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 on a naval ship. They later find connections between the experiments on the ship and Scully's child, William.