I hope it comes back for another season.
I am sorry to not have put a spoiler tag on my post. Please know that I did not intend to ruin it for others. I do regret my mistake.Not that I care about this show, but I'm sure someone will be perturbed by the presence of spoilers with no buffer.
I think the deal is that they have set up a continuation or spinoff with Miller and Einstein instead of Mulder and Scully. The ending just sets up Mulder and Scully as missing and leaves open a door for a cameo or closure someday.