Scully shows Mulder an MRI x-ray indicating a cancerous mass has been detected on the wall between her sinus and cerebrum. The tumor is inoperable and if it grows, the chance for survival is slim. 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 where Scully had met these women before. 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. The call is traced, and the agents apprehend Kurt Crawford, the man who downloaded the files. Crawford explains that he and Hagopian were both members of the same UFO network and 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 now hospitalized and near death from cancer.

     Scully visits Northern at the hospital, who reveals that Dr. Scanlon, who has been treating her cancer, may have isolated the cause. Seeing her future self in Penny's condition, Scully checks herself in and Dr. Scanlon begins treating her 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. When Scully asks Mulder to bring her overnight bag to the hospital, Mulder leaves Crawford in the basement to attend to Scully. 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 a federally-subsidized fertility clinic where all the female UFO network members were patients. 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. Near the breaking point, Mulder demands that Skinner 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, who tell him that the fertility clinic's mainframe is housed in a high-security federal research facility. The foursome infiltrate the research facility, and 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--including a vial with Scully's name on it. 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.