In an episode that is probably on par with Home on the horror scale, Mulder and Scully must track down a disgusting flukeman living in the sewers before it kills again.

On a Russian ship, a young Soviet seaman has the dirty job of inspecting the sewer system. Suddenly as he is doing this, he is yanked into the murky worker as the other workers frantically try to save him. The boss tells them to flush the tanks. Later he turns up as a John Doe in the New Jersey sewer system.

Mulder is relieved from the assignment he is working on to investigate this foul case which he doesn't seem to happy about, particularly as it just seems like a case that shouldn't be bothered with by the FBI. Mulder goes to see Skinner demanding to see him as he storms on a meeting that is being conducted. He complains that the case is meaningless and that he will not continue investigating it.

Mulder and Scully arrange another secret meeting on a park bench. Mulder tells her that he is thinking about quitting the FBI. Scully finds hope in this saying that he could request a transfer to Quantico where they could continue working together but Mulder replies saying that "They don't want us working together, Scully.".

Later, after a phone call with Scully, Mulder receives another anonymous call saying that he has a "Friend at the FBI". Meanwhile, Scully conducts an autopsy on the John Doe and discovers some sort of flatworm attached to the subject's liver. Back under the sewers, a sanitation worker is also pulled under the water by the flukeman but his fellow mate manages to save him. He discovers a strange bite on his friend's back which when analysed cannot be identified. Mulder goes to visit the man who is being checked over and is complaining of a strange taste in his mouth. Later, while in his shower, blood suddenly emerges from his mouth as he falls to the floor. A flatworm also comes out of his mouth as it disappears down the plug-hole back into the sewers.

Mulder goes to a sewage processing plant in an attempt to find out about this flukeman. Meanwhile, a sanitation worker spots something moving in the waters so flushes the system. He traps the 'thing' in a tube where they can all see the disgusting creature (I'm not talking about Darin Morgan by the way, folks). Mulder and Scully analyse the flukeman which appears to not have any sex organs.

Later, Scully (with the help of an anonymous tip) finds out the identity of the John Doe as a Russian. Meanwhile, an federal marshal is driving the flukeman in an ambulance to a fellow hospital but when he looks in his mirror the worm is gone. When he goes in the back to investigate he is killed. The flukeman, now free, crawls back into the sewers via the help of a portable toilet and a sewage tanker. Mulder realizes the flukeman is hiding back in the sewer plant so rushes back there. With the help of a foreman who gets dragged into the water by the flukeman, Mulder is able to kill it off forever by dropping a gate on it which chops it into two pieces (Eewww!).

Mulder and Scully again meet where Scully concludes that the creatures must have been formed by large amounts of radiation as a result of the disaster at Chernoybl. Mulder remarks that "species are disappearing off the planet everyday, you wonder how many new ones are being created" as we see, back in the sewers, the flukeman opening it's eyes ready to kill again....