In Boston, Peter and Bolivia go to dinner and discuss their fellow diners. The conversation turns to moral lines and judging other people without understanding their position. Peter finally says that he has to leave and get home to Walter before he panics. As they go, Bolivia asks for a minute and goes to the women's restroom to be alone.
The next day, Senator Van Horn is driving through Brookline, Massachusetts, and stops to get lemonade from two girls running a sidewalk stand. As he drives away, a truck slams into his car. At the hospital, the doctors confirm that he has no heartbeat... but he's still breathing.
Broyles arrives and reassures Van Horn's wife, Patricia. He then uses his identification to get access. In the operating room, the doctors are trying to stabilize Van Horn when Newton comes in. He shoots anyone who tries to interfere and then wheels Van Horn out on a gurney. Broyles tries to stop him, and Newton takes a nurse as a shield, shoots Van Horn in the eye, and makes his escape. Broyles runs to Van Horn... and discovers that he's bleeding mercury out of the eye wound.
At Massive Dynamic, Peter talks to Nina, who insists that she's okay with Walter owning the company. Meanwhile, Walter addresses the scientists on the matter of consciousness and his theory that the brain is God. As he starts to take off his pants, Peter comes in to collect him to investigate a kid. Nina admits that he's unorthodox, and Peter points out that he's tripping.
At the hospital, Broyles shows them surveillance footage of Newton's intrusion. They figure that Newton came there to retrieve Van Horn when he learned about the car crash. Broyles wants a full accounting of everything that the Van Horn shapeshifter was involved with. Bolivia goes to lock down Van Horn's office while Walter checks out the shapeshifter's body. Broyles calls the CDC to administer blood tests.
Walter examines the dead shapeshifter with the help of a bemused agent. He explains that it's part machine and part organic. Once Peter comes in, the agent leaves and Peter notes that Newton's shot was very specific. Walter concludes that Newton aimed specifically for the shapeshifter's power source, and agrees with Peter that they should try to fix it.
Newton is in the woods dosing himself with mercury when Bolivia calls him and warns that the Van Horn shapeshifter knew everything about her. He warns Bolivia that her cover is intact for the moment, but he figures that Peter has realized on some level that she's not the real Olivia. Newton tells her that if she isn't committed, she'll fail.
Walter is unable to reanimate the shapeshifter, and asks Peter to get the body moved to Massive Dynamic. When the shapeshifter's hand moves, Walter initially dismisses it as a hallucination. However, Peter confirms that Walter has triggered something. When Bolivia comes in, they tell her the good news.
Later, Astrid arrives at Massive Dynamic and brings Walter him everything he asked. He explains that he's building a treasure map of the shapeshifter's neural pathways using visual stimuli to trigger memories. As he talked, Astrid points out that he actually called her "Astrid," and Walter says it's the LSD.
Peter and Bolivia go through Van Horn's records for the last three years. She suggests that Peter go check on Walter, but Peter figures that his father is fine. He doesn't find anything but figures that the shapeshifter must have left something since he didn't know he was going to die. Bolivia takes a call from Newton, claiming it's Rachel, and tells him that the shapeshifter is alive. She tells Newton where the body is, and then signs off as Peter finds something: photos of all of the Fringe team, and all of their case files.
In Yonkers, the Duffy family is having dinner when Newton arrives at the door. The father answers the door, and discovers that it's Newton. Newton calls him Ray and gives him his assignment: break into Massive Dynamic after taking on a new body. Ray reluctantly agrees, noting it's been five years since they last met, and Newton tells him to erase all traces of his new life when he's done.
Broyles brings Bolivia and Peter into Massive Dynamic past the security teams. Walter greets them but they ignore him as Broyles explains that the blood tests so far have proven negative. When they pause, Walter says that they can ask the shapeshifter. In the lab, Walter demonstrates that it reacts to personal items such as a photograph of Van Horn's wife. He explains that to succeed in its mission, it played the role and a real emotional bond formed between it and Patricia. Bolivia objects, insisting that it's a bad idea, but Broyles says that they can trust her to keep the situation private.
