• Writer: Chris Carter
• Director: Kim Manners
• Original Broadcast: 11/5/00
• Guest Cast:
  • Assistant Director Walter Skinner (Mitch Pileggi)
  • Langly (Dean Haglund)
  • Byers (Bruce Harwood)
  • Frohike (Tom Braidwood)
  • Agent Danny Mosley (Marc Gomes)
  • Figure (Mr. Coeben) (Marty Zagon)
  • Deputy Director Kersh (James Pickens Jr.)
  • All-Business Agent/Agent Gene Crane (Kirk B.R. Woller)
  • Teacher (Arlene Malinowski)
  • Order Taker (Bryan Greenberg)
  • Principal (Jonathan Palmer)
  • Gibson Praise (Jeff Gulka)
  • Thea Sprecher (Christine Firkins)
  • Secretary (Jo-Ann Dean)
  • Agent TDB (Dondre Whitfield)

Scully searches for the truth about her missing partner, while she's simultaneously forced to contend with a resistant FBI bureaucracy and a skeptical new associate, Agent John Doggett, who reluctantly joins Scully in the search for Mulder. Part one of two.

• Writer: Chris Carter
• Director: Kim Manners
• Original Broadcast: 11/12/00
• Guest Cast:
  • Fox Mulder (David Duchovny)
  • Gibson Praise (Jeff Gulka)
  • Agent Danny Mosley (Marc Gomes)
  • Deputy Director Kersh (James Pickens Jr.)
  • All-Business Agent/Agent Gene Crane (Kirk B.R. Woller)
  • Agent Landau (Sal Landi)
  • Teacher (Arlene Malinowski)
  • Principal (Jonathan Palmer)
  • Alien Bounty Hunter (Brian Thompson)
  • Thea Sprecher (Christine Firkins)
  • Secretary (Jo-Ann Dean)

As Scully and Doggett continue their search for the truth about the missing Mulder, the skeptical Doggett is forced to acknowledge information that tests his unwillingness to believe in all things paranormal, and proves to him that no one is who he appears to be. Part two of two.

• Teleplay: Steven Maeda
• Story: Steven Maeda & Daniel Arkin
• Director: Pater Markle
• Original Broadcast: 12/10/00
• Guest Cast:
  • Martin Wells (Joe Morton)
  • Tall Guard (Roger Hewlett)
  • Al Cawdry (Lee Duncan)
  • Janet Wilson (Bellamy Young)
  • Bailiff (Derick Alexander)
  • Judge Kinberg (Jack Shearer)
  • District Attorney (Cynthia Martells)
  • Trina (Joanna Sanchez)
  • Hayley (Kayla Henry)
  • Brent Tufeld (J. Patrick McCormack)
  • Shorty (Guy Torry)
  • Spider-Man/Cesar Ocampo (Danny Trejo)
  • Reporter (Brien Blakely)
  • Vicky Wells (Anne-Marie Johnson)
  • Lead Cop (Shane Sinutko)
  • Homicide Detective (James Howell)
  • Gangbanger (Luis Rodriguez)

Scully and Doggett are called in to investigate the case of a man accused of murdering his wife. However, the man has no recollection of the crime. Initially skeptical of his claim, Scully and Doggett discover that time may not be on his side.

• Writer: Chris Carter
• Director: Chris Carter
• Original Broadcast: 11/19/00
• Guest Cast:
  • Tall George (Gary Bullock)
  • Elderly Woman (Annie O'Donnell)
  • Detective Abbott (Bradford English)
  • Little Old Lady (Eve Brenner)
  • Swanny Swanson (Jim Swanson)
  • Gravedigger (Brent Sexton)
  • Sheriff's Deputy (Bryan Rasmussen)
  • Myron Stefuniak (Dan Leegant)
  • Ernie Stefuniak (Gene Dynarski)
  • The Bat Thing (Jay Caputo)

Scully and Doggett investigate their first official case together -- a series of gruesome murders linked to a bat-like creature. Though skeptical of Scully's logic, Doggett finds a begrudging respect of her investigative process.

