Season 8 sees the addition of Robert Patrick to the main cast for the show as David Duchovny elected to return only as an intermittent main character, meaning that he appeared in only half of the episodes. And that took fans a long time (perhaps never) to adjust to as the show Agent Mulder’s defiance of the system and his search for proof of extra-terrestrial life was felt by many to be the heart of the show. Annabeth Gish, who would join the main cast in the 9th & final season appears as a guest star in 4 episodes in this season while Nicholas Lea also returns as Alex Krycek for 3 episodes.Season eight takes place after Fox Mulder’s alien abduction in the seventh season. The story arc for the search of Mulder continues until the second half of the season, when a new arc about Dana Scully’s pregnancy is formed. This arc would continue, and end, with the next season. The season explores various themes such as life, death, and belief.
An FBI taskforce is organized to hunt for Fox Mulder but Dana Scully suspects the taskforce leader, Special Agent John Doggett, and instead chooses to search for her lost partner with Walter Skinner (Mitch Pileggi). She is quite hostile to Doggett being assigned the search and his initial reluctance to reveal who he was pisses her off. At a remote school in the Arizona desert, Doggett, Scully, Gibson and Skinner – as well as a host of students and agents – do not know who to trust as the bounty hunter works among them; and – in a spaceship close by – Mulder is tested on. Having been assigned to the X-Files, John Doggett joins Scully to investigate a series of gruesome murders that appear to be the work of a bat-like creature. This being their first case together, Scully and Doggett find that their investigative techniques are less than similar. Working alone, Scully pursues a cult that worship a slug-like organism; but in her efforts to save an injured stranger, she discovers she’s in over her head. Doggett tracks her down and rescues her while killing off the slug. Having been kidnapped for ten years, a little boy mysteriously reappears but has not aged one bit. While the case stirs up painful memories for Doggett, suspicion stirs that the boy is not all he seems. After his wife is murdered, a lawyer friend of Doggett’s tries to clear his name of the crime but the days regress backwards.
Doggett and Skinner work to avert the murderous spree of a religious cult leader, while Scully takes time off to deal with the early stages of her pregnancy. The fatal shooting of a realtor while alone in a cinderblock jail cell has Doggett hoping motive will yield more than method, but they soon learn that there is more to this case than meets the eye. Doggett and Scully encounter a dead man who is still living – only somewhat changed. What they discover is a man made of metal, enacting vengeance on those he believes created him. When a mystic smuggles himself out of India, Scully and Doggett give chase as his murderous spree starts terrorising two families in suburban Washington, D.C. But Scully soon comes upon a crisis of faith when she realises how dissimilar her techniques are from Mulder, even as she tries to be the believer. It’s one of the most ridiculous concepts that the show has ever come up with. Doggett comes upon an old case about a professed ‘soul-eater’ that Mulder kept secret from Scully, which he hopes will ultimately prove the truth behind Mulder’s abduction. A string of bizarre deaths in the tunnels of the Boston subway system sees Doggett join a team of professionals underground to investigate. Meanwhile, Scully has to defy the train authorities above land, who are determined to get the trains up and running within hours. Scully becomes personally involved when she encounters several women who had no way of naturally conceiving but who claim to have been abducted and impregnated with alien babies. Doggett calls on another agent, Monica Reyes (Annabeth Gish), to assist in the Mulder case, but Scully’s fears about finding him come to a head with the sudden recovery of abductees seized at the same time.
Three months after Mulder’s funeral, a former abductee awakens from the dead and Scully pins her hopes on resurrecting her partner. Meanwhile, Alex Krycek offers Skinner a loathsome deal which he claims can save Mulder’s life. Mulder secretly conducts his own investigation after a man is gunned down on the White House lawn attempting to inform the President of a planned alien invasion. However, he is soon in over his head as he tries to expose further evidence of colonization. Reyes enlists Mulder’s help investigating a killer’s connection to the unsolved murder of Doggett’s son but Mulder soon finds himself clashing with Doggett. Mulder and Doggett are asked to investigate several deaths aboard an oil rig, but Mulder is convinced the rig is carrying an alien black oil; meanwhile a heavily pregnant Scully attempts to protect Mulder in absentia. With Scully on maternity leave, Doggett is paired with an enthusiastic young agent named Layla Harrison who knows everything about the X-Files, and her apotheosis of Mulder and Scully leads to him learning a thing or two. But when Harrison and Doggett disappear, Mulder defies orders in an attempt to find them. Mulder, Skinner and Doggett come up against the horrible consequences of the Syndicate’s pact with the aliens, as a hybrid attempts to erase all evidence of the tests – including Scully’s soon-to-be-born baby. The men call on Reyes, and – reluctantly – Alex Krycek to help them. Mulder, Doggett and Skinner face off with the alien replicants as they desperately try to expose the conspiracy within the FBI. Meanwhile Scully goes into labour in a remote location, but Reyes soon learns they may be no safer there.