After the eighth season finale "Existence", Fox Mulder (David Duchovny) goes into hiding. Dana Scully (Gillian Anderson) is again reassigned to the FBI Academy, and Monica Reyes (Annabeth Gish) becomes John Doggett's (Robert Patrick) new FBI partner in the X-Files office. Doggett asks Scully for help on a case involving an EPA official, Carl Wormus (Nicholas Walker), who died after his car was forced off a bridge by a woman he picked up. 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 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", 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.[3] 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. He is caught, however, after allegedly killing an apparently indestructible "Super Soldier", which causes him to be tried before a military tribunal. With the help of Kersh, Scully, Reyes, Doggett, Spender, Marita Covarrubias (Laurie Holden) and Gibson Praise (Jeff Gulka), Mulder breaks out, and Mulder and Scully travel to New Mexico to find an old "wise man", later revealed to be the "Cigarette Smoking Man" (William B. Davis). He tells the two that aliens will begin colonizing the planet on December 22, 2012. Cigarette Smoking Man appears to be killed by a missile, launched under the command of Knowle Rohrer (Adam Baldwin), who is revealed to be alive and well. Mulder and Scully escape, but become fugitives on the run from the FBI. The final scene of the season features the two in a motel room facing an uncertain—but possibly hopeful—future.