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In 35,000 B.C., two primitive men were attacked by an alien in North Texas. One of the primitives was killed by the creature, while the other was killed by the alien's toxic blood.

In 1998, a boy called Stevie found the remains of the primitives after falling into the cave where they had died. (The X-Files Movie)

The two primitives, who are shown in the opening shot of The X-Files Movie, were played by Craig Davis and Carrick O'Quinn.
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.