Starts in season 9 "the truth" but I will be changing things that have happened before that in regards to William and Scully...
Unknown Brig: The door opens and two guards walk in...
"What are you thinking?" The first guard gruffly asks a pitiful form on the ground,
Through the shadows we can see it's Mulder, not looking one bit intimidated by the impressive build and quick temper of his guard...
"Where am I?" He asks cockily,
"Wrong answer!" The guard violently hits the wall above Mulder, trying to intimidate him into submission...
"What are you thinking?" He asks again, testing to see if his show of force worked,
"I'm thinking about getting the hell out of here." It didn't, Mulder is still being his flippant self,
"Wrong… answer!" The guard grinds out through his clenched jaw, not liking the fact he can't break a man so much smaller than him, in height there weren't too different but Mulder had more of a lean build were this guard looked like he consumed Mulders weight for lunch and had it turned into muscle by dinner.
He hits Mulder in the abdomen, forgoing just the threat of violence for actual force showing Mulder he is done being jerked around. He leaves and the other guard instructs Mulder, "No sleeping!"
As his cell door is closed, Mulder is left in complete darkness.
The next time the door opens, letting light into Mulder's confinement, it is unclear how much time has passed, but the shadow of his growing facial hair tells us it's been a few days. The guard begins the same questioning over as before and it becomes clear this has been Mulder's life for a while now...
"What are you thinking?"
"About my son ... about his mother." Mulder replies allowing his mind to drift to when he was last able to hold his child, to see the peace come over Scully's face of having all of them together...
"Wrong answer!" His mental reprieve doesn't last for long as a large fist smashes into his face.
"Now, what are you thinking?"
Fed up Mulder snaps, "What do you want from me?!"
The guard sneers, "Wrong... answer!" he swings again but this time Mulder is prepared for him. He ducks out of the way and makes a grab for the guard's baton, unfortunately he is too strong for Mulder and the baton quickly finds it's way pressed against Mulder's neck causing him to gasp for air as more and more oxygen is deprived,
"I want answers, you hear me? I want answers!"
The two are in that locked position. Mulder continues to gasp as his vision starts to dim, finally the guard lets go and walks out. The metal door clangs shut leaving Mulder in darkness once again as he tries to refill his lungs.
When the door opens this time we see Mulder is lying naked on the cold floor, showing us his "What are you thinking" interrogation has been going on for a long time, and not to either the guard's or Mulder's satisfaction.
As the light seeps into the room Mulder winces and tries to cover his eyes from the sudden bright light.
"No sleeping!" The guard shouts kicking Mulder's hand away from his eyes,
"Did you hear me?" He asks,
"Yes." Is Mulder's cold reply.
"What are you thinking?" The guard asks, starting their dance from the top,
Mulder's voice is different then his earlier interrogations, it's lost some of it's fight, "What should I be thinking?" He dryly asks
The guard narrows his eyes at him, "You're a guilty man. You entered a government facility illegally in search of non-existent information! You failed in every respect!"
"Yes." Mulder lifelessly agrees with him,
"Say it!" The guard demands and pulls his hand back as if to start another beating but Mulder gives him his answer before his fists can do anymore damage,
"I'm a guilty man," He rushes out, "I failed in every respect. I deserve the harshest punishment for my crime."
The guard seems satisfied and walks out. Mulder moves to his corner and settles in again.
Skinner arrives at the heavily guarded facility, a door buzzes open and he shows his ID to another set of guards before being allowed to walk through. He comes to another door through a metal gate and waits for it to be opened for him.
On the inside he sees Mulder, looking pale, thin, beaten down, with a long beard, showing us how long he has been kept alone in this dark room.
Mulder get's up and looks past Skinner hoping to see his favorite red head behind him but she's not there, he looks to Skinner for an explanation, like she's parking the car but his expression tells him the answer isn't going to be as simple as that.
"Where is she?"
"I don't know."