In Boston, Massachusetts, Natalie calls her husband Randy. He claims to be leaving on a business trip but he's actually at home, leaving her flowers and a card as a surprise. As she says she'll be home in five minutes, the television switches on by itself. After Randy hangs up, he turns off the television and looks to see if anyone is there. A light goes off down the hall and he switches it back on. He puts the flowers and card by the door and the light goes off again. When he turns it on, a shadowy silhouette appears and walks toward him.
A few minutes later, Natalie arrives and sees the flowers and card. She finds him sitting on the couch, staring into space. She reaches forward to touch him and he dissolves into ash.
Broyles is at a restaurant and sees a little boy watching him. The boy briefly imitates him and hides behind his menu, but when Broyles gets a call, he quickly leaves. The Fringe team is at Randy's apartment examining the ash and determining there were no signs of forced entry or signs of a struggle. Walter notes that the couch shows no signs of burning and then asks for vacuum cleaners so they can take the dust to the lab. Broyles arrives and Olivia briefs him. He wonders if the man worked in a hospital or has visited one in the last 24 hours, and Broyles says he's seen the phenomenon before.
Broyles goes to a storage facility with the team and explains there were five similar killings four years ago. Each victim worked at or visited Tyson General Hospital. After the third death, he was contacted by an Eastern European man with details only the killer would know. The man offered to turn himself in if they could decipher his formula. Broyles gives them the formula that he has in storage, and Peter identifies it as a complex organic compound. Peter takes the notes to Walter while Olivia gets a call confirming that Randy visited his mother-in-law at Latchmere General Hospital in Boston.
At Latchmere, Nurse Darla is working when the shadow figure moves through the hallway behind her. It slips past her and continues down the hallway.
The next day, Broyles arrives with the team and asks to review the HR records. They present a warrant to go through their servers and set up in her office.
At the lab, Walter checks the ash for excessive radiation but the remains lack even the normal amounts of radiation. Olivia calls and Peter tells her that Walter believes the formula is a "she." He takes the phone and starts talking, and then realizes the formula has titanium tetrachloride.
As FBI agents go over the HR files to find an employee of Eastern European ancestry, Olivia suggests that Broyles go home while she waits. He refuses and Olivia asks him why the killer called him. Broyles explains that the man was distraught and couldn't control himself.
That night, a nurse is tending to a patient, unaware that the shadow figure is behind her. A fly lights on the patient, disrupting it and turning it into ash. The nurse sees it and screams, and Broyles and Olivia come to investigate. Broyles seals off the floor while the FBI agents come up with the name of Tomas Koslov, who worked at Tyson and then transferred to Latchmere. He didn't show up for his shift that night. They go to Tomas' apartment but he's nowhere to be seen and they figure he saw them at the hospital.
The FBI goes over Tomas' apartment and discovers he was building some kind of electrical equipment. Broyles determines that "Tomas Koslov" is an alias and the parts were made in Russia. There is a good print and Broyles has the team run it through the computers.
Back at headquarters, Broyles plays back a recording of his conversation with Tomas. In it, Broyles admits that they were unable to analyze the format and asks for a meeting, but Tomas hangs up on him. Senator Van Horn calls Broyles and arranges a face-to-face meeting. Van Horn reveals that a flag went up at the CIA when they got word of Tomas' fingerprints, and they're taking over the case. Broyles insists on pursuing the case and Van Horn explains Tomas is at the center of an international investigation conducted by the Russians. According to the Russians, Tomas removed property belonging to the Russian Federation. Broyles doesn't want to drop his case but Van Horn admits it's above his head and there's nothing he can do. Broyles offers his regards to Van Horn's wife and leaves.
Tomas checks into a hotel and hooks up a series of car batteries to his apparatus.
Broyles calls Olivia to tell her the CIA is now handling the case. He tells her not to put anything down on paper from now on. Olivia wonders who is going to protect Broyles if he doesn't comply with his superiors, but Broyles insists he knows what he's doing. A security guard goes over the footage and shows Olivia a shadowy figure with nothing to cast it. Olivia tells Broyles that he'll want to see it.
