At the Hennington Mental Health Institute in Boston, a man is examining a patient, Joseph Slater, and asking him to identify a girl in a red dress that he can visualize with flowers in her hair. As Slater provides more detail, the man cuts open the back of Slater's head and removes a small white object and places it in a container. As the man starts to close up Slater's skull, his assistant gets a call. Outside, the Hybrid leader, Smith, calls to warn them they have activity. The assistant looks out and sees an orderly approach and shoots him as he calls in an alert. He and his leader have no choice but to leave, with Slater's skull still open. The leader apologizes to Slater for leaving his skull open and they drive away as a nurse finds Slater, the back of his skull open and the skin peeled down.
The Fringe team arrives at the Hennington Institute and Dr. West informs them that Slater has been there for 14 years due to acute schizophrenia and delusions. However, after the break-in and the surgery, Slater is showing remarkable progress and there's no signs of any structural damage to his brain. Walter, clearly upset at the setting, asks to see tapes of Slater when he was a patient. They review the tapes, which show Slater talking about the girl and demanding that West bring her back. Slater doesn't recognize either man and talks of how he was suddenly free. Walter empathizes with his feelings. Once Olivia finishes questioning him, Slater's wife arrives and he goes to see her. Walter admits that Slater is lucky for having a wife who visits him, but apologizes when Peter seems concerned. Olivia asks Walter if he has any theories and he admits he hasn't but is eager to find a remedy for insanity.
The team reviews the security tapes and discovers the intruders used a state-of-the-art lock-breaking device. Olivia recognizes the leader as one of the heads stolen from the cryonics company, a head belonging to a Thomas Jerome Newton. Olivia reports their findings to Broyles and admits the name was an alias and has no other records. She reminds them that Bell claimed that Newton would open a corridor between worlds and cause global destruction. Olivia vows to stop him.
At the lab, Walter reviews Slater's medical record and asks Astrid to check on Dr. Simon Paris, the man who referred Slater to Hennington. He believes that someone induced Slater's insanity in the first place and notes that a cure for insanity is a fantasy. Astrid confirms there is no Simon Paris in the AMA files. While she looks for the Rx number on Slater's admission papers, she wonders why someone would make another person insane. Astrid then confirms Paris wrote an indefinite prescription for Slater as well as two other patients in the same week, at two other hospitals.
Olivia and Peter go to the Dunwich Mental Hospital to see one of the patients, Deborah Crampton, who suffered from arithomania: an obsession with the number 28. However, last Tuesday she woke up and the number was gone from her head. They check the back of her head and discover that there's a surgical scar but no sutures. It appears to have been sealed with a surgical laser. She only saw Dr. Paris a couple of times before she came to the mental hospital, but he only treated her for postpartum depression. The arithomania started after Paris sent her to the clinic.
Newton checks with Smith, who warns that they got to Slater too late and the specimen won't survive more than another five hours. However, their project will work until then. They hook up the two specimens to an electrical system and leave.
Peter and Olivia go to see Stuart Gordon, Paris' third patient. Like Crampton, Paris referred him to a hospital with a minor psychiatric ailment which then blossomed into schizophrenia, leading him to believe he was Sydney Greenstreet. Gordon was then miraculously cured two days ago. As they drive, Olivia admits that she can't get into Newton's head to figure out what his motive is. Peter assures her that it isn't just her fight.
Olivia confirms that Gordon has a surgical scar like Crampton. She calls Astrid, who passes the information on to Walter. He notices that Paris proscribed a drug only given to organ-transplant patients, but there's no record of an organ transplant. Walter realizes what's going on. When Peter and Olivia arrive, he explains that a human brain can be removed and given nutrients and electrical stimulation to be kept alive. Paris placed brain tissue inside of the three patients' brains. The brain scans show that they had foreign tissue, and Paris had proscribed anti-rejection drugs. The foreign matter caused the psychiatric conditions due to incompatibility. Once the tissue was removed, the patients were fine. Astrid gets a call from Dr. West, who tells her that they checked with affiliated facilities. Astrid finishes the call and tells Peter something privately. They both look at Walter and Peter asks his father if he had any visitors. Walter doesn't remember any. However, according to the records, Paris visited Walter on six separate occasions. Peter looks at the back of Walter's head and finds the same surgical scar, except older.
Peter takes Walter for a MRI. He warns Peter that the GPS chip is in his neck, but Peter reminds him it's made of silicon and suggests he takes some Valium. Walter admits he's worried about what Paris did to him, and Peter assures him that they'll find out. Peter watches through the observation window as Walter is slid into the MRI chamber. Afterward, Peter has Walter taken home and waits for the results, and Olivia comes to see Peter. Peter figures that Walter is hoping to find a way to restore his sanity. Olivia suggests that Walter going crazy may have made him a better person, and certainly made him a better father. Peter guiltily says he should have visited Walter at St. Claire's, but Olivia tells him he's making up for it now.
