Agents Mulder and Scully return from Antarctica to find their story of the deadly virus, alien spaceship, and subsequent escape disbelieved and their positions in the X-Files taken over by Jeffrey Spender and Diana Fowley. Although forced to work apart, the agents continue to secretly investigate information that passes through the X-Files office or comes to the clandestinely. Only after Cassandra Spencer returns saying that the aliens are about to colonise earth are Mulder and Scully reinstated to the X-Files. Then, an extraterrestrial artifact is found off the coast of Africa, an artifact which may hold the key to the very origins of life on earth - and which has a devastating effect on Mulder.

Episodes:
* Disc Four
Agua Mala
Monday
Arcadia
Alpha
* Disc Five
Trevor
Milagro
The Unnatural
Three of a Kind
* Disc Five
Field Trip
Biogenesis (1)
Special Bonus Features

Special Features:

* Deleted Scenes
* International Clips
* Audio Commentary
* Documentary "The Truth About Season Six"
* Featurette "Behind The Scenes of Season Six"
* 15 scenes with optional commentary
* 13 Special Effects sequences with commentary
* 30 promotional TV spots