Disc 1
- Deleted Scene From XF01-`The Blessing Way`: `Scully Looks For Comfort`
- Deleted Scene From XF04-`Clyde Bruckman`s Final Repose`: `Mulder
Wishes For A Real Psychic`
- International Clips
- Cast Credits For Each of The 4 Episodes on Disc 1
Disc 2
- Deleted Scene From XF05-`The List` : `Neech Goes To The Chair`
- International Clips
- Cast Credits For Each of The 4 Episodes on Disc 2
Disc 3
- Deleted Scene From XF11-`Revelations`: `Mr. Kryder Talks About
Armageddon`
- International Clips
- Cast Credits For Each Of The 4 Episodes On Disc 3
Disc 4
- Audio Commentary For XF16-`Apocrypha`
- International Clips
- Cast Credits For Each Of The 4 Episodes On Disc 4
Disc 5
- Audio Commentary For XF20-`Jose Chung`s From Outer Space`
- International Clips
- Cast Credits For Each Of The 4 Episodes On Disc 5
Disc 6
- Deleted Scene From XF21`Avatar`: `CSM Threatens Skinner`
- Deleted Scene From XF21-`Avatar`: "Skinner Visits His Wife`
- International Clips
- Cast Credits For Each Of The 4 Episodes On Disc 6
Disc 7
- Documentary: The Truth About Season Three : 다큐멘터리 : 시즌 3의 진실
- A Private Conversation With Chris Carter Creator of The X-Fiels or Chris
Carter Talks About Season Three
- 17 Behind The Truth
- 6 Deleted Scenes
- X-Files Visual FX Before & After or Special Effects Clips
- Promo Spots

Disc 1
- THE BLESSING WAY
- PAPER CLIP
- D.P.O
- CLYDE BRUCKMAN'S FINAL REPOSE

Disc 2
- THE LIST
- 2SHY
- THE WALK
- OUBLIETTE

Disc 3
- NISEI
- 731
- REVELATIONS
- WAR OF THE COPROPHAGES

Disc 4
- SYZYGY
- GROTESQUE
- PIPER MARU
- APOCRYPHA

Disc 5
- PUSHER
- TESO DOS BICHOS
- HELL MONEY
- JOSE CHUNG'S FROM OUTER SPACE

Disc 6
- AVATAR
- QUAGMIRE
- WETWIRED
- TALITHA CUMI