The theme of father-figures is one that is explored throughout "The X-Files", in relation to both Mulder and Scully. As well as their own fathers, a number of characters play a paternal role to the agents in later episodes, including Deep Throat, the Cigarette-Smoking Man and Senator Matheson. Both of the protagonists have deep-rooted family issues and this episode is the beginning of the exploration of that story arc. A motif often employed in the show is that of mirroring, doubling or cloning. Scully's relationship with her father, first dealt with in "Beyond the Sea", is mirrored by that of Mulder's with his father—also named William—who dies at the end of the second season.