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 Gibson Praise from an Alien Bounty Hunter disguised as the missing Mulder.

Scully isn't exactly warm to Doggett on their first X-File together in which they investigate a human bat.

Agent Scully is investigating a murder in a backwards town somewhere in Utah without the help of agent Doggett. This mistake would prove near fatal for Scully because the people in the town implant a deadly parasite into her back. It turns out that this parasite has been controlling everyone in the town and forcing them to do its bidding. Written by Ben Diamond

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 man lives the most recent 5 days of his life backwards and finds out that he is the main suspect in the murder of his wife.

While Scully tends to her secret, Doggett and Skinner team up to track a cult leader who may be a psychic assassin.

Doggett and Scully deal with a killer who may have X-Ray vision.

A man believed to be dead from Gulf War Syndrome comes back to life and slowly turns into metal.

A small Indian man on a creaky cart is believed to have the ability to leap into people's bodies.

Skinner and Doggett investigate a case Mulder was working on before he disappeared involving a family and a monster straight from Native American lore.

Doggett takes to the Boston subways to try to figure out where a deadly agent that is killing citizens is coming from.

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.

Billy Miles, thought dead, is found alive and Scully still thinks the still-dead Mulder can come back to life; meanwhile Skinner comes in contact with Krycek who may have a clue as to what exactly is happening with these dead-alive abductees. Written by UnforgivenSpaceCowboy

A man is shot on the White House lawn with a disk titled Fight the Future; Mulder, on the brink of expulsion from the X-Files, investigates while Doggett uses an old friend from the military, Knowle Rohrer, as an insider to the possibility of a conspiracy. Written by UnforgivenSpaceCowboy

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.

A bizarre reptilian creature captures Doggett and his new Mulder-obsessed partner underground and only a X-Files deposed Mulder can help them.

The X-Files team must protect Agent Scully and her unborn child as groups of Super Soldiers try to stop her pregnancy.

Agents Mulder, Doggett and Skinner investigate (along with Alex Krycek) the Super Soldier conspiracy, while Scully goes into hiding to have her child.