| # | Episode Name | Description | Quotes | Tag Line | Credits | Air Date | Rating |
| 1 | "Little Green Men" | The Second Season Première | "What am I looking for?" "Contact." |
THE TRUTH IS OUT THERE | W: Glen Morgan, James Wong D: David Nutter |
1994-09-16 (Fri.) | TT |
| 2 | "The Host" | The Fluke-Man Episode | " | W: Chris Carter D: Daniel Sackheim |
1994-09-23 (Fri.) | TTT | |
| 3 | "Blood" | The Subliminal Messages Episode | " | Story: Darin Morgan Script: Glen Morgan, James Wong D: David Nutter |
1994-09-30 (Fri.) | TT | |
| 4 | "Sleepless" | The Sleep Deprivation Episode | " | W: Howard Gordon D: Rob Bowman |
1994-10-07 (Fri.) | TTTT | |
| 5 | "Duane Barry" | The Episode with Duane Barry | "They're coming again, I can feel it." |
" | W: Chris Carter D: Chris Carter |
1994-10-14 (Fri.) | TTT |
| 6 | "Ascension" | The Abduction Episode | "Where is she?!" "They took her!" "Who?" "Them!" |
DENY EVERYTHING | W: Paul Brown D: Michael Lange |
1994-10-21 (Fri.) | TTTTT |
| 7 | "3" | The Episode with the Three Vampires | THE TRUTH IS OUT THERE | W: Glen Morgan, James Wong, Chris Ruppenthal D: David Nutter |
1994-11-04 (Fri.) | TT | |
| 8 | "One Breath" | The Episode Where Scully Comes Back | " | W: Glen Morgan, James Wong D: R. W. Goodwin |
1994-11-11 (Fri.) | TTTT | |
| 9 | "Firewalker" | The Volcano Episode | " | W: Howard Gordon D: David Nutter |
1994-11-18 (Fri.) | TTT | |
| 10 | "Red Museum" | The Beef Episode | " | W: Chris Carter D: Win Phelps |
1994-12-09 (Fri.) | TT | |
| 11 | "Excelsis Dei" | The Retirement Home Episode | "You think that Michelle
Charters was raped by a seventy-four-year-old schizophrenic?" "It's possible." "An invisible seventy-four-year-old schizophrenic." |
" | W: Paul Brown D: Stephen Surjik |
1994-12-16 (Fri.) | TTT |
| 12 | "Aubrey" | The "Brother"/"Sister" Episode | " | W: Sara B. Charno D: Rob Bowman |
1995-01-06 (Fri.) | TTT | |
| 13 | "Irresistible" | The Serial Killer Episode | " | W: Chris Carter D: David Nutter |
1995-01-13 (Fri.) | TTT | |
| 14 | "Die Hand die verletzt" | The Witchcraft Episode | "Mulder, toads just fell from
the sky!" "I guess their parachutes didn't open." |
" | W: Glen Morgan, James Wong D: Kim Manners |
1995-01-27 (Fri.) | TTTT |
| 15 | "Fresh Bones" | " | W: Howard Gordon D: Rob Bowman |
1995-02-03 (Fri.) | TT | ||
| 16 | "Colony" | The First Episode with Samantha | "Who is Mom talking to?" "Your sister." |
" | Story: Chris Carter, David Duchovny Script: Chris Carter D: Nick Marck |
1995-02-10 (Fri.) | TTTT |
| 17 | "End Game" | The Second Episode with Samantha | " | W: Frank Spotnitz D: Rob Bowman |
1995-02-17 (Fri.) | TTTT | |
| 18 | "Fearful Symmetry" | The Zoo Episode | " | W: Steve De Jarnatt D: James Whitmore Jr. |
1995-02-24 (Fri.) | TTT | |
| 19 | "Død Kalm" | The Boat Episode | " | Story: Howard Gordon Script: Alex Gansa, Howard Gordon D: Rob Bowman |
1995-03-10 (Fri.) | T | |
| 20 | "Humbug" | The Circus Freaks Episode | " | W: Darin Morgan D: Kim Manners |
1995-03-31 (Fri.) | TTTT | |
| 21 | "The Calusari" | " | W: Sara B. Charno D: Michael Vejar |
1995-04-14 (Fri.) | TT | ||
| 22 | "F. Emasculata" | " | W: Chris Carter, Howard Gordon D: Rob Bowman |
1995-04-28 (Fri.) | TT | ||
| 23 | "Soft Light" | The Evil Shadow Episode | " | W: Vince Gilligan D: James A. Contner |
1995-05-05 (Fri.) | TT | |
| 24 | "Our Town" | The Cannibalism Episode | " | W: Frank Spotnitz D: Rob Bowman |
1995-05-12 (Fri.) | TTTT | |
| 25 | "Anasazi" | The Second Season Finale | 'ÉÍ 'AANÍÍGÓÓ 'ÁHOOT'É' | Story: Chris Carter, David Duchovny Script: Chris Carter D: R. W. Goodwin |
1995-05-19 (Fri.) | TTTT |