Doggett and Walter Skinner (Mitch Pileggi) travel to a reclamation plant, looking for links between Wormus' work and death. After doing an illegal autopsy on Wormus, Alvin Kersh (James Pickens, Jr.) sends Brad Follmer (Cary Elwes) to locate Doggett. The investigation at the reclamation plant leads to an unknown woman, whose identity is later revealed to be Shannon McMahon (Lucy Lawless), 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 between the experiments on the ship and Scully's child, William. After Scully begins to miss Mulder, a complete stranger—the "Shadow Man" (Terry O'Quinn)—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", who is revealed to be a "Super Soldier" bent on killing Scully and Mulder. After a chase through a quarry, the "Shadow Man" is destroyed after being exposed to magnetite. Later, Scully, Doggett and Reyes find evidence of a dangerous UFO cult which has uncovered a second spacecraft similar to one Scully studied in Africa three 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 cult intends to kill the child. The cult, however, is successful in kidnapping the child. Concurrent with these events, Doggett is run over by a car, which sends him to the hospital. As Follmer and the "Toothpick Man" (Alan Dale) try to uncover the plans of the three agents, Scully and Reyes leave Washington, D.C. to find Scully's son. Doggett finds a strange disfigured man in the X-Files office; believing he is Mulder, Scully has his DNA tested, and the results reveal him to have the same pattern as Mulder. The disfigured man sticks a needle into William, which the other agents believe to be a virus of some kind, but it is later revealed to be a cure for William's powers. The unnamed man is later revealed to be Jeffrey Spender (Chris Owens), Mulder's half-brother. In the season finale, Mulder returns from hiding in the attempts of finding classified information at an army base.