Episode 1: Nothing Important Happened Today (1)
Air Date: Nov 11, 2001
Doggett and Reyes investigate the death of an EPA official. Scully who has returned to her teaching position at the FBI Academy in Quantico was asked to help out. Doggett and Reyes might have found the woman who possesses knowledge of a possible government cover-up involving Scully's baby.
Episode 2: Nothing Important Happened Today II (2)
Air Date: Nov 18, 2001
Doggett has found Shannon McMahon who killed the EPA official. She claims to be a super solider. Meanwhile, Scully's baby is showing signs of being extraordinary.
Episode 3: Damonicus
Air Date: Dec 2, 2001
Doggett and Reyes investigate a double homicide that has all the signs of a satanic ritual killing. While Doggett is convinced that a doctor is orchestrating the crimes from within the hospital, Reyes believes it points to the existence of an evil entity.
Episode 4: 4-d
Air Date: Dec 9, 2001
Doggett is clinging to life in the hospital following a shooting and Reyes has been accused of attempted murder after a witness identifies her as the shooter.
Episode 5: Lord Of The Flies
Air Date: Dec 16, 2001
Doggett and Reyes asked Scully to help them to investigate the bizarre death of a teenager who died while performing a stunt for a cable TV show.
Episode 6: Trust No 1
Air Date: Jan 6, 2002
Scully has to decide whether she should put Mulder's life in danger by looking for him after a couple claims that their baby has the same abilities as William and they will only talk to Mulder about the information they have revolving around the super soldier program.
Episode 7: John Doe
Air Date: Jan 13, 2002
An amnesic Doggett is wandering in a small Mexican town. Meanwhile, Scully and Reyes went searching for him.
Episode 8: Hellbound
Air Date: Jan 27, 2002
Doggett and Reyes investigate a series of murders where the victims were skinned alive. Scully was called in to help out and they found the murders to be linked to a case from 1960.
Episode 9: Provenance (1)
Air Date: Mar 3, 2002
Scully decides to take drastic measures to protect William when she suspects that he may have more special abilities than she knew.
Episode 10: Providence (2)
Air Date: Mar 10, 2002
Scully desperately wants to rescue William from his kidnappers, so she enlists the help from the Lone Gunmen.
Episode 11: Audrey Pauley
Air Date: Mar 17, 2002
Reyes is in a coma after a car accident. Scully and Doggett desperately search for a way to help her while Reyes found herself in a strange place.
Episode 12: Underneath
Air Date: Mar 31, 2002
Scully, Doggett and Reyes have to reopen one of Doggett's old cases to determine whether the man dubbed as The Screwdriver Killer and has recently been released from prison was really guilty or not.
Episode 13: Improbable
Air Date: Apr 7, 2002
Using numerology, Reyes managed to deduce that a single killer is behind a series of murders. Reyes and Scully also discover some clues left by a mysterious stranger.
Episode 14: Scary Monsters
Air Date: Apr 14, 2002
Agent Leyla Harrison asks Doggett and Reyes to investigate the death of a woman who was presumed to have stabbed herself repeatedly. Harrson suspects a man who can control terrifying creatures is behind the murder.
Episode 15: Jump The Shark
Air Date: Apr 21, 2002
Scully, Doggett and Reyes ask for the help of the Lone Gunmen when Morris Fletcher gives them information about the Super Soldiers.
Episode 16: William
Air Date: Apr 28, 2002
A severely deformed man is captured in the X-Files office while trying to steal documents about Mulder's sister. Doggett and Scully becomes suspicious of his real identity when his DNA is found to match that of Mulder.
Episode 17: Release
Air Date: May 5, 2002
An FBI profiler links a series of murders to the killing of Doggett's son. However, soon Doggett and Reyes start to wonder about his involvement in the murders.
Episode 18: Sunshine Days
Air Date: May 12, 2002
The agents are investigating a mysterious death outside the house which the original Brady Bunch series was filmed. There, they meet a man who is obsessed with The Brady Bunch.
Episode 19: The Truth (1)
Air Date: May 19, 2002
Mulder is on trial before a military tribunal that seeks to justify and prove the existence of an alien conspiracy and The X-Files.
Episode 20: The Truth (2)
Air Date: May 19, 2002
Although several witnesses testified to help Mulder, he was found guilty by the military panel and sentenced to death by lethal injection.