WHEN SCULLY IS DIAGNOSED WITH CANCER, MULDER HUNTS FOR RESEARCH FILES PERTAINING TO A GROUP OF FEMALE ABDUCTEES WHO ALSO CONTRACTED THE DISEASE.
Scully shows Mulder an MRI x-ray indicating a cancerous mass has been detected on the wall between her sinus and cerebrum. The tumor's placement makes it inoperable. Instead of requesting a leave of absence, Scully opts to follow another avenue of investigation: contacting a group of purported female abductees who experienced similar symptoms after having implants removed from the base of their necks.
The agents travel to the home of Betsy Hagopian in Allentown, Pennsylvania. A realtor informs them that Hagopian (one of the female abductees) passed away two weeks earlier. While searching through Hagopian's house, the agents realize someone is downloading computer files via phone modem. A tap is placed on the line, and the source of the call is pinpointed. The agents take Kurt Crawford, the man who downloaded the files, into custody. Crawford explains that he and Hagopian were both members of the same UFO network. He claims he downloaded Hagopian's files because the government is out to destroy them. Crawford also reveals that all of the women who claimed they were abducted by aliens died of similar tumors-with the exception of Penny Northern, who is confined to a hospital bed.
Scully visits Northern at the hospital. Northern reveals that a Dr. Scanlon, who has been treating her cancer, may have isolated the cause. Dr. Scanlon begins treating Scully's cancer. Meanwhile, Mulder and Crawford search through hard files in Hagopian's basement. They discover that all of the woman abductees, including Northern, were treated at the same fertility clinic in Pennsylvania. Mulder leaves Crawford in the basement to attend to Scully (who decides to check into the hospital). Later that evening, the Gray-Haired Man (the same man who killed X) shows up and kills Crawford, whose body melts into a pool of green liquid.
Meanwhile, Mulder breaks into the fertility clinic. Inside, he discovers Kurt Crawford (Mulder is unaware of the other Crawford's death). They access a computer terminal and download a directory containing Scully's name. Mulder then approaches Skinner and attempts to arrange a meeting with The Cigarette-Smoking Man. But Skinner refuses, insisting The Cigarette-Smoking Man deals only in lies. Nonetheless, Skinner secretly enlists The Cigarette-Smoking Man's help.
Mulder turns to the Lone Gunmen. The foursome infiltrate the research facility via a subterranean tunnel. Once inside, Mulder realizes Dr. Scanlon is on staff. He instructs Byers to find Scully and stop her treatment immediately. As he continues through the building's corridors, Mulder encounters additional Crawfords and realizes Kurt is a clone. He finds several of them dressed as doctors inside an incubator room housing tanks containing human forms, including those of Samantha. One of the Kurts shows Mulder a cold storage room containing vials of human ova. The eggs were harvested from women during their abduction, which were later used for reproduction. Mulder realizes the women are the Kurts' birth mothers-and the clones are actually working to save their mothers' lives.
The Gray-Haired Man arrives at the clinic and traps Mulder between two security doors in a quarantine wing. The Gray-Haired Man opens fire, slowly cracking the bullet proof glass that stands between himself and his prey. Working feverishly, Frohike breaks a computer code from a remote location, allowing Mulder to open the outside door and run to safety.
When Mulder returns to the hospital, he finds Scully at Penny's bedside. Byers arrived in time to stop Scully's treatment, but Penny Northern had died and Dr. Scanlon was gone. Scully tells her partner she has decided to fight the disease and continue her work.