| Episode | Description |
|---|---|
| NOTHING IMPORTANT HAPPENED TODAY I | EPA agent killed by a woman hitchhiker |
| NOTHING IMPORTANT HAPPENED TODAY II | EPA agents preparing the water supply |
| DAEMONICUS | Investigation of a murdered couple in west virginia | 4-D | agent Doggett is both the shooter and the shooted |
| LORD OF THE FLIES | A local cable reality show goes horribly wrong |
| TRUST NO 1 | Scully is approached by a couple who claim their baby has the same abilities as William but they will only talk to Mulder |
| JOHN DOE | Reyes and Scully team up to find a missing agent Doggett |
| HELL BOUND | A man found skinned alive |
| PROVIDENCE I | Pieces of a spaceship beached in Africa appear and Scully takes drastic measures to protect William |
| PROVIDENCE II | Scully and the Lone Gunman investigate the kidnapping of Scully's son |
| AUDREY PAULEY | After a car accident, Reyes finds herself in a very gray area |
| UNDERNEATH | The Trio investigate an old case that Doggett dubbed "The Screwdriver Killer". |
| IMPROBABLE | A serial killer is driven by numerology while Mr. Burt dispenses confusing "advice". |
| SCARY MONTERS | Doggett and Reyes investigate a boy's claim that monsters killed his mother, |
| JUMP THE SHARK | Morris Fletcher claims Yves Adele Harlow is one of the "super soldiers" |
| WILLIAM | Scully must allow herself to send William away for his own safety. |
| RELEASE | an FBI cadet with amazing profiling skills claims to know the killer of Doggett's son |
| SUNSHINE DAYS | Doggett and Reyes investigate a murder outside the house that the original Brady Bunch series was filmed in. |
| TRUTH, THE | Mulder Returns to Scully with "the truth" |