Olivia takes the footage to the lab and Walter goes over it. He believes the stolen Russian technology allowed Tomas to become a shadow, and admits even 40 years ago the Russians were doing work in Fringe science.
At headquarters, Broyles receives a top secret file from Van Horn. The information reveals that Tomas, whose real name was Timur Vasiliev, abducted his brother Alex, a cosmonaut. According to the Russian government, they don't know what happened to Timur's brother. Since then, Timur has been moving his comatose brother from hospital to hospital. Broyles figures that Timur's brother is still at the hospital in the coma ward.
Walter explains to Astrid and Peter that the shadow entity is absorbing radiation from the victims, causing them to disintegrate. Each victim was undergoing radiation treatment, while Randy had a window seat on a flight and absorbed relatively high levels of radiation from the sun. The entity then followed him from the hospital.
At Latchmere's coma ward, the power goes out and a nurse, Maxine, goes to check on the patients. She turns and finds Tomas there. He tells her he needs to take his brother and disconnect the monitors, and regrets the fact she's there. He prepares to inject her with a hypodermic.
A few minutes later, Broyles and his team arrive. The patients are all there but Maxine has disappeared. They find her shoe and follow the trail to a bed. She's been sedated and they realized Timur swapped her for his brother and escaped.
Olivia and Broyles go to the lab where an agitated Walter is going over the formula. He explains that there's something inside of the cosmonaut. He took a spacewalk and brought something back. Walter believes that the organism can project a version of itself, the shadow entity, while remaining inside the cosmonaut's body. Broyles wants to know if they can leave a message telling Timur that they have solved the formula, and Walter believes he can. He says he needs something from home first and leaves.
Later, Timur checks his voice messages while tending to his brother. Broyles has left his number and the information that he has solved the formula. Timur hooks Alex up to the batteries and turns on the power, containing the shadow entity as it tries to escape. However, his efforts prove temporary and the entity tries to escape again. Timur manages to contain it and Alex briefly flatlines. Finally he revives and Timur sighs in relief.
Peter follows Walter home and his father gets out a box of Tinkertoys from his luggage.
Astrid prepares to trace Timur's call while Olivia asks Broyles why the case is so important to him. He finally tells her that the government started depriving Fringe Division of necessary funds. Broyles obsessed about the case and drove his wife away as a result.
Walter builds a physical representation of the formula using the Tinkertoys but realizes something is wrong.
Timur talks to his comatose brother and admits he's tired of running. He then calls Broyles while Olivia calls Walter. Walter tells her the bad news: it's impossible to remove the entity from Alex without killing them both. Broyles tells Timur about the merge and says that his people can help, but only if they examine Alex. Timur insists he doesn't want his brother harmed and can contain the entity, and Broyles says he can trust them. However, the entity gets loose and kills Timur before escaping.
Astrid runs the trace and they go to the hotel, where they discover Timur dead. Alex is in the van where Timur had placed him before dying. Walter examines Alex and says they need a lead case. However, he realizes that the shadow has left. Peter suggests they draw the shadow back by distressing the host body with electro-shocks. Walter agrees to try.
A young girl, Tara, is watching TV in her hotel room. Broyles hears her scream and shoots Alex in the head, killing him.
In the hotel room, the girls' mother checks on Tara and confirms she's alive. Tara says that there was a shadow man and he disappeared.
Russian agents arrive to take Alex's body away in a shielded containment unit.
Later, Broyles goes to see his wife Diane. He tells her that he closed the case and she congratulates him, and then invites him in to dinner with her and her new husband. He declines and wishes her good night. As he goes to his car, a man appears from the shadows and says he has a friend in Senator Van Horn. However, the man warns that when someone disobeys the CIA's cease and desist, it can lead to danger. He emphasizes that there shouldn't be a report and starts to walk away. Broyles asks what they did with the cosmonaut. The CIA man admits that they had no choice once Alex started breathing again, and looks up at the sky before driving away.