A powerful, invisible force shakes the darkened, deserted streets of Fairfield, Idaho. Two janitors watch in horror as the force smashes a plate glass window and crumples a car. A construction worker is killed as the force rumbles down a highway. Then, suddenly, a ten-foot tall Indian elephant materializes out of thin air. The pachyderm runs off until, finally, it grows exhausted and lays on the ground. As residents of the community watch, saddened, the elephant dies.
     Mulder and Scully investigate the incident. Mulder believes the invisible force and the elephant-whose name is Ganesha-are somehow connected. Ed Meecham, a worker at the Fairfield zoo, tells the agents that the animal's cage is still locked. At Meecham's suggestion, the agents question Willa Ambrose, a naturalist hired by the zoo's board of supervisors. Ambrose explains she was hired to redesign the zoo's restrictive pens to make them more humane environments. She explains that Meecham is from the "old school" and resents her involvement. Mulder and Scully interview Kyle Lang, an animal rights activist and member of the Wild Again Organization, who believes Ganesha was treated in an inhumane fashion by Meecham. But he is just as contemptuous towards Ambrose, whom he claims is attempting to gain custody of a gorilla so it can be kept in a cage at the zoo.
     Believing that members of the W.A.O. are responsible for releasing the elephant, the agents stake out the zoo. One night, a red-haired boy sneaks into the zoo with a night-vision camera. The animals become enraged. As the boy watches, horrified, a tiger dematerializes inside its cage. An invisible force strikes at the boy, ripping him to pieces. Mulder becomes convinced that some invisible force-not an escaped tiger-is responsible for the boy's death. He is intrigued by reports that no animals kept at the zoo are able to reproduce. Scully performs an autopsy on the elephant, and discovers that it was once pregnant. Ambrose assures her that the animal could not possibly have given birth without her knowledge. Shortly thereafter, the missing tiger turns up at a construction site. The agents, Ambrose and Meecham attempt to capture the animal. But when the tiger charges Ambrose, Meecham kills it.
     Mulder tells Ambrose about a theory of his involving aliens impregnating zoo animals for some unknown purpose. Using sign language, Ambrose questions Sophie. The gorilla relays her fears about a baby flying "into the light." Meanwhile, the zoo's board of directors, in an effort to cut costs, eliminates Ambrose's job. Sophie is prepped for her return to the wilderness despite Ambrose's conviction that the gorilla will be killed by poachers.
     Kyle returns to the zoo one evening looking for Willa. Instead, he finds Sophie's empty cage. Suddenly, a large crate crashes into Kyle, killing him. Scully discovers evidence that Kyle was murdered with a cattle prod. She arrests Ambrose for his death. Ambrose admits she and Ed Meecham joined forces and transported Sophie to an abandoned factory.
     When Mulder arrives at the factory, he finds Sophie in an uncontrollable rage. He and Meecham attempt to tranquilize the animal, but suddenly Meecham runs off, leaving Mulder alone with the gorilla. Sophie lashes out of the darkness and strikes Mulder. As Mulder loses consciousness, the animal disappears in a blinding flash of light. Later, Sophie's dead body is discovered on a roadside. Ambrose weeps and embraces the animal.