Inside a retirement home, Michael Lanyard opens a box filled with memorabilia. Amongst the many items contained within is a small wooden matryoshka doll. In flashback, in the year 1945, a much younger Agent Lanyard meets with Clyde Tolson, then Assistant Director of the FBI. Tolson shows Lanyard a slide of a mangled body. He explains that the victim was Dr. Carew, a physicist who had been hard at work on an experiment critical to the Allied victory in the war. Back in the present day, the elderly Lanyard places a gun to his head and pulls the trigger.
Baldwin and Emma are assigned to investigate Lanyard's death. Baldwin dismisses the incident as a simple suicide. But Emma's interest is piqued when she discovers Peter Watts' name listed in the retirement home's guest register. She and Frank access folders containing Lanyard's case files and begin to read the contents within.
In flashback, Lanyard drives towards Los Alamos. He is intercepted by General Groves, who attempts to set ground rules for the murder investigation. But Lanyard counters that his authorization goes all the way to President Truman himself. He requests to be driven to Dr. Alexander's residence. When he enters Alexander's home, he finds it vacant. Lanyard searches through some drawers and comes upon a receipt for $10,000 to bail out a man named Warren Kroll. Dr. Alexander interrupts Lanyard's progress. Lanyard demands that he identify Warren Kroll, but the conversation is interrupted when Alexander's young daughter, Natalie, runs into the room. Alexander scoops Natalie (who clutches a matryoshka doll) into his arms, ending the discussion. Later, Lanyard reports back to Tolson by phone. He explains that Warren Kroll was jailed for assault two days before the murder, and was later bailed out of jail by Alexander's nanny, Lily Unser. It turns out that the bail money was withdrawn from Alexander's account. Later, as Lanyard observes the Alexander house from the shadows, he hears a fight break out. Lanyard races inside, where he is attacked by a wild-eyed Kroll. Several M.P.s storm into the house and pin Lanyard to the floor.
Back in the present day, Emma and Frank finish reading the file. On the reverse side of the last piece of paper in the file is an ouroboros, doodled in pencil. Later, Emma approaches Watts at Lanyard's funeral. Watts denies that Lanyard was ever a Group member. He tells Emma that Alexander defected to Russia with plutonium. With the case seemingly at a dead end, Emma researches Lily Unser's name on her computer. She discovers that Unser is a patient at a mental hospital. Unser tells Emma and Frank that Kroll is dead. After performing more research, Frank concludes that Kroll is buried at Los Alamos and labeled as a "John Doe." Frank has Kroll's coffin unearthed. He discovers a lead box, covered with cautionary radioactive symbols, inside. The "hot" box is moved to a nuclear containment room. Inside is a well-preserved male body. Frank recognizes the corpse's face as Dr. Alexander's.
When Lily learns that Alexander's body has been exhumed, she become more cooperative. She tells Emma that Lanyard was arrested by the M.P.s and ordered to stay off the base. Instead, he returned to Alexander's house and, fearing for Natalie's safety, attempted to take the little girl away. However, Alexander detected his presence. Lanyard handed the little girl to Lily and instructed her to leave at once. Suddenly, Alexander literally transformed into Kroll. Moments later, Lanyard discovered a hidden lab inside Alexander's house. Alexander told Lanyard to bring the matryoshka doll to his daughter, as it contains pages explaining everything. Alexander then reached inside a lead vessel and retrieved some plutonium. He morphed into Kroll and attempted to walk out of the lab. But Lanyard knocked him to the ground. Before Alexander expired, he asked Lanyard to save his daughter. Lanyard attempted to retrieve the matryoshka doll, which rolled into a crevice at the side of the room during the scuffle. Suddenly, the sound of a car's engine filled the room. Lanyard rushed outside only to see Lily drive off with Natalie.
Back in the present day, Frank finds the matryoshka doll, still wedged in the crevice of Alexander's home. He tells Emma and Baldwin that Kroll and Dr. Alexander were the same person. It turns out that Alexander became obsessed with finding out how good men could create something so evil as the atomic bomb. So he experimented with plutonium, and attempted to split off the evil he felt inside himself. In doing so, he split off Kroll.
Frank realizes that Lanyard killed himself after he viewed a television news magazine featuring an adult Natalie performing secret biological research. Frank travels to a race track, where he confronts Peter Watts. Watts explains that, many years earlier, the Group had asked Lanyard to become a member of the organization. Frank pulls out the matryoshka doll and hands it to Watts. He asks him to give the doll to Natalie.
In flashback, Tolson and J. Edgar Hoover approach Lanyard about joining the Group. They tell him that Lily has already become a member. Lanyard is outraged that the men had Natalie kidnapped. He promises to turn in his letter of resignation and exits the room. After he exits, Hoover shows Tolson his drawing of the ouroboros, sketched on the back of the report.
In the present day, Natalie enters her office and discovers the matryoshka doll perched on the edge of her desk and the crumpled pages of her father's journal inside.