After what happened during the season finale of season eight, Fox Mulder goes into hiding. Dana Scully is again reassigned to the FBI Academy and Monica Reyes becomes John Doggett's new FBI partner at the X-Files office. Doggett asks Scully for help on a case involving an EPA official, Carl Wormus, who died after his car was forced off a bridge by a woman he picked up. Doggett and Walter Skinner travel to a reclamation plant, to find any links between Wormus' work and death. After doing an illegal autopsy on Wormus, Alvin Kersh sends Brad Follmer to locate Doggett. The investigation at the reclamation plant leads to an unknown woman, whose identity is later found to be Shannon McMahon, one of Doggett's former Marine associates. She reveals to Doggett that she is a "Super Soldier". This leads them to a clandestine laboratory where a secret experiment is taking place on board on a naval ship. They later find connections with the experiments on the ship to Scully's child, William.

Hopeful about reuniting with Mulder, a complete stranger offers his service to drive Mulder out of hiding. Scully takes the offer, but unknowingly gets herself and Mulder in even more danger. The "Shadow Man", a government agent, follows Scully. It is then discovered that he is a "Super Soldier" bent on killing Scully and Mulder. As confirmed in this episode, a "Super Soldier"'s only weakness is magnetite, which leads to the death of the "Shadow Man". Later on, Scully, Doggett and Reyes find evidence of a dangerous UFO cult which has found a second spacecraft similar to one Scully studied in Africa two years ago. Misled by the FBI, the agents enlist the help of The Lone Gunmen to protect Scully's son after they learn that the UFO cult apparently intend to kill the child. Doggett is run over by a car, leading him to be sent to the local hospital. As Follmer and the "Toothpick Man" are trying to uncover the plans of the three agents, Scully and Reyes leaves Washington, D.C. to find Scully's son.