S2E2 · The Host

On a Russian freighter off the coast of New Jersey, a crewman trying to fix the ship's toilets is pulled into the septic system. His water-logged body appears in the sewers of Newark days later. Fox Mulder is assigned the case and is shown the still-unidentified body. Mulder initially assumes the case is simply a gang-related murder, and angrily confronts Assistant Director Walter Skinner, feeling he has been given this "wild goose chase" as a form of punishment. That night, Mulder talks to Dana Scully, telling her that he is thinking of leaving the FBI. Scully performs the autopsy on the crewman's body, finding a Russian language tattoo on his arm and a flukeworm inside his liver.

In a Newark sewer, a city sanitation worker named Craig is rescued when an unseen creature pulls him underwater. Believing he was attacked by a python, he visits a doctor with Mulder observing. An examination of his back reveals an abnormal four-pointed wound. Shortly afterwards, Mulder receives a call from a mysterious man, telling him he has a friend at the FBI. Scully shows Mulder the flukeworm, whose mouth, though much smaller, matches the wound on Craig's back. That night, Craig dies in his shower after coughing up a flukeworm. Mulder visits a sewage processing plant and, along with a foreman named Ray, finds a large humanoid mutant with a fluke-like mouth.

At the FBI Academy, someone slips a newspaper article under Scully's door enabling her to identify the original body. Mulder and Scully meet at the processing plant and observe the "Flukeman". Skinner wants to prosecute the creature and subject it to a psychiatric evaluation, which Mulder thinks would be difficult. Skinner tells Mulder of Craig's death and admits that this should have been an X-file. Mulder insists that Craig's death could have been prevented if the X-files had remained open, but Skinner implies that the decision came from higher up the chain of command.

That night, as the Flukeman is being transported by van, it escapes its restraints and kills the driver. It hides in a portable toilet, is soon suctioned into a septic truck and is brought back to the sewage processing plant. Meanwhile, Mulder receives another call from the mysterious man, telling him that the X-files must be reopened. Scully tells Mulder that the flukeworm she discovered is a larva, revealing that the Flukeman is capable of asexual reproduction. Meanwhile at the plant, the Flukeman is spotted in a storm drain overflow pipe, with Mulder realizing it is using the drain to make an escape back to the ocean. Mulder and Ray then investigate the overflow pipe, but Ray is pulled underwater by the Flukeman. Mulder rescues him, bisecting the Flukeman at the waist with a sewer grate.

Scully concludes her investigation, hypothesising that the creature was brought to the U.S. by a Russian freighter that was hauling salvage material from the Chernobyl disaster, and that the creature was created in a "soup" of radioactive sewage. Elsewhere, in the drains beneath Newark, the Flukeman's eyes remain open.

In the 2013 comic continuation of The X-Files called Season 10, a two-issue story, "Hosts", continues the story almost twenty years later after the events of this episode. According to the comics, the Flukeman escaped to Martha's Vineyard and began to multiply, abducting multiple beach-goers. The Flukeman and its offspring were nearly all killed, however, by a man revealed to be one of the Chernobyl liquidators. In addition, the story expanded upon the Flukeman's backstory, revealing that he was a liquidator named Gregory, who, after being locked in a sewage tanker truck at Chernobyl, gestated the mutated flukeworm that grew into the original Flukeman after he was exposed to irradiated cooling water from the still-burning nuclear reactor and to flatworms in the sewage tank.