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.