#1 - Existence (2) 8.46
Season 8 - Episode 21
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.
#2 - Anasazi (1) 8.46
Season 2 - Episode 25
When Mulder obtains what could be the original and uncut MJ documents containing information about the government's knowledge of extraterrestrial life; his shadowy enemies step up their harassment of him, eventually leading to his apparent murder.
#3 - Bad Blood 8.45
Season 5 - Episode 12
After Mulder chases down and kills a young man who he believes to be a vampire, the agents return to DC aware of the mistake they just made. Faced with a lawsuit from the family of the man, they recount each of their sides to the story leading up to the event. In the extremely humorous stories that follow we see how Scully and Mulder both perceive each other.
#4 - Redux II (3) 8.45
Season 5 - Episode 2
The Cigarette-Smoking Man helps Mulder to obtain Scully's cure and also lets him see his real sister who doesn't turn out to be as happy to see Mulder as he would've liked. In return for this, the Cigarette-Smoking Man asks that Mulder quit the FBI and work for him in the Syndicate where he could have power and respect which Mulder turns down, deciding to stay on the side of justice. While Scully's cure appears to have worked, the Cigarette-Smoking Man faces his own enemies and disappears, presumed dead.
#5 - The Erlenmeyer Flask 8.38
Season 1 - Episode 24
When Deep Throat points out a news story about a fugitive who apparently drowned, Mulder and Scully cannot see what makes the case special but follow it up anyway. With Deep Throat's insistence, they discover evidence of a secret government project code-named Purity Control, which uses human test subjects and infects them with extraterrestrial DNA. However, the evidence and everyone who has seen it is quickly being eliminated.
#6 - One Son (2) 8.37
Season 6 - Episode 12
The Cigarette-Smoking Man reveals all the government secrets from the past 50 years in order for his son, Jeffery Spender, to join him in his work. Mulder learns that the final stage of the conspiracy will soon begin with the hybridization of the Syndicate members, and he must stop it from happening. Agent Spender deceives his father and arranges for Mulder and Scully to be reassigned to the X-Files, which doesn't sit too well with the Cigarette-Smoking Man.
#7 - The End 8.32
Season 5 - Episode 20
The Cigarette-Smoking Man returns as Mulder investigates the attempted assassination of a young boy with psychic powers who may be the proof that he has looked for all his life.
#8 - Paper Clip (3) 8.31
Season 3 - Episode 2
A.D. Skinner and Scully are at a standoff when Mulder bursts in and discovers that Skinner has the digital tape. Reunited, Mulder and Scully travel to a secret vault inside a mine and find an elaborate filing system of medical records which reveals that Mulder's sister may not have been the first choice for abduction. Meanwhile, Skinner deals with the Cigarette-Smoking Man for their safety.
#9 - Musings of a Cigarette Smoking Man 8.30
Season 4 - Episode 7
Frohike pieces together and recites to Mulder and Scully what could be the possible life story of the Cigarette Smoking Man; from a young captain in the U.S. Army recruited to assassinate President Kennedy, to becoming the mysterious man in the shadows at the height of a global conspiracy. What measures will the Cigarette Smoking Man take to ensure that he remains a mystery forever?
#10 - Redux (2) 8.29
Season 5 - Episode 1
Scully helps Mulder fake his own death in order for him to go undetected through the Department of Defence and find out the answers to his new questions about the government hoax concerning the existence of extraterrestrial life. Meanwhile, at a joint FBI/DOD inquiry, Scully's attempt to drive out the Conspiracy's informant is halted as her cancer takes a bad turn.
#11 - Herrenvolk (2) 8.28
Season 4 - Episode 1
Jeremiah Smith and Mulder are on the run from the alien bounty hunter, and Smith takes Mulder to a small farm tended to by identical sets of children, and all the girls are clones of his sister when she was still a child. Mulder prepares to take Jeremiah and one of the clones to see his mother in the hospital, but the bounty hunter catches up with them. Meanwhile, the Syndicate suspects that they have a traitor in their midst and plan a trap which results in X being executed by the Cigarette-Smoking Man.
