes the woman saw something. After being assured by Olivia that she will not get into trouble, the woman reveals that she was trying to get reception on her cellphone when she saw the suspect leaving the scene and took a picture of him. With this piece of evidence, Olivia compliments Lincoln for his observation. When Lincoln does not understand why the killer is involved in two apparently unrelated murders, Olivia tells him that is not just two.
Lincoln is brought to a facility where he meets Agent Philip Broyles, who hands him documents stating that he will be persecuted if he disclosed what he is about to see. Lincoln enters a room with Olivia and Broyles and discovers that there are more bodies whose deaths are identical to the two murders he saw, which apparently happened within the last three days. Broyles tells Lincoln, that they are unable to find out the cause of death, just that the victim suffers a massive hematoma around their faces and their hearts stopped. They are looking to see if the attacks have anything to do with different ages, blood type, race or cholesterol levels but have been unable to link to anything. Lincoln tells the agents that Robert had Crohn's Disease and had to take iron pills. He tells Olivia that Robert was like family to him and Robert believed that everything happened for a reason, but now Lincoln has a hard time believing that there is a reason for all the people's deaths, including Robert's.
Meanwhile, September is buying some electronic stuff from a junk shop. The shopkeeper tells him that he found an electron gun which was salvaged from a TV cathode ray tube, so he has to charge September the full price of the TV as well. When asked what he is going to do with all the stuff, September replies that he needs to erase someone from time.
Olivia and Lincoln return to the lab and Astrid asks them if they have seen Walter, who has disappeared when he asked her to get him a sandwich. While Olivia and Astrid search for Walter, Lincoln finds Walter emerging from the isolation tank. Walter is disturbed, and as the others find him, he tells them that there was a man who appeared in the mirror when Walter was looking at it. Olivia manages to calm Walter down. As the group observes the latest victim from the car crash, Walter has checked with Lincoln's observations for any manner of iron-related diseases with the victims. Although the victims have a variety of symptoms such as hair loss, he has found all the victims share a disease in common: heavy metal poisoning such as lead, zinc, or mercury. Although they have these problems before, the levels of metals in their body have returned to normal at their point of death as though their blood have been cleaned. Walter has no hypothesis on why the killer is taking metal particles from the victims' blood, but it's clear he needs a lot more. At an unknown location, the killer extracts and injects an orange substance into his arm and continues taking notes.
Back at the lab, Lincoln is appalled that Walter will be taking samples from the victims for experimentation. He is told by Olivia that the victims' bodies will not be returned to their families, and instead they will be officially declared missing and the families will be informed the authorities will continue to search for them. Lincoln tells Olivia that she doesn't understand that the families will always be wondering about what happened to their loved ones and will continue to search for them. Olivia explains the reason they do not disclose the cause of death of the victims is that they need to file official documentation which will draw attention to the Fringe division.
Astrid has found that one of the victim's credit cards has registered a charge. However, it's a false alarm as it was an automatic renew of the victim's commuter pass's monthly charge. Lincoln suggests that the killer may have picked up his victim at the commuter rail parking lot. Olivia goes to trace the victims' location of death and discovers that the killing patterns are not random at all, with four killzones centered on the commuter rail stations. She tells Astrid to call Broyles and tell him to put out an identification of their suspect at all rail stations around that region and three teams of agents to watch the stations. Meanwhile, the killer's arm spasms while writing his notes and discovers that he is growing a new fingernail rapidly. Removing it, he observes his data and finds something interesting.
At Avon Station, Massachusetts, Olivia and Lincoln watch for the killer in their car. Olivia tells Lincoln that she can understand how he feels as she lost a partner, John Scott, before. She recruited Walter from the mental institution so as to better solve the case and save her partner's life. However, Walter could not save John Scott in time, which differs from the earlier timeline when Peter was around. Before Lincoln can respond, they received a transmission that other agents have identified the suspect and is now heading to an industrial area. As two agents try to track him down, the killer grabs one of them underneath the track while the other fires his gun in his direction.
Olivia and Lincoln find the first agent, who is already dead, and the second one in critical condition. Olivia tells Lincoln the agent will bleed out and die, but Lincoln tells her to go after the killer and assures her that he will take care of the injured agent. Olivia tracks the killer to a warehouse which is his hideout. She hears noises upstairs as the killer burns his notes and prepares to flee. Before he can leave, Olivia holds him at gunpoint and tells him to drop his briefcase, but he slams it into her and they get into a fight. Olivia is at the losing end, but she manages to pick up her gun and fires multiple times into the killer. Lincoln hears the gunshots and is relieved to see Olivia safe and sound. While he assures the injured agent, who has regained consciousness, the latter warns him that there is more than one suspect. Lincoln looks up and sees the second suspect rush past the tracks. He follows after him and as he rounds a corner, he and the suspect fire simultaneously at each other. The suspect misses Lincoln and is killed by Lincoln's shot. Lincoln looks over the suspect and realizes he is the same man that killed Robert, giving him a measure of revenge for his partner.
Later, as the two bodies of the suspects are wheeled away, Lincoln asks Olivia who they were and what they were looking for. Olivia replies the better question is what were they. Unknown to them, a woman watches from the top of a storage tank. She has the same translucent skin condition as the first two suspects and as she concentrates, her skin regresses back to normal. She turns and leaves the scene.
Back at FBI headquarters, Lincoln packs up Robert's belonging including his badge and card. He is handed a sealed envelope by another agent. Meanwhile at the Harvard lab, Olivia watches Astrid poring over the remains of the killer's burnt notes while Walter does an autopsy of the killer's body. Lincolns arrives and thanks Olivia for releasing Robert's body back to his family. Olivia tells him that although they still do not have all the answers they seek, she hopes that her actions can bring some measure of closure to what Robert deserves and because of what he meant to Lincoln.
Walter tells Olivia that he has found a biological device that looks similar to the ones employed by people on the other side. Although, Olivia and Astrid try to alleviate his suspicions, he maintains that this technology couldn't have been from their own dimension. Lincoln doesn't understand what the group is saying, so she brings him to a top secret facility where is given an ID pass. They walk deeper and enter a decontamination room. While undergoing decontamination, Olivia tells Lincoln that she understands how it feels to have a hole in her life like he said before, and she was invited by Broyles to join the Fringe division so as to find her own answers. But she says sometimes answers lead to more questions.
As they exit into a large room, it is revealed to be the hangar which stores the doomsday device and both dimensions' Fringe divisions have set up their facilities inside. Lincoln is stunned to see another Olivia, which is Bolivia, coming to meet them. Olivia shows Bolivia the biological device Walter found and informs her that it's powering a new form of shapeshifters who were originally human. As Bolivia leaves with the device to research on it, Lincoln is shocked to see an airship from the Other Side passing by from the rooftop window.
Outside the Harvard lab, September prepares his device as he watches Walter moving inside. Walter is revealed to be using the lab as he quarters as he prepares to sleep. September looks as though he is about to power up the device, but he switches it off and leaves. When Walter switches off the television and goes to bed, he sees Peter's reflection on the TV instead of his own. He shouts in fright causing the agent watching over his room to run in. Walter has smashed the TV screen with his remote and tells the agent that he saw the same man from the mirror.