Mulder receives an encrypted computer disk containing the defense department's top secret files on extraterrestrial life and becomes a target. Scully takes him to a Navajo family that unearthed a buried secret to decipher the disk.

Scully finds her career with the FBI in jeopardy as Mulder is still missing and the Cigarette Smoking Man is pursuing the stolen files. The Navajo elders find Mulder's body in a cave and perform an ancient ceremony to call the spirit back to the empty vessel.

A.D. Skinner and Scully are at a standoff when Mulder bursts in and discovers that Skinner has the digital tape. Reunited, Mulder and Scully travel to a secret vault inside a mine and find an elaborate filing system of medical records which reveals that Mulder's sister may not have been the first choice for abduction. Meanwhile, Skinner deals with the Cigarette-Smoking Man for their safety.

Two scientists confer about each of their metal objects that were found in Africa and they theorize that the objects are pieces of a puzzle which could be undeniable proof that human, plant, and animal life did not originate on this planet. When one of the scientists is killed and the objects are stolen, the agents investigate and Mulder begins to experience severe neurological pain caused by the objects.

Scully frantically searches for a way to help her ailing partner without having anyone to turn to for help, while a catatonic Mulder's dreams lead him away from his mission and the X-Files to a place which he believes is a better life.