In a shocking revelation, Scully is diagnosed with cancer and Mulder must locate the group of female abductees shown in Nisei and 731 who also have the same disease.

At the start of the episode, Scully shows Mulder an X-ray indicating that she has cancer. Mulder is shocked. Scully remembers the MUFON members whom she met and quickly wants to contact them for help. When they reach the house of one of the abductees, Betsy Hagopian, they find that she has died and that someone is tapping into her computer files. They scan a trace on this and find that the man who downloaded the files is Kurt Crawford, another member of the UFO network. He tells the agents that all of the members have died apart from Penny Northern who is currently in hospital. Scully visits her in hospital and decides to be treated by Dr. Scanlon for cancer also.

Meanwhile, back at Hagopian's house, Mulder and Crawford are going through her files and discover that all of the abductees had been treated at the same fertility clinic. Mulder leaves and goes to visit Scully in hospital. Later, Crawford is shot and killed by X's assassin where he disappears in a pool of green bubbly liquid. He is obviously an alien clone.

At the fertility clinic, Mulder breaks in and discovers the real Kurt Crawford although he thinks it is the same one as before. They access the clinic's files and download the directory named 'Scully'. Mulder tries to convince Skinner to arrange a meeting with the CSM but he refuses. Nevertheless, Skinner still secretly receives help from him.

With all options down, Mulder turns to the help of the Lone Gunmen who break into the research facility via a tunnel. Realizing Dr. Scanlon is on staff, Mulder orders Byers to stop Scully's treatment immediately. Mulder comes across more Kurt Crawford's and realizes they must be clones. He comes across an incubator room containing many human clones including some of Samantha Mulder.

Suddenly the Gray Haired Man appears again (X's assassin) and traps Mulder between two security doors where he starts opening fire slowly breaking the glass standing between him and Mulder. But Frohike is just in time and breaks a code which enables Mulder to open one of the doors and run to safety. Mulder runs back to Scully where he finds her against Penny's bedside. She had died and Scanlon has left the hospital. Scully tells her partner that she is determined to fight the disease and continue her work on the X-Files.