In Boston, Massachusetts, Natalie Rancik calls her husband on her cellphone. She thinks he's on the way to the airport on a business trip but he's actually at home preparing a surprise get-together for their anniversary. She says she'll be home in five minutes and hangs up. Randy hears the television turn on by itself and goes to check it out. He turns it off, unaware that a shadowy figure is following him. A light goes on by itself and he turns on the light, only to find himself confronting the shadowy figure... which has nothing to cast it. A few minutes later, Natalie arrives and sees Randy sitting on the couch. She touches him... and he breaks apart into ash.
Broyles is eating at a restaurant and a little boy starts imitating him. Broyles plays along until he gets a phone call from Olivia and quickly leaves. He goes to the Dancik apartment where Olivia, Peter, and Walter are examining what's left of Randy's body. There are no signs of forced entry or a struggle. Walter determines there are no signs of burning on the couch Randy was sitting on. Olivia briefs Broyles on what happened and he asks if Randy was either a patient or a visitor at a hospital in the last 48 hours. He tells Olivia that he seen a similar phenomenon before.
Broyles takes Olivia and Peter to the storage facility where he kept the evidence of the case from four years ago. He explains that there five similar deaths at Tyson General Hospital. An Eastern European man contacted Broyles after the third death and proved he knew about the murders. He offers to turn himself in if Broyles could solve a specific formula. Broyles gives the formula to Peter, who identifies it as a complex organic compound. Peter takes the formula to Walter while Olivia and Broyles confirm that Randy was recently at Latchmere General Hospital visiting Natalie's mother.
At Latchmere, the shadow entity stalks the halls. The next day, the FBI set up at Latchmere and present a warrant to search the HR records and set up.
At the lab, Walter uses a Geiger counter to check Randy's ashes for radiation, but realizes that it has less radiation than human ash normally would. He starts calling the formula "she" as he tries to understand it.
Olivia and Broyles wait while the FBI team goes over the HR files. She suggests that Broyles go home and she can wait for the results. He refuses and she wonders why the killer called him. Broyles tells her that the man he heard from was distraught and seemed to regret what was happening, and apparently couldn't control himself.
That night, a nurse checks on a patient in ICU and discovers that they've been transformed into ash. Broyles and Olivia come in and Broyles seals off the floor. The FBI agents tell him that they've confirmed that one employee, Tomas Koslov, worked at Tyson four years ago and is now at Latchmere. However, he didn't show up for his shift that night. They search Tomas' apartment and discover that he's already fled. There are electrical parts scattered all over the place. Broyles confirms that the man was using an alias and the parts are Russian. They lift a fingerprint from the components and start running a check.
The next day, Broyles listens to a tape recording he made of his conversation with Tomas, where the man hung up after Broyles was unable to solve the formula. He then meets with Senator Van Horn in a park. Van Horn explains that the fingerprint flagged a check at CIA headquarters. The CIA is taking over the investigation but Broyles refuses to let it go. The senator warns that Tomas is wanted by the Russian Federation, who claims he stole property from them. Broyles thanks Van Horn for his help, asks briefly after his wife, and leaves.
The man known as Tomas checks into a motel and brings in car batteries, and hooks them up to his equipment.
Broyles is at the airport and calls Olivia at the hospital to tell her they're going to continue with the case, but that they should keep everything off the record. Olivia worries that Broyles could get in trouble and wonders who will protect him. The security guard finishes reviewing the footage and tells Olivia that there's a shadow on the recording, despite the fact there's no one there to cast it. She takes it to the Harvard lab and Walter examines it, and he believes that the Russians developed their own Fringe science and somehow learned how to transform Tomas into a shadow.
Van Horn secretly sends a file to Broyles about "Tomas," whose real name is Timur Vasiliev. Timur abducted his brother Alex, a cosmonaut who returned from a space mission in a coma. Since then, Timur has brought Alex to the U.S. and has been moving him from hospital to hospital. They realize that Alex is still at Latchmere.
Walter realizes that the shadow entity is absorbing radiation rather than projecting it. It absorbs the high levels of radiations from its victims, stripping the atoms of their energy and causing them to transform into ash. Randy, the only non-patient, had a window seat on a high-altitude passenger plane and absorbed radiation. The entity noticed him at the hospital and followed him home to feed on the energy.
At Latchmere, the power goes out and a nurse goes to investigate. She finds Timur, who injects her with a sedative. Broyles and the others arrive a few minutes later and find the unconscious nurse. They determine that Alex is gone.
Walter calls Olivia and Broyles to the lab and explains that he now believes that the entity is inside Alex. It somehow got inside of Alex when he was in space, and projects the shadow entity to feed itself. Walter believes they can now solve the formula but needs something at home.
Broyles calls Timur and tells him that they are close to solving the formula. Timur is at the motel and hooks Alex up to the batteries. He triggers the electricity, shocking Alex and containing the entity. His brother briefly flatlines but finally revives.
Peter and Walter go to their house and Walter digs out a box of Tinker Toys.
While they wait for Timur's call, Astrid prepares to trace the call and Olivia asks Broyles why he's obsessed with the case. He admits that at the time, the government was threatening to cut off funding to Fringe Division. He became obsessed with the deaths and his wife left him as a result.
Walter uses the Tinker Toys to build a physical representation of the formula and solves it, but realizes that there's something wrong. He calls Olivia while Timur finally calls Broyles. Walter tells Olivia that he's learned that Alex and the entity have bonded and there's no way to remove it without destroying both of them. Broyles passes the news on to Timur, who insists he can contain the entity. He tells Broyles that he knows they need 60 seconds to trace the call, and Broyles tries to convince him that they can be trusted. The sixty seconds pass and the line stays open: Timur is dead, turned to ash because the creature has escaped.
They trace the call and go to the motel. Timur had transferred Alex to the van before he died. Walter examines the cosmonaut and believes they can contain the entity within a lead casing. However, the entity has projected the shadow again. As Walter starts to panic, Peter suggests that they use Timur's electrical equipment to shock Alex and bring the creature back. Walter agrees to try it.
In a nearby room, a young girl, Tara, is watching TV. The TV picture goes out and something moves in the closet.
Broyles hears Tara scream, draws his gun, and shoos Alex in the head.
Tara's mother runs to check on her daughter, who is staring at the television. Tara says that there was a shadow man in her room but he disappeared.
Agents in protective suits place Alex's body in a lead case with Russian lettering and take him away.
Later, Broyles goes to see his wife at her home. She tells him that he children aren't there but he says he's there for her. He tells her that he finally closed the case and starts to go. She invites him to come in for dinner with her husband, Rob, but Broyles gently turns her down and walks toward his car. A CIA agent is waiting for him in the street and congratulates him, saying that Senator Van Horn is a loyal friend. He warns Broyles that it's dangerous when people disobey CIA cease & desist orders. He tells Broyles not to file a report and starts to walk away. Broyles asks what they did with Alex and the CIA agent says that Alex didn't die despite the lethal head wound. They had no choice but to send him back. The man glances up at the sky and then leaves.
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