FBI special agents Fox Mulder and Dana Scully are assigned to the X-Files, a unit that investigates unsolved cases involving paranormal phenomena, alien encounters, and government conspiracy. Mulder, a believer driven by the childhood abduction of his sister, seeks definitive proof of extraterrestrial life, while Scully, a medical doctor and skeptic, is initially placed alongside him to apply scientific analysis and debunk his theories. Their dynamic of faith versus reason drives every investigation.

The three-volume manga adapts six key episodes from the first season of the television series. Volume 1 presents the Pilot, in which Mulder and Scully investigate a series of abductions linked to a mysterious alien abductor, and Ice, where a team of scientists at an Arctic research station becomes infected by a parasitic extraterrestrial organism. Volume 2 covers Squeeze, the hunt for a mutant killer who can compress his body through vents and ductwork, and Beyond the Sea, in which a convicted serial killer claims to have psychic visions that may help locate a kidnapped woman, challenging Scully’s skepticism when she experiences her own paranormal connection. Volume 3 includes Fire, involving a pyrokinetic assassin targeting a British diplomat’s family, and Shadows, where a deceased industrialist’s vengeful spirit uses telekinesis to protect his daughter and expose corporate wrongdoing.

Throughout these cases, the agents uncover hints of a larger shadow organization that controls information about extraterrestrial life, and their partnership deepens as they confront monsters, mutants, and forces beyond conventional science. The manga faithfully recreates the show’s eerie atmosphere and balances standalone horror stories with the ongoing mythology of alien colonization and government secrecy.