New Deputy Director Kersh has Agent John Doggett investigate the missing Mulder case. Doggett's skeptical treatment of Mulder's disappearance puts a thorn in Scully and Skinner's sides.
Scully leads Skinner and an unhappy Doggett to Arizona to protect child prodigy Gibson Praise from an alien bounty hunter disguised as the missing Mulder.
Doggett is a little dismayed when Scully investigates a murder in a barely inhabited town in Utah without him. When Scully's car breaks down and she finds the town people aren't as sweet as they seem she struggles to find a way out of the demented town.
Doggett and Scully once again butt heads on their latest X-File which involves a boy who has returned after being missing for ten years but still appears to be seven years old, the age he was the day he was abducted.
A small Indian man on a creaky cart with powers of illusion is believed to have the ability to take over people's bodies and kill them by leaping into their anal cavity. Doggett and Scully try to stop his gruesome killing spree.
Skinner and Doggett investigate a case Mulder was working on before he disappeared involving a family and a monster straight from Native American lore.
Scully stumbles upon a woman whose abductee experience and symptoms are amazingly similar. The fear now is that both their upcoming births will be to non-human offspring.
Jeremiah Smith appears out of nowhere and formerly dead abductees are coming back to life, giving Scully and Skinner the idea that Mulder may have a shot at still being alive.
Three months after Mulder's funeral, another dead alien abductee comes back to life. Skinner exhumes Mulder hoping that he too can be revived. Skinner faces an impossible decision when Krycek offers him a vaccine that can save Mulder.
Mulder requests reassignment to the X-Files but is denied by Kersh. When a man with information about an alien invasion is killed on the White House lawn, Mulder conducts his own investigation to find further evidence of colonization.
Upon being fired, an office worker murders his employers, believed to be under the influence of pure evil. Agent Reyes believes this evil may be linked to the death of Doggett's son.
Doggett and Mulder unwillingly team up investigating an oil rig where some mysterious murders have happened and the possibility of the Black Oil being involved is a haunting reality.