Episode/Production # /Title

Plot Synopsis

Continuity Notes

Dates

Code

Season 9: Episode 1

9x01 Nothing Important Happened Today

John Doggett begins his investigation of Deputy Director Alvin Kersh and the search for Fox Mulder.

Lone Gunmen appear.

First appearance of Shannon (Lucy Lawless) and Assistant Director Brad Follmer (Cary Elwes)

The main portion  of the episode begins on Monday, 48 hours after the prologue.  Kersh is under investigation by Doggett, who still bears the bruises from the end of Season 8.  However, Frohike has a blue face, a direct reference to his appearance in The Lone Gunmen: 1x13: All About Yves, which takes place on May 14, 2001. William is telekinetically moving his crib's mobile.

Mid-May 2001

X

Season 9: Episode 2

9x02 Nothing Important Happened Today II

Shannon McMahon, a former Marine associate of Doggett's, reveals to Doggett that she is a "Super Soldier." This leads them to a clandestine laboratory where secret experiments are taking place aboard a naval ship.

Late May 2001

X

Season 9: Episode 3

9x03 Daemonicus

With Dana Scully  reassigned to the Quantico Training Academy, Doggett and Monica Reyes investigate their first X-File together – a series of satanic ritual murders.

Scully is back at work, now teaching at Quantico.

June 2001

Season 9: Episode 4

9x05 4-D

A vicious murderer threatens Doggett and Reyes and then vanishes. Doggett is shot and Brad Follmer discovers that Reyes' gun was used.

Late June 2001

Season 9: Episode 5

9x06 Lord of the Flies

Scully, Doggett and Reyes investigate when a teenager dies while performing a daredevil feat for a television show, but his death is soon revealed to be caused by a disturbing family secret.

Early July 2001

Season 9: Episode 6

9x08 Trust No 1

Scully is hopeful about reuniting with Mulder when a complete stranger offers new information about what drove him into hiding. Yet her trust in the stranger may place Mulder in even more danger. The tagline of this episode is "They're Watching."

No explicit date give, but it's noted that "several months ago" Scully saw her son affect movement on the mobile above his crib, an event that happened in episodes 1 and 2 of this season.

Mid July 2001

X

Season 9: Episode 7

9x07 John Doe

With no knowledge of his identity or his past, Doggett is found wandering a dusty Mexican town. While he struggles to piece together his memory, he finds himself embroiled in a smuggling plot. Across the border Scully and Reyes attempt to find him.

Doggett goes missing for two weeks

August 4-18, 2001

Season 9: Episode 9

9x10 Provenance

When rubbings from the spaceship resurface, the FBI hides its investigation from the X-Files. Meanwhile, Scully is forced to take drastic measures when she discovers a threat to William.

The Lone Gunmen appear.

William Scully is abducted

Rubbings from the spaceship refer to events from Season 6, Episode 6x22: Biogenesis and Season 7, Episode 7x03: The Sixth Extinction, which occurred in October 1999.  In this episode, Scully refers to that event as having happened two years ago.

September 2001

X

Season 9: Episode 10

9x11 Providence

Distrustful of both Skinner and Follmer, Scully circumvents the FBI's investigation into William's kidnapping and performs her own, assisted by Reyes and The Lone Gunmen.

William Scully is rescued.

September 2001

X

Season 9: Episode 11

9x13 Audrey Pauley

Awakening in a surreal hospital – which a companion believes to be Death's Waiting Room – after being hit by a car, a comatose Reyes struggles to wake herself up before her organ donor card is acted upon.

No internal dates mentioned. Takes place from Friday to Sunday.

Fall 2001

Season 9: Episode 12

9x09 Underneath

Doggett is determined to find an error in the DNA evidence that freed the convicted "Screwdriver Killer", whom he nearly caught in the act 13 years earlier.

The 13 year old case occurred in 1989

Early 2002

Season 9: Episode 1

9x04 Hellbound

Reyes takes the lead while investigating an X-File case surrounding a man found skinned alive. When she discovers that he had visions of a similar thing, she calls on Scully's expertise to help with the investigation.

Victim died on the same month and day as his birth date, March 8th, revealed on a file Scully shows Reyes. Victim died five days prior.

March 13, 2002

Season 9: Episode 13

9x14 Improbable

In the race to catch a serial killer, Scully and Reyes find themselves relying on numerology, their powers of deduction, and a mysterious, card-playing stranger.

No internal dates provided. As the number three is a large factor in this episode on numerology, perhaps it takes place in the third month of the year.

March 2002?

Season 9: Episode 12

9x12 Scary Monsters

Special agent Leyla Harrison takes Reyes and Doggett on a drive into the mountains after a woman stabs herself repeatedly and her widowed husband refuses to let anyone see their son.

