In Fairfield, Idaho, two janitors witness an invisible force storm down a city street; a road worker is later killed by the force on the highway. The next day, an elephant suddenly materializes in front of an oncoming big rig. The driver manages to stop in time, but the elephant soon collapses and dies, over forty miles away from where it disappeared the night before at the Fairfield Zoo.

Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) survey the damage in the city, which appears to have been caused by an elephant even though none was seen. Ed Meecham, an animal handler at the zoo, recounts how he came to the elephant’s locked cage to find it empty. His boss, Willa Ambrose, tells the agents that the zoo is in danger of closing due to other animal disappearances. She blames the zoo’s decline on an animal rights group which is known to free captive animals. The group’s leader, Kyle Lang, denies any involvement in the elephant’s release. Lang tells them that Ambrose is being sued by the Malawi government over a lowland gorilla she took from their country ten years prior.

Mulder contacts Frohike and Byers, who say that Fairfield is known for its animal disappearances and UFO sightings. They also mention Ambrose’s gorilla, who is known to communicate using American Sign Language. Meanwhile, Scully follows one of Lang’s activists as he sneaks into the zoo, running into Meecham inside. The activist attempts to free a tiger, but after a flash of light, the tiger seemingly disappears. The activist is promptly mauled to death, with the killing captured on his night vision camera. When questioned, Lang denies any responsibility for the death. Ambrose introduces the agents to the gorilla, Sophie, who has been cowering in her cage and expresses an apparent fear of light.

Scully performs a necropsy on the elephant, revealing it to be pregnant — which is impossible, since the animal had never been mated. The tiger reappears at a Boise construction site, and is shot dead by Meecham when it charges at Ambrose; the zoo is shut down the next day over the incident. Mulder tells Ambrose that the tiger was also pregnant, and explains his theory that extraterrestrial aliens are impregnating all the female endangered animals as part of “their own Noah’s Ark.” Mulder thinks that Sophie too is pregnant and that she is worried that her baby will be abducted. Sophie confirms Mulder’s suspicions when she makes signs for “baby go flying light”.

Sheriff’s deputies order Ambrose to release Sophie into protective custody, presumably to be sent back to Malawi. Ambrose unsuccessfully seeks help from Lang, her former boyfriend, but he advises to let Sophie return to the wild. Lang later goes to see Ambrose at the warehouse where Sophie is being prepped for shipping, but finds her cage empty. He is then mysteriously killed by a falling crate. Scully finds that Lang was struck with a cattle prod and suspects Ambrose of killing him, but she claims that Meecham is responsible. Mulder goes to arrest Meecham, who is keeping an angered Sophie at another warehouse near Boise. Meecham suddenly locks Mulder in Sophie’s room, where the enraged gorilla attacks and injures him.

A bright light appears and causes Sophie to vanish, but not before she gives Mulder a final message in sign language. When Mulder gives the message to Ambrose the next day, she says it means “man save man.” Ambrose and the agents are then called to the highway, where Sophie has been struck by a car and killed. Ambrose and Meecham are both charged with manslaughter for Lang’s death. As the agents leave Idaho, Mulder says through narration that he believes alien conservationists were behind the events in Fairfield.[1][2]