The opening shot of The Beginning - the Season 6 premiere of The X-Files, set soon after the majority of the movie - shows two male scientists from Roush Technologies running across a barren landscape, towards camera. The depiction of this shot from the episode's script mentions, "Anyone who saw the Movie will recognize a wink at the opening shot. Except these figures, we see as they approach, are not the primitives from 35,000 years ago, but scientists".
Footage of the primitives from the movie is shown in the teaser of Biogenesis and in The Truth.
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