Ray takes a hidden gun from a hidden security safe, and then removes the shapeshifting device. He put on his policeman's uniform, leaves his sleeping wife and goes to see his son, Nate, who says there's a monster hiding beneath his bed. Ray confirms there aren't any monsters there, and talks about how some monsters are capable of love and can become a best friend. As Ray starts to go, his son asks him to check on him when he gets back, and Ray promises that he will.
Patricia arrives at the lab, and admits that she can't believe that her "husband" was a shapeshifter. However, she insists on helping so that she can find out who killed her husband. She addresses the shapeshifter and Walter has her talk to it, and then caress it. Patricia understands and agrees, and tells him about their children and grandchildren. The shapeshifter's neural activity increases as Patricia apologizes, admitting she didn't know that he was gone and blaming herself. Astrid detects activity in its spine, and the shapeshifter suddenly comes to life and starts reciting numbers and names. Peter finally shuts it down, and Patricia explains that all of the names were hotels, and the numbers were the dates that they were going to go on their anniversary. Broyles assures her that she's done more than enough and takes her home.
As Walter explains that the shapeshifter's system is too badly damaged, Bolivia secretly takes a text message saying that she needs to get everyone out in 15 minutes. She suggests that Walter take a walk to clear his head and they go to the cafeteria. Walter blames himself for disturbing Patricia, but then gets an idea as they talk about dinosaurs. He goes back to the lab by himself, but Ray gets into the elevator with him. As they go up, Walter explains that the stegosaurus had a brain in its spine, a massive cluster of nerves. He's unaware that Ray is getting out his shapeshifting device. The elevator arrives at the top and the guard lets Walter in. However, he warns Ray that he's not allowed on the floor.
In the cafeteria, Peter talks about how Patricia must have made excuses to avoid confronting the fact that her husband had changed. He says that he's been doing that with Bolivia, and notes that she's been a completely different person since she got back from the Other Side. Before he can pursue that line of thought, Astrid comes over and Peter realizes that Walter has gone.
Walter flips over the shapeshifter's body and cuts into its spine. Ray comes in and holds Walter at gunpoint, and then removes the disc. Walter grabs a knife and stabs it into Ray's stomach, but Ray knocks him out.
Peter and Bolivia get into the elevator to go upstairs, and Ray goes past them. Peter notices mercury on the buttons and realizes that Ray is a shapeshifter. Bolivia says she'll go after him and tells Peter to check on Walter. Peter gets upstairs and finds Walter, unconscious but alive. Bolivia arrives and tells them that she lost Ray, and Walter explains that Ray took the data out of Van Horn. Peter accesses the security cameras to identify the shapeshifter.
Ray drives home and finds Newton waiting for him outside. When Newton notes that he didn't shift, Ray says that he didn't have to and gives him the disc. As he starts to go inside, Newton tells him that he disposed of Ray's wife and child. When Ray reacts, Newton says that he didn't, and now he knows that Ray has become attached. He reminds him that they were created to keep moving on, but Ray insists on staying with them. Newton shoots him dead and prepares to leave, just as Bolivia and Peter arrive.
Newton drives off and Peter drives after him. They enter a tunnel and Newton's car flips. As Peter holds back the civilians, Bolivia takes the disc from the unconscious Newton's body. He wakes up and grabs her hand, and stares at her intently. Bolivia pockets the disc and moves away from the car.
Later, Bolivia goes to the federal detention center and visits Newton. She assures him that the disc is secure and then gives him a small metal chip. He warns her that she'll have trouble without him, but she insists that he's just a machine. Newton notes that she is good, but she is trying to convince herself that she doesn't care. Finally, he warns her that there are matters of integrity and self-respect that she isn't willing to pursue, but figures it's not his problem anymore. Bolivia turns without a word and walks away.
Peter is drinking at a bar when Bolivia sends him a text message asking him to come over and talk.
In his cell, Newton takes the chip and swallows it.
Bolivia tells Peter that she lied to him, but then insists that she doesn't want to talk and kisses him.
Newton convulses and then dies, leaking mercury.
Peter and Bolivia end up in bed.