Within

Newly appointed Deputy Director Kersh organizes a manhunt for Mulder and assigns Agent John Doggett to head the team. Scully and Skinner go along with the investigation but are warned by Kersh that they will be fired if anything is said about aliens. Scully , along with the Lone Gunmen, surmise that the Bounty Hunter is trying to erase all evidence of abductions and they realise that he may be going after Gibson Praise, who is now living at a school in Arizona. Agent Doggett comes to the same conclusion and his team race Scully and Skinner to the school where they find Mulder trying to kidnap Gibson.

Without

As the search for Mulder intensifies in the Arizona desert, Gibson Praise leads Scully to believe that she is truly closer to her target. Meanwhile AD Kersh informs Agent Doggett that he has been assigned as Mulder's sucessor on the X-Files.

Patience

While tackling his first X-File case about a series of gruesome murders surrounding a bat-like creature, Doggett quickly learns that his investigative techniques are somewhat dissimilar to Scully's.

Roadrunners

Scully evades Doggett's help in investigating a vicious murder in a remote area of Utah and she is trapped in the small town by a religious cult that believe a slug-like creature is the second coming of God who needs a human host to survive.

Invocation

In 1990 a little boy unexplainably disappeared from his crowded school playground and was never seen again; that is until now, ten years later, and he hasn't aged a day since.

Redrum

A prominent lawyer wakes to find himself in jail and about to be prosecuted for the murder of his wife. He has no memory of this event however, and when the days begin to regress backward towards the murder, he realizes that he has been given a second chance.

Via Negativa

Working without Scully's input, Doggett and Skinner try to avert the mysterious murder spree of a drug-induced, religious cult leader and it becomes clear that the man can enter the dreams of the people he knows and can kill them in their sleep.

Surekill

When a real estate agent is shot inside a prison cell by someone who apparently fired from the roof, Scully and Doggett track him to two exterminators, one of whom has x-ray vision.

Salvage

A man whose blood is rapidly changing into metal alloy enacts revenge on those who caused his condition.

Badlaa

An Indian mystic whose son died in a chemical plant accident smuggles himself into the United States and takes his revenge on two families in suburban Washington D.C.

The Gift

Doggett comes upon an old case that Mulder kept secret from Scully and he follows up the investigation, hoping to find a possible connection to Mulder's disappearance.

Medusa

Scully and Doggett must race against the clock to investigate and fight off a contagion lurking in the subway tunnels of Boston.

Per Manum

When Scully and Doggett are contacted by a man who claims his wife was murdered shortly after giving birth to an alien baby, Scully digs deeper into reports of alien fertilization on humans and she begins to question her own pregnancy and it's conception.

This Is Not Happening

When Teresa Hoese, the woman Scully & Mulder met the previous spring in Oregon just before Mulder was abducted, is found in a desert, returned from testing done on her by aliens, Doggett alerts Scully that this could have something to do with Mulder and his whereabouts. Skinner joins them and they travel to the hospital where Teresa is, clinging to life by a thread, and Scully realizes that this is exactly what's going on with Mulder. The agents catch up with Richie Szalay, who found Teresa Hoese and was looking for his friend, and talk to him. Richie says that the area has been heavily covered with UFO activity and thought he might find his friend here but instead found Teresa. Meanwhile, Jeremiah Smith is back with his friend, Absalom, who belives in the coming alien apocalypse. Jeremiah has been taking the returned abductees and secretly healing all their wounds so that they wouldn't die. Being a shapeshifter, Jeremiah walked into the hospital that Teresa Hoese was in and posed as her doctor, transfering her out to his place in the woods so that he might heal her, too. That night, Scully goes to talk to Skinner about how she's afraid that they're going to find Mulder like Teresa, near death or already dead. Skinner says they'll find him alive. The next day, Doggett calls Scully and Skinner out to a field to get another point of view from an FBI agent from New Orleans that worked on his son's murder case with him. Her name is Monica Reyes and she specializes in ritualistic crimes and religious cults. Monica thinks that Mulder may have joined some sort of UFO cult but Scully disagrees. That night, Reyes is driving back when she spots a UFO. She gets out, only to stumble onto the body of Richie's friend. With evidence, Scully, Skinner, Doggett, and Reyes storm the house of Jeremiah Smith, Absalom, and all the abductees that have been healed, looking for Mulder. Scully interviews Jeremiah, asking about Mulder, and Jeremiah says that he was trying to help Mulder when the FBI came storming in. Before she could do anything, Skinner pulls Scully out of the room to tell her that they found Mulder. They rush out to the field where people are standing over the lifeless body of Fox Mulder. Seeing that Mulder is dead, Scully rushes back to get Jeremiah to help but before she reaches the house, Jeremiah is abducted...

DeadAlive

Shortly after Mulder is buried, Billy Miles is found very dead but somehow comes back to life. Skinner and Scully put all their hopes into digging up Mulder and discovering that he too, is still alive. As Mulder lies in hospital without indication that he is going to fully recover, Krycek comes to Skinner and offers him a vaccine to the virus that has infected Mulder - but the cost of the vaccine is that Skinner has to kill Scully's unborn child.

Three Words

Mulder's request for reassignment to the X-Files is denied by Kersh, who hopes that Mulder will simply quit the FBI. When a census worker is killed on the White House lawn trying to get information to the President, Mulder gets in over his head trying to discover what the man knew.

Empedocles

Special Agent Reyes enlists Mulder's help in investigating a supernatural killer's connection to the unsolved murder of Agent Doggett's son, Luke.

Vienen

Mulder and Doggett are reluctantly thrown together to investigate several deaths on an oil rig. Mulder becomes convinced that the rig is really carrying the alien black oil.

Alone

While Scully takes maternity leave, Doggett is partnered with a young agent who is fascinated with the X-Files and has followed Mulder and Scully's careers. She and Doggett investigate the death of an old man and the disappearance of his son but when they disappear as well, Mulder, despite having left the FBI, heads out to search for them.

Essence

Mulder and Doggett join forces to investigate the arson attack on a genetics lab where one of the doctors suspected of experimenting with alien impregnation is killed. They encounter Billy Miles, who has been changed into an alien replicant after his recent abduction and is attempting to erase evidence of the tests; part of the Syndicate's conspiracy with an alien race. When a woman helping Scully out at home is found to be a part of the conspiracy, the agents, along with Monica Reyes and Alex Krycek, know they must protect Scully and her baby from Billy Miles and get her out of the city.

Existence

Mulder, Doggett and Skinner attempt to fight off the alien replicants and they find a connection to the conspiracy that leads into the FBI, while Reyes and Scully head to a remote farm to safeguard the birth of Scully's child.