Return of Leyla Harrison

Takes place Friday. Leyla Harrison says she enjoyed her big adventure last year, an event that refers to Season 8: Episode 19: Alone, which took place in early 2001.

April 2002

Season 9: Episode 15

9x15 Jump the Shark

When Morris Fletcher approaches the agents with information related to the "Super Soldiers", they turn to The Lone Gunmen. But the Gunmen are already knee-deep in a bio-terrorist's plot which has links to the mysterious Yves Adele Harlow.

Return of Jimmy Bond, Yves Harlow and Morris Fletcher.

The Lone Gunmen appear to die.

Frohike, Langly and Jimmy say that Yves disappeared a year ago, a reference to The Lone Gunmen, Episode 1x13 All About Yves, which occurred in late May 2001.

May 2002

X

Season 9: Episode 16

9x17 William

Doggett finds a strange, disfigured man in the X-Files office and, on a whim of Scully's, they test his DNA. The surprising answers they find become even more surprising when William's life is put on the line. Jeffrey Spender returns.

No internal dates provided

2002

X

Season 9: Episode 17

9x16 Release

When one of Scully's students displays an inordinate ability to profile serial killers, his insights reopen the murder case of Doggett's son, Luke.

Doggett says that nine years have passed since the abduction of Luke Doggett, but that's incorrect as he was abducted on 8/12/97, according to the file Agent Reyes shows Mulder in Season 8: Episode 8x17: Empedocles, which is five years ago.

2002

Season 9: Episode 18

9x18 Sunshine Days

Doggett, Reyes, Scully and Skinner stumble on to a bizarre murder case where the main suspect is Oliver Martin, a man with an unusual obsession with The Brady Bunch.

Scully notes that she's worked on the X-Files for nine years and nearly two hundred cases.

2002

Season 9: Episodes 19 & 20

9x19 The Truth

9x20 The Truth

After not knowing Mulder's whereabouts for the last year, Skinner and Scully learn he's being held for the murder of a military man he couldn't possibly have killed: Knowle Rohrer, one of the government's secret "Super Soldiers." Mulder breaks out of prison with help of Skinner, Reyes, Doggett, Scully and Alvin Kersh. Mulder and Scully travel to New Mexico where black helicopters destroy an Anasazi cliff dwelling ruin along with the Cigarette Smoking Man.

Final appearance of Gibson Priase, Jeffrey Spender and Marita Covarrubias

Gibson Praise hid Mulder in the desert "for the last year" from the Super Soldiers and the New Syndicate.  Mulder discovers the December 22, 2012 date for the mobilization of alien forces. Jeffrey Spender says he worked for the X-Files until 3 years ago (2/10/99). Skinner says Doggett's been on the X-Files for two years (June 2000). Mulder and Scully are said to have worked on the X-Files for nine years (March 1993)

An adult Gibson Praise appears again in the non-canonical Season 10 comic-book series.

2002

X

Movie: I Want to Believe

Book: I Want to Believe

Mulder and Scully are called back to duty by the FBI when a former priest claims to be receiving psychic visions pertaining to a kidnapped agent.

According to the novelization, this second X-Files film takes place roughly five years after the close of Season 9, episode 19/20: "The Truth."

Mulder and Scully are living together, with the former now a recluse, still a fugitive from the FBI, and the latter a doctor. By story's end, Mulder is no longer wanted by the FBI.

2007

D/E

Short Story: "It's All in the Eyes"

From the book: The X-Files: Trust No One (IDW)

(Coming soon)

October 30, 2009

Episode Theme Codes

A: Artificial Intelligence, technology and machines gone bad

B: Bugs, creepy-crawlers and parasitic pests

C: Cults, tribal practices and bizarre religious rites

D: Drama

E: Evil experiments and other scientific blunders

F: Fantasy, Philosophic theory, and Time paradoxes

G: Government conspiracies (unrelated to the mythology)

H: Humor

K: Killers (serial & spree), psychopaths; the human monster

L: Local legends: Bigfoot, lake monsters, ghosts & goblins

M: Monsters, mutants and malformed menaces

N: Nightmares, Dreams and Visions

O: Occultism, devil worship, demons and dark forces.

P: Psychic manifestations (telepathy, telekinesis, etc.,)

R: Reincarnation, transmigration and other pagan beliefs

S: Spirits, ghosts and apparitions

U: UFO's (unrelated to the mythology)

V: Viruses, bacteria and other nasty microbial matter

W: Werewolves, vampires and zombies

X: The Alien/Conspiracy main plot thread of the mythology

?: Unknown