Dr. West shows them the MRI, which reveals three scars that go all the way into the gray matter. Brain matter was removed from the hippocampus, which controls long-term memory and inhibitions. Peter takes the MRIs of the other three patients and combines them, and it reveals a perfect fit.
Astrid takes Walter home, and Walter is still dizzy after having miscalculated the dosage. He refuses to go to a hospital and says he needs an album from the lab to help come down from his Valium high. Astrid leaves to go get it.
Peter figures that Paris removed Walter's memories of how to open the door between worlds, and that Newton will need Walter to interpret all the memories. They call Astrid and tell her to get back to the house.
Walter is still recovering from the Valium when he hears a pounding on the door. He answers it and finds Newton there to greet him.
Olivia and Peter arrive to find that Astrid has already discovered that Walter is gone. Peter gets the tracking device for the implant chip that Walter placed in his neck.
Smith puts a device on Walter's head while Newton's team leader gives Walter a sedative.
While Peter and Olivia follow the signal, Newton explains to Walter that the brain isn't static and they need to calculate where the new connections are. They start to scan Walter's brain.
Peter, Olivia, and a FBI team follow the signal to a public restroom. Peter finds the implant in a sink and then kicks in a toilet stall door in frustration.
Newton shows Walter a series of photos and asks him to tell the truth about what he sees. Walter realizes that he's using associations to map his brain function and locate his neural pathways. He asks if Newton is trying to fix him, but Newton admits that he isn't. They proceed and several of the images remind him of Peter… including a coffin. Smith warns that Walter isn't making the connection and Newton says they need something more powerful. He realizes that sound and smell should provide a stronger stimulant to Walter's memories.
Back at the lab, they figure that the brain tissue will only last so long so the Hybrids must be close. Peter realizes that the three patients' obsessions all tie together. Slater's girl in the red dress lived across from Peter at Cambridge. She lived at 2828 Green Street, and Peter concludes that Newton and the Hybrids will take Walter back to his old home to stir his memories.
Newton and his people arrive at Walter's old house, where the Rabels currently live. Walter talks about the trees. Newton explains that in his world, the trees and the grass were killed by the Blight. He then connects Walter to the three brain fragments in their nutrient baths. Walter takes on a more arrogant demeanor and demands to know where his wife and son are. Newton asks him how he built the door between worlds. Walter asks how things are on his side of door and Newton admits it's getting worst, and then asks if Walter is willing to lose Peter again.
As Olivia and Peter approach the house, Smith calls the team leader and informs them they have company. Newton has what they need and they quickly dismantle their equipment and give Walter an injection to render him unconscious. Peter bursts in seconds later and runs to Walter. His father wakes up and says "Hello, Son," while Olivia frees the Rabels and goes after Newton. She gets to the street and fires at the team leader as he drives their van away. The van crashes and Smith bursts out. Olivia shoots him in the head and tells Newton to come out. He raises his hands and carefully emerges. She slams him to the ground and handcuffs him.
At the house, Walter tells Peter that his brain tissue is dying and he'll never get back the memories they contained. Walter says "Hello, Son," says it again, and then gags and collapses.
In the street, Newton tells Olivia that he injected Walter with a neurotoxin. It will kill him in four minutes unless he's released. Olivia calls Peter and confirms that Walter is dying. Newton tells her to tell Peter there are three vials in a medical kit that must be injected in the correct order. He tells her she has 40 seconds to give her the phone and run back to Peter, and he'll tell her the sequence. As Peter begs Olivia to help, she finally gives up the phone and runs back to the house. When she arrives and talks to Newton via Peter's phone, Newton tells her the correct sequence. As Peter gives Walter the injections, Newton tells Olivia that he now knows how weak she is and hangs up. Walter revives and complains about a headache and a craving for chicken wings, and Peter embraces him.
Later, Olivia admits to Broyles that she made an emotional choice. The brain tissue is dead and they don't know what Newton got from Walter. She's worried that they've got nothing, but Broyles tells her that they've given their enemy a name and a face, and she saved Walter. He assures her that she made a rational choice: they could do without Newton, but there's only one Walter Bishop and they'll need him before it's over… and they'll need her, too.
Walter goes in for another MRI and Peter apologizes for not visiting him at St. Claire's. Walter assures him that if Peter had come to see him, he wouldn't have remembered. Peter goes out and the MRI scan begins. As Walter undergoes the scan, he remembers "Dr. Paris," actually William Bell, prepping him for surgery. Bell admits that there's no other way to remove the memories of how to build the doorway. However, he'll put the memories in a place that only he can find. He then tells Walter to think about the door he designed.