At the end of the seventh season finale, "Requiem", Fox Mulder (David Duchovny) was abducted by aliens. Dana Scully (Gillian Anderson) meets Special Agent John Doggett (Robert Patrick), the leader of an FBI taskforce organized to conduct a search for Mulder.[2] Although the search ultimately proves unsuccessful, Doggett is assigned to the X-Files and works with Scully to look for explanations to several cases. When Scully learns that several women have reportedly been abducted and impregnated with alien babies, she begins to question her own pregnancy and fears for her unborn child. 
Doggett introduces Scully to Special Agent Monica Reyes (Annabeth Gish), an FBI specialist in ritualistic crime, shortly before Mulder's deceased body suddenly appears in a forest at night. Following Mulder's funeral, Assistant Director Walter Skinner (Mitch Pileggi) is threatened by Alex Krycek (Nicholas Lea) that he must kill Scully's baby before it is born. Billy Miles (Zachary Ansley), a multiple abductee who disappeared on the same night as Mulder, is returned deceased but his dead body is resurrected and restored to full health.[6] Mulder also returns from death, with Scully supervising his recovery. Fully rejuvenated, Mulder investigates several X-Files, against orders to do so, but soon gets fired, leaving Doggett in charge of the cases. Mulder continues to provide input in an unofficial capacity. 
Reluctantly accepting Krycek's assistance, Mulder, Doggett and Skinner learn that an alien virus recently created in secret by members of the United States government has replaced several humans, including Miles and several high-ranking FBI personnel, with so-called alien "Super Soldiers". Krycek claims that the soldiers are virtually unstoppable aliens who want to make sure that humans will not survive the colonisation of Earth. They have learned that Scully's baby is a miraculously special child and are afraid that it may be greater than them. They have only recently learned of the baby's importance, which is why Krycek told Skinner to kill the unborn child earlier. When Miles arrives at the FBI Headquarters, Mulder, Doggett, Skinner and Krycek help Scully to escape along with Reyes, who drives her to a remote farm. Shortly after Skinner kills Krycek, Scully delivers an apparently normal baby, while the alien super soldiers surround her. Without explanation, the aliens leave the area as Mulder arrives. While Doggett and Reyes report to the FBI Headquarters, Mulder takes Scully and their newborn son, William, back to her apartment.