Alternatively, Scully’s qualifications as a medical doctor suggest she could have been Mulder’s physician, tasked with monitoring his mental health. The mystery of Samantha Mulder’s disappearance is explored in multiple episodes throughout The X-Files, but it is primarily resolved in Season 7, Episodes 10 and 11, “Sein und Zeit” and “Closure.”
In “Sein und Zeit,” Mulder discovers a link between his sister’s disappearance and other missing child cases, leading him to the belief that Samantha’s abduction was part of a broader pattern of abductions.