William

When Scully and Doggett are contacted by a man who claims his wife was murdered shortly after giving birth to an alien baby, Scully digs deeper into reports of alien fertilization on humans and begins to question her own pregnancy and its conception.

Mulder and Doggett join forces to investigate the arson attack on a genetics lab where one of the doctors suspected of experimenting with alien impregnation is killed. They encounter Billy Miles, who has been changed into an alien replicant after his recent abduction and is attempting to erase evidence of the tests; part of the Syndicate's conspiracy with an alien race. When a woman helping Scully out at home is found to be a part of the conspiracy, the agents, along with Monica Reyes and Alex Krycek, know they must protect Scully and her baby from Billy Miles and get her out of the city.

With otherworldly factions in pursuit, Mulder and the agents race to safeguard the birth of Scully's child. Scully and Reyes take refuge in an abandoned town where Doggett grew up. Meanwhile Doggett and Skinner have the final showdown with Alex Krycek and continue to fight off the replicants but how successful will they be?

Doggett catches an intruder trying to steal documents from the office; the mystery man baffles everyone with enough knowledge of the X-files to make them suspect that he just might be Mulder, despite disfigurement. Scully's fears regarding her son's safety are triggered, when the stranger interacts with him, and subsequent rethinking leads her to make a heartbreaking sacrifice.

When a pair of teenage girls attack one another, each believing the other to be a monster, Mulder and Scully find that their investigation could possibly lead back to their long-lost son, William.