Begins at the end of 9x20 "The Truth"
Out in the desert Mulder and Scully make their way into a ancient Anasazi pueblos carved in the rocks. Led by an old indigenous woman they travel through a narrow passageway at the mouth of the cave, at the end where it opens up into a living space, CGB Spender is sitting waiting for them.
He looks much older, older than then the rocks that surround them.
"What's the matter, Agent Mulder?" Spender asks taking a drag of his cigarette through the trachea hole in his neck.
"You come to see the wise man but you look as if you've seen a ghost." He taunts the agents.
"You're no wise man. You're a dead man. Just like Krycek and X."
Spender seems amused by Mulder's hostility,
"You see a dead man, Agent Scully?" He asks turning to Mulder's prettier half.
"I hoped and prayed you were dead you chain-smoking, son of a bitch."
"You waste your time... ask Mulder, he knows the futility of hopes and prayers. He knows the truth now." CSM tells Scully.
She looks confused at what Spender is saying. CSM zeroes in on this immediately and begins to exploit it as he's done so many times before.
He smiles condescendingly to Mulder, "You have told her the truth haven't you, Fox? I helped you find it."
Mulder looks a little sick, "You didn't help me. You sent me to that government facility knowing exactly what I'd find."
"And now you refuse to speak it." He taunts, "Not to Scully, not to anyone. You've even refused to testify what you learned ... even though it would have saved your life. You damned me for my secrets ... but you're afraid to speak the truth." For Mulder hiding the truth is a sin neither agent thought he'd be capable of.
CSM takes another drag from his cigarette letting Mulder stew in the awkwardness of being called out in front of his partner... the love of his life.
"You call me afraid? Look at you sitting here alone in the dark like a fossil."
CSM exhales a puff of smoke around him.
"It's the final refuge." He explains, "The last place to hide from those who are insidiously taking power now."
"Who?" Scully steps forward and asks.
"The aliens. They fear this place ... its geology. Magnetite, like that which brought down the original UFO in Roswell. Indian wise men realized this over 2,000 years ago. They hid here and watched their own culture die... the original shadow government."
After taking a break to fill his rotting lungs with more smoke, Spender continues,
"It leaves me to tell you what Mulder's afraid to, Agent Scully."
Mulder turns to Scully, "Come on, let's go." He says trying to prevent the inevitable, trying to get her out of there before she learns the truth he knows, and like him can't un learn it.
But Scully doesn't budge,
"It's a scary story. You want to come sit on my lap?" CSM asks leering at Scully.
"You don't scare me." Scully says staying strong,
CSM just smirks, "My story's scared every president since Truman in '47."
"You don't have to hear this," Mulder tells her.
Scully shakes her head, "No, I want to hear it, Mulder."
"Ten centuries ago the Mayans were so afraid that their calendar stopped on the exact date that my story begins. December 22, the year 2012. The date of the final alien invasion. Mulder can confirm the date. He saw it at Mount Weather ... ...where our own "Secret Government" will be hiding when it all comes down."
Scully looks at Mulder but he doesn't return her gaze, instead his eyes stay trained on CSM, who has a wild glint in his eye - almost a crazed look...
"Yeah, you smile ... feeling drunk with power. The power to do nothing." Mulder accuses CSM.
"My power comes from telling you. Seeing your powerlessness hearing it. They wanted to kill you, Fox. I protected you all these years ... waiting for this moment ... to see you broken. Afraid." Spender taunts his biological son.
Mulder schools his features to reveal nothing,
"Now you can die." CSM tells him.
Outside the agents here a commotion,
Looking out the second level doorway Mulder and Scully see Doggett,
"Mulder, get out of there!" He yells to them, "They know where you are!"
Above two black helicopters, both very heavily armed, continue to the ruins.
Mulder grabs Scully's hand and tries to race down and outside the ruins but it's too late.
There is a loud bang of an explosion and rocks start falling crushing both agents, killing them.
CUT TO:
The last thing Dana Scully felt was the crushing weight of rocks as she was flattened to the ground, her eyes fly open and she gasps for breath.
It takes a moment for her to realize she's in a car, she looks around not expecting death to look like this and immediately finds Mulder in the drivers seat, but he's different, he looks about a decade younger then he did a second ago.
He's trying to start the car but it won't go.
"What happened?" She asks afraid.
"We lost power, brakes, steering, everything." He looks at his watch, There is something about this that seems very familiar to Scully,
"We lost nine minutes." He tells her and gets out of the car and screams into the sky as rain pours down on him.
Suddenly it hits her, she already lived this, on their first case together in Oregon.
She gets out of the car and races over to him,
"We lost what?" She screams out over the rain,
"Nine minutes. I looked at my watch just before the flash and it was nine-o-three. It just turned nine-thirteen." He tells her excitedly, giving no indication that he remembers just a moment ago they both died,
He starts running down the road.
"Look! Look!" He's standing over the pink X he marked earlier that's now only a few feet from the car.
"Oh-ho, yes!" He cheers, "Abductees... people who have made UFO sightings, they've reported unexplained time loss."
He looks to Scully waiting for her reaction but it's not one he ever saw coming...
"Oh holy fuck, no."