• Writer: Vince Gilligan
• Director: Rod Hardy
• Original Broadcast: 11/26/00
• Guest Cast:
  • Hank Gulatarski (David Barry Gray)
  • Female Bus Driver (Rusty Schwimmer)
  • Gas Station Man (William O'Leary)
  • Mr. Milsap (Lawrence Pressman)
  • Sheriff Ciolino (Conor O'Farrell)
  • Lead Agent Mayfield (Todd Jeffries)
  • Disabled Man (Bryan Dilbeck)

Scully, while investigating on her own a murder in the New Mexico desert, discovers a small, remote town housing a paranormal cult that keeps a terrible secret. Scully's discovery of the cult's secret puts her life in danger, and she must rely on Doggett to track down her hidden whereabouts and save her life.

• Writer: David Amman
• Director: David Compton
• Original Broadcast: 12/3/00
• Guest Cast:
  • Billy Underwood (Kyle and Ryan Pepi)
  • Lisa Underwood (Kim Greist)
  • Josh Underwood (Colton James)
  • Doug Underwood (Erich Anderson)
  • Principal (Stave Stapenhorst)
  • Sheriff Sanchez (Barry Cullison)
  • Marcia Purnell (Sheila Shaw)
  • Ronnie Purnell (Rodney Eastman)
  • Cal Jeppy (Jim Cody Williams)
  • Sharon Pearl (Maggie Baird)
  • Lisa's friend (Leslie Sachs)
  • Luke Doggett (Jake Fritz)

Scully and Doggett investigate the reappearance of a young boy kidnapped ten years ago, who returns to his family having not aged at all. Doggett takes a very personal interest in the case, and he and Scully discover that although the boy appears to be normal, things are not what they seem.

• Writer: Frank Spotnitz
• Director: Tony Wharmby
• Original Broadcast: 12/17/00
• Guest Cast:
  • Assistant Director Walter Skinner (Mitch Pileggi)
  • Frohike (Tom Braidwood)
  • Langly (Dean Haglund)
  • Byers (Bruce Harwood)
  • Deputy Director Alvin Kersh (James Pickens Jr.)
  • James Leeds (Kevin McClatchy)
  • Angus Stedman (Lawrence Lejohn)
  • Nurse (Mary Ostrow)
  • FBI Agent Gene Crane (Kirk B.R. Woller)
  • Anthony Tipet (Keith Szarabajka)
  • Senior Agent (Wayne Alexander)
  • Homeless Man (Wayne A. King)
  • Andre Bormanis (Grant Heslov)
  • E.R. Doctor (Christopher Jacobs)

With Scully in the hospital for reasons she does not disclose to her partner, Doggett investigates the mysterious deaths of 20 cult members and two FBI agents, all of whom died in identical fashion.

• Writer: Chris Carter & Frank Spotnitz
• Director: Kim Manners
• Original Broadcast: 2/18/01
• Guest Cast:
  • Fox Mulder (David Duchovny)
  • Assistant Director Walter Skinner (Mitch Pileggi)
  • Duffy Haskell (Jay Acovone)
  • Kath McCready (Megan Follows)
  • Dr. Lev (David Purdham)
  • Dr. James Parenti (Steven Anderson)
  • Delivery Nurse (Diana Castle)
  • Second Nurse (Elizabeth Cheap)
  • Receptionist (Victoria Gallegos)
  • Mrs. Hendershot (Saxon Trainor)
  • Agent Joe Farah (Christopher Stanley)
  • Dr. Miryum (Jennifer Griffin)
  • First Associate (Karl T. Wright)
  • Second Associate (Alexandra Margulies)
  • Knowle Rohrer (Adam Baldwin)

Scully and Doggett are called in to investigate reports of alien impregnations on human subjects. As their discoveries become even more disturbing, Scully is forced to question whether she should reveal the secret of her pregnancy to Doggett. Clues to the identity of who - or what - is the father of Scully's baby may be revealed.

