The video release has additional footage not shown in the theatrical release:
- In the opening scene you now see more of the alien. In the theatrical release we see it fight off one of the cavemen, killing it, and the other caveman gets up to see it lying on the ground draining out the black blood (or what fans know as black oil). In the video release, we see it run off after it kills one of the cavemen, and when the other caveman gets up, he tracks it down and then kills it using the broken end of his torch.
- In the scene with Mulder talking to the Well Manicured Man in the car, he reveals to Mulder that Samantha, Mulder's sister, was abducted by aliens at the request of her father, William Mulder, so she could be part of the colonization project, thus ensuring her survival in the colonization of Earth by the visitors. Also revealed is that when plans went awry, Mulder was intended, by his father, to seek the truth and reveal what had been done.
- There is also an added scene in the video release with Mulder running down the street after the hospital scene.