The newly appointed Deputy Director Kersh has organizes a manhunt for Mulder and assigns Agent John Doggett to lead the team. He even warned Scully and Skinner that they will be fired if anything is said about aliens. Scully and the Lone Gunmen suspect that the Bounty Hunter might go after Gibson Praise.

Gibson Praise makes Scully believes that she is close to her target. Meanwhile, Agent Doggett has been told to be Mulder's successor in the X-Files by AD Kersh.

Doggett is investigating his first case in the X-File. The case revolved around a series of gruesome murders linking to a bat-like creature.

Without Doggett, Scully alone is investigating a brutal murder in Utah. However, she became trapped in a small town occupied by a religious cult.

Ten years after a little boy mysteriously disappeared from his school playground, he reappeared again and he hasn't aged a day since.

A lawyer wakes up and finds himself in jail for the murder of his wife, but he has no recollections of that event. What's more puzzling is that the days begin to regress backward towards the murder.

Doggett and Skinner are investigating the mysterious murder spree of a religious cult leader. They suspect him to be able to enter the dreams of the people he knows and can kill them in their sleep.

Scully and Doggett are investigating a case where a real estate agent was shot from the roof, inside a prison cell. One of the murderers might have x-ray's vision.

A man takes revenge on those who has caused his blood to change rapidly into metal alloy.

When his son died in a chemical plant accident, an Indian mystic smuggles into the USA to take revenge on two families in Washington D.C.

Doggett found an old case which was investigated by Mulder and was kept a secret from Scully. He decides to follow up the investigation, in order to find any leads into Mulder's disappearance.

Scully and Doggett are investigating a plague of bacteria in the subway tunnels of Boston which eats away human flesh.

When a man claimed that his wife was murdered after giving birth to an alien baby, Scully and Doggett were called in to investigate. Scully began to question her own pregnancy and its conception.

Doggett, Scully and Skinner thought they may have found a lead into Mulder's whereabouts when Teresa Hoese, an abductee was found returned in a desert. However, Scully feared that they are going to find Mulder just like Teresa, near death or already dead.

After Mulder was buried, Billy Miles who also was dead, somehow comes back to life. Skinner and Scully immediately dig up Mulder and found him to be alive too. Krycek offers Skinner a vaccine for Mulder's virus infection but he wants him to kill Scully's unborn child.

Mulder has requested to be reassign back to the X-Files, but he is denied by Kersh. Mulder starts investigating the death of a census worker who was killed on the White House lawn.

Reyes seeks Mulder's help in investigating a killer's connection to the murder of Doggett's son.

Mulder and Doggett investigate several deaths on an oil rig. Mulder is convinced that the oil in the rig is really the alien black oil.

A young agent has been assigned to the X-files when Scully has to take maternity leave. Together with Doggett, they investigate a case revolving a deadly reptilian creature. When they went missing, Scully and Mulder heads out to search for them.

Mulder and Doggett are investigating the death of a doctor who was suspected of experimenting with alien impregnation in an arson attack on a genetics lab. They discovered that Billy Miles who has been changed into an alien replicate, is trying to erase all evidence of the tests. Now, together with Reyes and Krycek, they must protect Scully and her baby.

Mulder, Doggett and Skinner are fighting off the alien replicates while Reyes takes Scully to a remote farm to safeguard the birth of her baby.