• Writer: Greg Walker
• Director: Terrance O'Hara
• Original Broadcast: 1/7/01
• Guest Cast:
  • Tammi Peyton (Kellie Waymire)
  • Dwight Cooper (Michael Bowen)
  • Randall Cooper (Patrick Kilpatrick)
  • Carlton Chase (Tom Jourden)
  • Capt. Al Triguero (Joe Sabatino)
  • First Officer (Ty Upshaw)
  • Second Officer (James Franco)
  • First Gangbanger (Noel Guglielmi)
  • Second Gangbanger (Greg Boniface)

Scully and Doggett investigate a seemingly impossible string of murders committed by an assailant with no apparent access to the victims. As they gain more information about the mysterious murderer and the circumstances surrounding the case, they uncover an unprecedented medical anomaly.

• Writer: Jeffrey Bell
• Director: Rod Hardy
• Original Broadcast: 1/14/01
• Guest Cast:
  • Ray Pearce (Wade Andrew Williams)
  • Nora Pearce (Jennifer Parsons)
  • Dr. Tom Puvogel (Arye Gross)
  • Larina Jackson (Tamara Clatterbuck)
  • Harry Odell (Dan Desmond)
  • Curt Delario (Scott MacDonald)
  • SWAT Cop (Randy Walker)
  • Owen Harris (Kenneth Meseroll)
  • Owen's Wife (Colleen Quinn)
  • Owen Harris' Little Boy (Reece Morgan)
  • Ray's Double (Jack Forbes)

Scully and Doggett investigate a series of bizarre and unexplained deaths in a small Midwestern town. The killer appears to be a man who was previously thought dead.

• Writer: Frank Spotnitz
• Director: Kim Manners
• Original Broadcast: 2/4/01
• Guest Cast:
  • Fox Mulder (David Duchovny)
  • Assistant Director Walter Skinner (Mitch Pileggi)
  • Byers (Bruce Harwood)
  • Frohike (Tom Braidwood)
  • Langly (Dean Haglund)
  • Creature (Jordan Marder)
  • Sheriff Kurt Frey (Michael McGrady)
  • Paul Hangemuhl (Justin Williams)
  • Marie Hangemuhl (Natalie Radford)
  • Rustic Woman (Caroline Lagerfelt)

A case Mulder kept secret from Scully comes to light as Doggett investigates circumstances that may ultimately relate to Mulder's unexplained disappearance.

• Writer: John Shiban
• Director: Tony Wharmby
• Original Broadcast: 1/21/00
• Guest Cast:
  • Beggar Man (Deep Roy)
  • Mr. Burrard (Christopher Hutson)
  • Bellboy (Winston Story)
  • Customs Agent (Kiran Rao)
  • Quinton (Jordan Blake Warkol)
  • Quinton's Father (Andy Hubbell)
  • Quinton's Mom (Ruth de Sosa)
  • Mr. Potocki (Calvin Remsberg)
  • Mrs. Holt (Jane Daly)
  • Red-Headed Kid (Jacob Franchek)
  • Teacher (Mimi Savage)
  • Trevor (Michael Welch)
  • Trevor's Mom (Maura Soden)
  • Trevor's Dad (Tony Adelman)
  • Chuck Burks (Bill Dow)

Scully and Doggett investigate a string of mysterious murders linked to a mystical being that is inhabiting its victims' bodies. As they gain more information about this inexplicable culprit, Scully and Doggett must race to stop it before it chooses its next victim.

• Writer: Frank Spotnitz
• Director: Richard Compton
• Original Broadcast: 2/11/01
• Guest Cast:
  • Deputy Chief Karras (Ken Jenkins)
  • Lt. Bianco (Vyto Ruginis)
  • Hellura Lyle (Penny Johnson)
  • Steven Melnick (Brent Sexton)
  • Dr. Kai Bowe (Judith Scott)
  • Passenger/Transit Cop Philbrick (Adam Gordon)
  • Kid (Christopher and Kevin Graves)
  • Gangbanger (Bill Jacobson)
  • Woman (Mary-Kathleen Gordon)

Scully and Doggett race to investigate a string of bizarre deaths in the tunnels of the Boston subway system linked to a mysterious killer.

