Ok, sweet, finally I can feel superior in this forum, knowing (hopefully, if no one comes up to spoil my title
) more about X-Files than the rest of you guys.
Let me explain.
Mulder gets abducted at the end of season 7, in the episode Mekt has mentioned.
In season 8, Mulder is totally absent for the first part of the season, but he appears in form of flashbacks.
The "new guy", as Quarto said, is actor Robert Patrick (the T-1000 guy from Terminator 2), who plays agent John Doggett, a friend of Walter Skinner. He is the new assigned partner for Dana Scully.
In this new season, the producers and directors wanted to give X-Files the original stance i.e.
Mulder investigating paranormal cases, and
Scully being there to question his judgement, and provide a scientific opinion...
In the first seasons, Mulder "believed", Scully was the "skeptic"...
In this new season, the roles have changed: Mulder is gone, and Scully has seen so many things she could not explain in the past seasons, that she has started to "believe" as well!
Moreover, her partner has disappeared, and she really thinks he was abducted!! That's where Doggett comes in, taking Scully's "role" of the first seasons: the "skeptic" character!!
At any rate, we're way after mid-season by now, and Mulder has just reappeared in the last episode: he has been "returned" by the Aliens...
AHA, but unfortunately in the last episode it appears that he is dead, that he did not survive the tests the aliens performed on him!!
As always, Chris Carter leaves us in doubt...
To answer you last question Mekt, Mulder and Scully should make "guest apperances" in the
Lone Gunmen series, yes!
As a matter of fact, the next episode on Friday should feature Walter Skinner already...
Mulder should appear later, but the episode in which he appears has not been filmed yet...