in the last season of the x-files, scully gives birth to mulder’s baby but then has to give him up for adoption because he’s in danger, or evil, or a superbaby, or something. she gives him to a farm couple who resemble clark kent’s parents, thereby fueling the whole superbaby theory.in the last episode, mulder gets arrested for murdering this dude named knowle rohrer. since knowle rohrer is a supersoldier and can’t be killed and therefore isn’t actually dead, scully and mulder and skinner and robert patrick know that the allegations are bullshit. to prove mulder’s innocence, they hold a military trial during which they recap the ENTIRE SERIES and invite back every single recurring character from the last nine years. it’s just like the final episode of seinfeld, but without that green day song.
despite the stirring retrospective, mulder is found guilty and sentenced to death by lethal injection. can they really sentence someone to death by lethal injection without a jury trial? there’s no time for questions like that, because scully busts mulder out of jail and now they’re on the lam! while they’re on the lam, mulder stops to take a piss and talk to the ghosts of the lone gunmen, who were killed off earlier in the season, in an episode cleverly titled “jump the shark.”
anyhow, mulder and scully drive to a pueblo in the desert to see the cigarette-smoking man. they climb up into his lair, where they find him all decrepit and white-haired and smoking through a hole in his throat. he tells them that the aliens are going to take over in 2012, and that’s when the world is going to end, and the mayans knew this back in the day and that’s why their calendar ends in 2012. i don’t think the smoking man actually used the phrase “back in the day,” but you get the idea.
meanwhile, outside the pueblo, robert patrick runs into knowle rohrer. it turns out that magnetite is a supersoldier’s kryptonite, so robert patrick kills him with the magnetite bullets he keeps in his purse for just such an occasion. hey, he didn’t walk away from those terminator movies without learning a little something about metal.
mulder and scully climb down from the pueblo and drive off in their car. and just in time, too, because some black helicopters show up and bomb the shit out of the pueblo, killing the smoking man and ruining thousands of precious native american artifacts.
later, mulder and scully sit around in a seedy motel room. they talk about The Truth, and then they make out. the end.
i hope this answers your question.