• Writer: Chris Carter & Frank Spotnitz
• Director: Kim Manners
• Original Broadcast: 2/25/01
• Guest Cast:
  • Fox Mulder (David Duchovny)
  • Assistant Director Walter Skinner (Mitch Pileggi)
  • Agent Monica Reyes (Annabeth Gish)
  • Richie Szalay (Judd Trichter)
  • Dr. Strauss (Bernard White)
  • Skinner's Assistant (Arlene Pileggi)
  • Teresa Hoese (Sarah Koskoff)
  • Night Nurse (Roz Witt)
  • Jeremiah Smith (Roy Thinnes)
  • Absalom (Judson Scott)
  • Nike Man (Randy Ross)
  • Uniformed Cop (John McGonegle)
  • Gary Cory (Eddie Kaye Thomas)

The search for Mulder intensifies as FBI agent Monica Reyes joins the hunt for the missing Mulder. As Scully and Doggett's difference of opinions about the missing Mulder heighten, Doggett enlists Reyes' help to bring her own viewpoint and expertise to the mysterious Mulder X-File. Part one of three.

• Writer: Chris Carter & Frank Spotnitz
• Director: Tony Wharmby
• Original Broadcast: 4/1/01
• Guest Cast:
  • Fox Mulder (David Duchovny)
  • Assistant Director Walter Skinner (Mitch Pileggi)
  • Deputy Director Alvin Kersh (James Pickens Jr.)
  • Absalom (Judson Scott)
  • Billy Miles (Zachary Ansley)
  • Dr. Lim (Nelson Mashita)
  • Dr. Francis Orovetz (Richard McGonagle)
  • Alex Krycek (Nick Lea)
  • Arthur Gaffin (Gibby Brand)
  • 1st Deck Hand (Larry Rippenkroeger)
  • Minister (David Doty)
  • Nurse (Mary Wickliffe)
  • Pathology Assistant (Larry Dorf)
  • Mrs. Scully (Sheila Larken)
  • Byers (Bruce Harwood)
  • Frohike (Tom Braidwood)
  • Langly (Dean Haglund)
  • Skinner's Assistant (Arlene Pileggi)

Scully's frantic efforts to save Mulder were not successful and he is finally put to rest as the episode opens. Three months later, Doggett has been offered the chance to transfer out of the X-Files, while he and Scully re-open the investigation into Mulder's death when a man abducted with Mulder makes an impossible reappearance. Part two of three.

• Writer: Steven Maeda
• Director: Rod Hardy
• Original Broadcast: 4/29/01
• Guest Cast:
  • Fox Mulder (David Duchovny)
  • Assistant Director Walter Skinner (Mitch Pileggi)
  • Dep. Director Alvin Kersh (James Pickens Jr.)
  • Bo Taylor (M.C. Gainey)
  • Diego Garza (Gregory Norman Cruz)
  • Chef (Kevin C. Loomis)
  • Simon de la Cruz (Luis Villalta)
  • Ed Dell (Steve Wilcox)
  • Martin Ortega (Miguel Sandoval)
  • Yuri (Lee Reherman)
  • Saksa (Casey Biggs)

Mulder and Doggett are begrudgingly thrown together to investigate several mysterious deaths aboard an oil rig in the Gulf of Mexico. While Mulder believes the deaths on board to be part of the alien conspiracy, he races to convince the skeptical Doggett that the ship may not be pumping traditional oil.

• Writer: Greg Walker
• Director: Barry K. Thomas
• Original Broadcast: 4/22/01
• Guest Cast:
  • Fox Mulder (David Duchovny)
  • Special Agent Monica Reyes (Annabeth Gish)
  • Det. Franklin Potter (Ron Canada)
  • Dr. Mary Speake (Denise Crosby)
  • Gary Garber (Bruce Wright)
  • Jeb Dukes (Jay Underwood)
  • Katha Dukes (Wendy Gazelle)
  • Mia Dukes (Amanda & Caitlin Fein)
  • ER nurse (Cheryl Francis Harrington)
  • Roberta Toews (Dayna Beilenson)
  • Agent Joe Farah (Christopher Stanley)
  • Pimply-Faced Pizza Delivery Man (Devlin Elliott)
  • Distraught Woman (Louise Melilli)
  • Payphone Woman (Veronica Brown)
  • Luke Doggett (Jake Fritz)
  • ICU Nurse (Jennifer Hammon)

Mulder, Scully, Doggett and Reyes investigate a killer's mysterious connection to the unsolved murder of Doggett's son.

