As Section Chief Blevins expresses his concern with the direction of the X-Files department, Mulder is personally affected by the abduction of a young girl, whom he speculates might have been abducted by aliens — a scenario similar to that which he believes occurred to his younger sister, Samantha, who went missing Nov. 27, 1973, at age 8.
Scully and Mulder are contacted by a young girl who keeps her identity secret. The girl states that a boy named Greg Randall got Ruby pregnant, and that he couple were planning to elope together. Kevin Morris' doodles turn out to be part of a top secret binary defense satellite transmission. The boy is taken into custody by NSA Agent Holtzman and then released. New doodles taken from the Morris home turn out to be digital renderings of everything from Shakespeare passages to bars from a Brandenburg concerto. Mulder believes the boy has become a conduit for alien transmissions. The agents return to the site of the abduction. They find evidence of intense heat.
They also find Greg Randall's body buried in a shallow grave. Mulder discovers a handwritten note in Randall's wallet noting a doctor's appointment. The handwriting matches that of the mysterious girl encountered earlier. By questioning the doctor, the agents locate the mysterious girl, who turns out to be Tessa Sears. Scully informs Tessa that officials know that it is she-and not Ruby-who was impregnated by Greg Randall. Sears admits she shot Greg when she discovered he was having an affair with Ruby. But she insists she did not murder Ruby. Scully and Mulder return to the Morris home and find it abandoned. They also find a large portrait of Ruby formed with binary numbers. The agents travel back to Lake Okobogee. Mulder finds Kevin floating in a strange fog. Just as Mulder pulls Kevin away, a group of bikers drives by them and Ruby's unconscious body is discovered nearby. Darlene forbids Mulder from speaking with her daughter, insisting that as far as she is concerned, Ruby had simply run off with bikers. That night, Mulder listens to tape recordings of his hypnosis session in which he described his belief that one day his sister will be returned to Earth unharmed.