Mulder receives a cryptic tip from Deep Throat regarding an incident in which a fugitive eluded police after a high speed chase. During the escape, the suspect was shot and wounded by police before he fell into a lake. Despite many hours of dredging, the fugitive's body is not recovered. After some investigating, Mulder realizes that someone deliberately switched the car the suspect was driving with another vehicle.

The agents trace the original car to a Dr. Berube, a scientist who is not eager to cooperate with the FBI investigation. With the puzzling case at a dead end, Mulder prepares to give up. Yet Deep Throat makes contact and convinces him that the case is of extreme importance. Meanwhile, Dr. Berube's dead body is discovered inside the lab.

The police end their search for the fugitive without recovering a body. When they leave the lake, the mysterious fugitive resurfaces from beneath the water. Tiny gills in his neck allowed him to remain submerged for a long period. The fugitive makes his way to the city, and after attempting to contact Berube collapses on the street. As paramedics rush the fugitive to a hospital, they insert a needle into his skin. Suddenly, a rush of toxic gas is emitted from the fugitive's body. The paramedics are overcome by the fumes and the fugitive escapes.

With the help of Dr. Carpenter, Scully analyzes a flask taken from Dr. Berube's lab. The bacteria inside is suspected of being extraterrestrial in origin.

Mulder discovers a storage room containing human bodies suspended in a clear liquid. When he returns to the room with Scully, he finds that it has been emptied. Deep Throat explains that Dr. Berube had been experimenting with extraterrestrial viruses. He used humans afflicted with terminal illnesses as his guinea pigs. The experiment was funded by the US government, but officials were interested only in technology-not the patients' well being. One of those patients was Dr. Secare, a friend of Dr. Berube's. When it became clear that the government wanted Secare eliminated, Berube warned his friend and gave him his car to escape. When Secare was hunted down by police, he used his mutation to his advantage and hid beneath the lake.

Scully is stunned to learn that Dr. Carpenter was killed in a car accident. Shortly thereafter, Mulder locates Dr. Secare hiding in the attic of his house. The pair are surprised by a government official who shoots and kills Secare.

When Mulder disappears, Scully makes contact with Deep Throat. Deep Throat arranges for Scully to gain access to a top secret containment facility in Maryland. Scully steals an alien fetus, and with Deep Throat's help, arranges to exchange the fetus for Mulder. After Deep Throat makes the exchange, he is shot and killed by the government agents.

Later, Mulder tells Scully that the government is shutting down the X-files.