In this shot, we see Janke (our Hades stand-in) pulling out of a parking lot followed by three barking Rottweilers. Now we know Janke has a multi-headed dog, so here we are seeing Hades again in his chariot, with the three dogs standing in for Cerberus, the three-headed dog who stands at the gate of the Underworld.
UPDATE: Reader Jim made a fascinating connection between this visual- a representation of Cerberus and a "UP" gas station and this article about the BP disaster. Very interesting indeed.
Janke picked up a prescription for an animal tranquilizer here, which links us to theories about the descent to the underworld motif. Persephone was picking narcissus flowers when Hades first saw her, which have narcotic properties.
As Janke drives off we see three ravens (a common symbol of death) fly ahead of him. But Carter may well be referencing Poe here, linking again to Hades/Pluto: 'Tell me what thy lordly name is on the Night's Plutonian shore!'/Quoth the raven, `Nevermore.'
But keep an eye on that chap on the street there....
Just as we saw the visual link between Scully and the dog in the hospital, we see this very quick visual juxtaposition, a hooded (and hollow-eyed, thanks to his quite unnecessary sunglasses) man standing and Mulder sitting in his car.
A familiar visual arrangement seen in depictions of Charon, the ferryman to the Underworld...
...who is often seen in contemporary depictions as a hooded figure with a skull for a head, or sometimes as a blind man.
This motif is germane since Mulder takes on his traditional role as Osiris and is tricked and trapped by Janke, who then "murders" him on the road/river.
Immediately after Mulder's "death" we see Carter himself clutching a very canopic-looking funerary urn (containing the ashes of his dog, who died during the film's production). Symbolically-speaking, this shot doubles up, since it also identifies Scully with Isis, via the 'Dog Star'.
This is now the sequence where we see DNA Scully crowned with the Amanita Muscaria Grail of Light, similar to that of Isis-Aphrodite. She realizes Mulder is in the Underworld, signaled by the photos of the two-headed dogs (three heads might have seemed too obvious).
Again, we see her explicitly identified as the Mater Dolorosa, and here we see an analog of Isis casting spells to raise Mulder from the dead...
... with this double-entendre. We see Mulder's sarcophagus, and shortly after...
....he rises from the dead as Osiris-Dionysus-Orpheus, descending to the Underworld to rescue Cheryl-Semele-Eurydice, and where he also encounters his anima, the dismembered Monica.
What does it mean? Well, I'm not sure, but just like that Sirius-soaked Cleopatra exhibit in Phila(e)delphia, it all seems to point to DNA and the mysteries it holds. The X-Files was the first place I heard of junk DNA, something that Intervention Theorists are focused on as well.
At the same time the theme of the film comes from Huston Smith and the Billy Connolly character was inspired by Alan Watts. Both men were pioneers in the field of entheogenic theory, and mushroom motifs are all over the place in the film.
One thing that I do realize about The X-Files was that the point is not wrap things up in a simple bow (ie., close the door) but to create a kind of disoriented state in which the viewer is encouraged to provide his or her own interpretations (meaning to open the door). We'll not being seeing that kind of daring on network TV again soon.
But maybe at this stage in the game all we can do is keep that door open. There is no doubt in my mind that information is being kept from us on any number of vitally important topics pertaining to human origins and our place in the Universe.
And as frustrating as it is, I'd say a good question is much better for you than a crummy answer.
UPDATE: We'd see a more explicit take on this entire Charon motif in The X-Files 2016 revival episode, "Babylon."
POSTSCRIPT: I was just reading a critical work on The X-Files, which has its extremely frustrating moments in that the writer didn't understand the Mythology at all. I mean at all. Now, there was a stretch in the Mytharc- from 'Nisei' to 'Redux II' (and excepting 'Tempus Fugit/Max') where I didn't really understand it either. But after watching the episodes in order I realized that they were chapters, not episodes.This all started right at the time episodes of The X-Files were being released on home video and Chris and Frank knew that the whole series would be released at some point (The X-Files was the first TV show to be be released on DVD). I later realized that they were experimenting with the storytelling format, though they seemed to judge the experiment a failure and returned to more tightly-focused Myth eps with 'Patient X' (and forget most of the season nine Mythology, since they obviously thought they were finally finished with it for good at the end of season eight).But the point is that the author obviously realizes that Chris was a determined envelope-pusher (see Triangle, Post-Modern Prometheus, Improbable, etc. etc.) but didn't bother to rewatch the Myth eps in order and realize that A., they do all fit together and B., they're not confusing at all when you watch them that way. Like too many fans the author also didn't realize that a lot of the problems that people complain about in the series were down to network decisions.