Season profiles
1. Within: Part 2 of 3. Sculley returns to work, with only Skinner knowing the truth about her pregnancy. The investigation into Mulder's disappearance is handed to Detective Doggett and Sculley attempts to find Mulder on her own.
2. Without: Part 3 of 3. The search brings them to finding Gibson Praise-The Beginning Episode- and a Mulder clone that is trying to take him. Doggett gets assigned to the X Files.
3. Redrum: Martin Wells wakes up and finds that time is jumping backwards. He must peice together what happened to his wife before she gets killed all over again.
4. Patience: Mulder and Dogett investigate what appears to be a vampire attack.
5. Roadrunners: Sculley, on her way to investigate a body found in the desert, gets stranded in a smalll quiet town. What she doesn't realise until it's too late, is that the towns folks are worshipping a worm like creature that burrows into the spine of humans and she's been picked as the next victim. Will Doggett get there in time?
6. Invocation: Billy Underwood disappeared when he was seven years old without a trace. His family have given up hope until 14 years later, he appears looking the same as he did when he left. Only his now 14 year old baby brother thinks there's something not right about him.
7. Via Negativa: Sculley is admitted to the hospital for tests, leaving Doggett alone on his first solo xfile. A man seems to be killing people while they are asleep-in a nightmares coming true sort of way. Has he opened his third eye or are drugs the culprit?
8. Per Manum: Sculley is upset to hear that a fellow abductee who became pregnant after being told it was impossible, died while giving birth. She sets off to investigate.
9. Surekill: A man gets shot while in police custody. The only suspects are a blind man and his brother but they were nowhere near at the time.
10. Salvage: A car crash at a salvage yard leads the new partners to find a theory about Gulf War syndrome. Could it be a simple death or something more sinister?
11. The Gift: A fake case leads Doggett on a wild goose chase and Skinner gets caught up in it.
12. Badlaa: Agents Scully and Doggett investigate an indian beggar who appears to have the power to alter perception.
13. Medusa: The Centre for Disease Control call in Agents Scully and Doggett to investigate an organism that consumes human flesh, discovered in the Boston subway system.
14. This Is Not Happening: Part 1 of 2. When news reaches the FBI that Teresa Hoese, abducted from Bellefleur, Oregon the night before Mulder, has turned up in a hospital in Helena, Montana. Agents Scully and Doggett travel to interview her and are joined by Assistant Director Skinner and Agent Monica Reyes. The doctor caring for Teresa tells them that she shows signs of being experimented on. This shakes Doggett, however it raises hope for Scully that Mulder will be found.
15. Dead Alive: Part 2 of 2. Scully's hopes for Mulder are raised further when Billy Miles, another abductee from Bellefleur, Oregon is dragged from the sea, barely alive. Scully also encounters Jeremiah Smith, who appears to be trying to help the abductees to return. But is it too late for Mulder?
16. Vienen: When a man dies in unusual circumstances on an oil rig in the Gulf of Mexico. Mulder fears a link to the black oil and argues that the case should be an X-file. Deputy Director Kersh agrees and sends agent Doggett to investigate, but Mulder makes his own way to the rig.
17. Empedocles: When the New Orleans Police Department uncover a series of ritualistic killings they ask the FBI for assitance. Agent Reyes is sent to investigate but soon contacts Mulder for his assistance, with his experience of such cases. Mulder however directs her to Agent Doggett, but she seems reluctant to deal with him.
18. Three Words: A man breaks in to the White House and is shot, as he lies bleeding he screams that he must tell the President that aliens are taking over the country. Secret service agents surround the dead man, however none of them shot him. In his hand he clutches a CD with the words, 'Fight the Future' on.
19. Alone: With Scully on maternity leave, Doggett is assigned a new partner to help investigate a case. Leyla Harrison who worked in the accounts department and has followed Mulder and Scully's work over the years, dreamed about being an agent assigned to the X-files. But her enthusiasm gets the better of her and conflicts with Dogget's investigation techniques.
20. Essence: Part 1 of .
21. Existence: Part 2 of .