The second to last episode of season 6 doesn’t really build up to anything. Though it starts off quite promising. Scully and Mulder find some skeletons in the woods, who have only been there a few days, and Mulder discovers their owners nearby, alive and well.
</span>From then on Mulder is convinced aliens are involved, and actually argues with Scully stating he’s been 98.9% right on all X-Files cases. He then goes on to explain they always have the logical reasoning come out of Scully’s mouth to begin with, only to go on and prove Mulder right – Scully wonders just how many X-Files they’ve actually solved, but to cut a long story short… they’ve been eaten by a large underground plant that feeds them dodgy mushrooms to make them hallucinate while being slowly digested by acids.
That’s where the skeletons came from and everything after that was a dream. Skinner manages to find them underground and everyone lives. Interesting side note – when we see Mulder’s bedroom in on of Scully or Mulder’s hallucinations – there is no water bed.