We’ve been talking in another thread about what a vast suckorama the last episode of The X Files was. But it seems to me that there are few ways that they COULD have ended the show while staying true to the idea that we’re never really going to know everything.
So, given the chance, how would you have scripted the final episode?
I think a killing spree was in order, starting with Chris Carter.
Well, to start with… Skully would be naked and writhing in ecstasy.
With Reyes. Yeah, that’s the ticket…
Actually, I think they should have had an alien invasion. Something out of Childhood’s End.
…but, seriously, folks. 
It woulda helped Mulder if that alien-judge revealed himself ala Alien chest-burster.
Well, since the basic plot of the X-Files was this impending alien invasion, I would have ended it in one of two ways:
The aliens are somehow prevented from invading.
The aliens invade and kill everyone.
Mulder walks up to the camera, reaches offscreen, yanks a cameraman into view of the other actors.
“The truth is, we are ALL characters in a television show!”
Oh, and I’m all for that naked Scully-Reyes thing.
I would have ended it by having Mulder, Scully, Skinner, Kirsch, Reyes, Corraruvius(that blonde lady who used to work for the UN), Dogget, and Gibson form the new syndicate, like I was led to believe they were planning to do two seasons ago. It would have been cool to see them turn into what they’ve been looking for all this time. They would become the conspiracy.
Imagine a fast forward at the end of the series, 9 years from now:
A young FBI hot shot seeking the truth has just reopened the X-files and leaves the assistant director’s office. As the door closes, the assistant dierector turns to a shadowy part of his office, where an older looking Mulder, looking very ominous, lights up a cigarette. Fade out and role credits.
Now how cool would that have been?
Idea #1
They give up on the pretense of a trial. The judge admits he’s an alien because all the other judges have known for quite a while. The bad guys admit Mulder’s innocence. Then, the guards shoot Mulder, Scully, Dogget, Reyes, and psychic boy.
Idea #2
The episode actually answers all the questions that the series has asked. But, these lead to new and unexpected questions. That way, the series ends with a nice payoff for viewers but with enough new questions to fuel the coming films.
Idea #3
Scully reveals that Mulder has never actually seen an alien. For years she has been hypnotizing Mulder, donning a bizzare latex bodysuit and probing his rectum. This all comes to light after he discovers the bodysuit, a strange glowing rod and a Bend Over Boyfriend video in Scully’s closet.
Idea #4
The Conspiracy is destroyed by a second conspiracy. Mulder begins investigating this new Cabal and discovers it is led by a strange figure wearing a mortarboard and a paperbag
Scully looks at her watch and says “Mulder, we’ve somehow lost 9 minutes!.”
And they are back in the forest of the “Pilot episode” searching for Billy Miles. The last 9 seasons never happened.
How would I have ended it?
Umm… is “5 years ago” an acceptable answer?
I would have let Mulder win. Have him publicly expose the Alien conspiracy. And then have suprise both sides when the public won’t buy it. [“My life’s work and no one believes me” and “We’ve been trying so hard to hide and everyone believes it’s just some promotional gimmick”]
There is no secret cabal!
Heh. I like it.
Well, since they’re using the Mayan timeline point of change as the Alien invasion date, it would be pretty cool if Mulder and Scully headed down to Mexico/Guatamala where that prophecy is well esconced. Mebbe they could hook up with some shamans and get a bit of a grip on the situation. I’m assuming that the shiny new Ford Expedition that got them to the SW pueblos is good for a few more miles…
Supposedly, the next movie will be a stand-alone story. What’s the point? Why go into the future a few years. Or at least let us know what happened to Reyes, Skinner, and Doggett (Robert Patrick, BTW, did a damn good job in spite of the pressure and the size of the shoes he had to fill).