Mulder and Scully desperately try to protect the life of Jeremiah Smith. Not only is this mysterious man a link to the colonization plan-- his paranormal healing powers are Mulder's only hope of saving his mother's life. Close on their trail is the relentless alien bounty hunter: an assassin who is hard to escape. And harder to kill.

     With the assassin close behind, Smith leads Mulder to an eerie, isolated farm community. There, Mulder is stunned to see clones of his sister Samantha, who had been abducted by aliens as a child. Smith tells Mulder that these children have been bred as worker drones. Before Smith can reveal more about the "Colonization" conspiracy, they are set upon by the alien assassin. Mulder is helpless to save Smith or Samantha.

     Back in Washington, Scully's investigations into Smith's background lead her to a disquieting conclusion. All five of the identical men named Jeremiah Smith were secretly cataloguing the entire human population. But at whose orders? And why?

     Meanwhile, the Cigarette-Smoking Man and the Elder have identified X as a traitor. He is ambushed and gunned down. As he dies, he leaves behind one last ambiguous clue: the letters "SRSG" scrawled in blood.

     With his mother still in a coma, a despondent Mulder follows the last of his meager clues to the end of the line: the United Nations office of Special Representative to the Secretary General. An enigmatic official denies the Colony ever existed...as she hands him a folder containing photographs of the farm and of Samantha.