#12 - Gethsemane (1) 8.24
Season 4 - Episode 24
While investigating the discovery of a preserved alien body found in the mountains of Canada, Mulder is contacted by Michael Kritschgau. He tells Mulder about a government conspiracy to make people believe in aliens without question, and Mulder has been the prime target.
#13 - End Game (2) 8.23
Season 2 - Episode 17
The alien bounty hunter kidnaps Scully and wants to trade her for Mulder's sister, who is revealed to be a clone herself. After the trade goes badly and Mulder discovers the truth about Samantha, he tracks the bounty hunter to his ship buried in the arctic ice and demands the whereabouts of his real sister.
#14 - Clyde Bruckman's Final Repose 8.22
Season 3 - Episode 4
In the midst of a psychic sideshow while on a murder case, Mulder and Scully enlist the help of a man who may have a true psychic ability to foresee how people will die to help the agents catch a man killing fortune tellers.
#15 - Two Fathers (1) 8.21
Season 6 - Episode 11
While the Cigarette-Smoking Man recites to an unseen listener everything about the work of the Syndicate involving a global conspiracy in cooperation with an alien species, Cassandra Spender reappears and is pursued by the scientists who would rather kill her than keep her alive. Cassandra runs to Mulder's apartment and demands that he shoot her because she is the culmination of 50 years work - a living alien/human hybrid - and colonization will begin if the aliens find out about her.
#16 - Colony (1) 8.21
Season 2 - Episode 16
After the obituaries of four identical men are e-mailed to Mulder, the agents are contacted by a shadowy CIA agent who tells them about a bounty hunter sent to wipe out the beginning of a colony of clones. Meanwhile Mulder is distracted by the sudden reappearance of his sister Samantha.
#17 - Dreamland (1) 8.21
Season 6 - Episode 4
While being detained near the famed "Dreamland" Area 51, a strange craft flies overhead and Mulder swaps bodies with an Area 51 "Man-in-Black". While the other agent has fun in Mulder's body, Mulder himself finds it difficult to fit into someone else's life, especially a shadowy one. Mulder contacts Scully about the body swap and tries to get her the flight data recorder from the UFO test flight, but his alter ego uses Mulder's FBI persona to have him arrested.
#18 - Ascension (2) 8.21
Season 2 - Episode 6
When Mulder finds out that Scully was kidnapped by Duane Barry, he risks the wrath of his superiors and the annoyance of Agent Krycek in order to do whatever it takes to find her. Meanwhile, Krycek is found to be reporting Mulder's activities to the Cigarette-Smoking Man.
#19 - The Blessing Way (2) 8.20
Season 3 - Episode 1
Scully finds her career with the FBI in jeopardy as Mulder is still missing and the Cigarette-Smoking Man is pursuing the stolen files. The Navajo elders find Mulder's body in a cave and perform an ancient ceremony to call the spirit back to the empty vessel.
#20 - Duane Barry (1) 8.19
Season 2 - Episode 5
Mulder is called to a hostage situation involving Duane Barry, a former FBI Agent who claims to be an alien abductee and wants to get back to the abduction site with someone who will be taken instead of him. Unfortunately, the someone he eventually chooses is Scully.
#21 - Without (2) 8.18
Season 8 - Episode 2
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, A.D. Kersh informs Agent Doggett that he has been assigned as Mulder's successor on the X-Files.
#22 - Essence (1) 8.18
Season 8 - Episode 20
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. 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.
#23 - Small Potatoes 8.17
Season 4 - Episode 20
Five babies in the same town are all born with tails and the local OB-GYN is blamed for tampering with fertilized eggs. However, Mulder discovers the culprit to be a simple man with a genetic deformity who may have the ability to alter his appearance.
#24 - The Truth (2) 8.15
Season 9 - Episode 20
When an unexpected person comes to Mulder's rescue, Mulder refuses to slip north over the border to safety. Instead, he heads southwest to the Anasazi ruins of New Mexico seeking a mysterious wise man who the Indians call "The Keeper of the Truth".
#25 - Talitha Cumi (1) 8.13
Season 3 - Episode 24
Mulder and Scully search for a mysterious man with the power to heal. His actions risk exposing the existence of aliens on Earth, while a confrontation between Mrs. Mulder and the Cigarette-Smoking Man leads Mulder to the discovery of the only weapon which can kill the aliens.