Mulder and Scully's encounter with a man and his handicapped brother leads them to an indifferent genie whose willingness to grant wishes belies a deeper motive.
Mulder and Scully return to the site of their first investigation together when a series of abductions take place. However, Scully's failing health, and Mulder's concern that she is in danger, cause him to take her off the case. Meanwhile, the Cigarette-Smoking Man—on his deathbed—reunites with Marita Covarrubias (Laurie Holden) and Krycek in an attempt to revive the project.
While Mulder is away in England, Scully is led by coincidences, chance, fate and possibly a higher power to a married man with whom she had an affair during medical school, and a look at the life she didn’t choose, forcing her to make choices about her future.
While protecting a man due to testify against the Morley cigarette company, Skinner is horrified when the witness dies mysteriously. What the agents soon discover is that a new brand of cigarette has a dangerous secret.
An entrepreneurial Hollywood producer and college friend of Skinner picks up the idea for a film based on the X-Files division, however the agents find that the level of realism in their fictional portrayal is somewhat questionable.
Mulder and Scully cross paths with a pair of doppelgangers whose close proximity yields unlimited mayhem. Splitting up in two, the agent tries to find out "why" and "what" they are doing.
The Lone Gunmen summon Mulder and Scully to the headquarters of a video game design company when the new virtual-reality game, which the Gunmen helped design, is taken over by a bizarre female computer character whose power is much more than virtual.
After a prominent doctor discovers his father-in-law dead and the word "Theef" written on the wall in blood, Mulder suspects hexcraft may be the source of threats against the doctor's family.
After a young boy with cancer, whose parents do not believe in medical treatment because it is against God’s will, recovers miraculously, Scully is intrigued. What she soon discovers is that his cure is not miraculous, but scientific. Eager, if wary, to learn of the truth behind his secrets, Scully agrees to travel with the Cigarette Smoking Man to get the cure to all mankind’s diseases.
Mulder investigates what appears to be a missing case of a woman from a small town, but soon turns out to be a murder by a spirit summoned from the underworld. Scully, meanwhile, must endure an uncomfortable stakeout.