• Writer: Chris Carter & Frank Spotnitz
• Director: Tony Wharmby
• Original Broadcast: 4/8/01
• Guest Cast:
  • Fox Mulder (David Duchovny)
  • Deputy Director Kersh (James Pickens Jr.)
  • Frohike (Tom Braidwood)
  • Langly (Dean Haglund)
  • Byers (Bruce Harwood)
  • Absalom (Judson Scott)
  • Dr. Lem (Nelson Mashita)
  • Howard Salt (Gary Bristow)
  • Knowle Rohrer (Adam Baldwin)
  • Prison Armed Guard (Dwight Hicks)
  • White House Lead Guard (Joe Basile)
  • FBI Guard On Intercom (J.C. Murad)
  • Prison Trustee (Ric Sarabia)

Mulder secretly conducts his own investigation after a man is gunned down on the White House lawn attempting to inform the President of a planned alien invasion. Part three of three.

• Writer: Frank Spotnitz
• Director: Frank Spotnitz
• Original Broadcast: 5/6/01
• Guest Cast:
  • Fox Mulder (David Duchovny)
  • Assistant Director Walter Skinner (Mitch Pileggi)
  • Agent Leyla Harrison (Jolie Jenkins)
  • Gary Sacks (Tony Ketcham)
  • Arlen Sacks (James Otis)
  • Pathology Assistant (Lisa Kaseman)
  • Herman Stites (Zach Grenier)
  • Salamander Man (Jay Caputo)

With Scully on leave due to her impending delivery and Mulder still barred from his official investigative duties, Doggett, with the aid of a new and very green FBI agent, finds himself hot on the trail of a deadly creature. But when the situation turns and they become the hunted, Mulder and Scully must race against time to rescue them.

• Writer: Chris Carter
• Director: Kim Manners
• Original Broadcast: 5/13/01
• Guest Cast:
  • Fox Mulder (David Duchovny)
  • Assistant Director Walter Skinner (Mitch Pileggi)
  • Special Agent Monica Reyes (Annabeth Gish)
  • Margaret Scully (Sheila Larken)
  • Alex Krycek (Nick Lea)
  • Lizzy Gill (Frances Fisher)
  • Dr. Lev (David Purdham)
  • Dr. James Parenti (Steven Anderson)
  • Dr. Speake (Denise Crosby)
  • 1st Woman Party-Goer (Arlene Pileggi)
  • 2nd Woman Party-Goer (Karon Kearney)
  • Duffy Haskell (Jay Acovone)
  • Billy Miles (Zachary Ansley)

Long-simmering plot twists converge and details about Scully's pregnancy are revealed as Mulder, Doggett, Skinner and Reyes must put aside their differences and work together to protect Scully's unborn child. Part one of two.

• Writer: Chris Carter
• Director: Kim Manners
• Original Broadcast: 5/20/01
• Guest Cast:
  • Special Agent Monica Reyes (Annabeth Gish)
  • Alex Krycek (Nicholas Lea)
  • Agent Gene Crane (Kirk B. Woller)
  • Deputy Director Alvin Kersh (James Pickens, Jr.)
  • Melvin Frohike (Tom Braidwood)
  • Richard Langly (Dean Haglund)
  • John Byers (Bruce Harwood)
  • Knowle Rohrer (Adam Baldwin)
  • Dr. James Langenhahn (Austin Tichenor)
  • Pathologist's Assistant (Tom Martin)
  • Billy Miles (Zachary Ansley)
  • Game Warden (Dale Dickey)
  • William Scully Jr. (Jerry Shiban)

Mulder, Doggett, Skinner and Reyes race against time to protect Scully and her unborn child from unknown pursuers as the possibility of an extraterrestrial conspiracy solidifies and a potential link to the FBI is questioned. Part two of two.