Clause

Sombra woke. He wasted no time, neglecting to dress himself, and eating as quickly as possible.
He had considered skipping breakfast, but he would need top performance for the task ahead.
Opening the slot on the cell door, he could faintly make out Fluttershy huddled in a corner.
Showtime.
Sombra opened the door, and shut It quickly behind him. There would be no escape attempts, no runaways.
Sombra closed in on Fluttershy, a savage grin spreading further and further across his muzzle the closer he got to her.
Fluttershy could do nothing but shrink back in fear.
With a single, deft movement, Sombra had her in his masterful grip.
He lifted Fluttershy up to eye level, and began kissing her hungrily again
He savored her warm, sweet saliva as his tongue wandered around her mouth
Fluttershy began to relax slightly, this would be easier than he thought.

Easily overpowering Fluttershy, Sombra lifted her to the table, and secured her restraints
She struggled, but to no avail.
She still had a glimmer of hope left – That had to be dealt with.
Sombra scanned the room. What would he use first? Whips, Chains, So many possibilities.

After contemplating, Sombra decided.
There was no rush. He would be able to put her through a wide variety of torture. Scanning the walls, he picked out a decently sized paddle.
Flipping Fluttershy over ,and turning down the lights, Sombra began the paddling.
Each connection made a satisfying SLAP, and provoked a cry from the mare.
As Sombra paddled more and more, fluttershy's cries got louder, and her rump became redder
After a fair few strikes, Sombra stood back to admire his work. Her blank was most certainly tender by now, but there was more he could do.
Putting the paddle back onto the wall, Sombra looked for his next toy.
His eyes landed on a cat 'o' nine tails, and he took it in his hooves. Fluttershy, oblivious to what was heading her way, could only whimper and sob.

Holding the Cat'o'nine tails firmly, Sombra continued the Flagellation. Fluttershy cried out as the whips made contact, further adding to the pain in her rump.

Sombra ignored her cries, and continued whipping. Harder and harder, faster and faster.
After several minutes of brutal flogging, Fluttershy had taken all she could.
She broke down once more, crying and begging for reprieve. Sombra was not about to comply.

Tears streaming down her face, Fluttershy could only struggle in her restraints. Sombra continued to whip Fluttershy mercilessly, until her mane was wet with tears. Sombra decided it was time for some vocal encouragement.

Loud vocal encouragement.

“WHO IS YOUR MASTER?”
“y...you..a...are...”
Sombra whipped again, with considerable force.
“I CANT HEAR YOU. WHO DO YOU BELONG TO?”
“y...you”
Another strike. Fluttershy cried out once more.
“I AM ONLY GOING TO ASK ONCE MORE. WHO DO YOU BELONG TO.”
“YOU!”
Sombra stopped immediately.
He walked around to Fluttershy's head
“Excellent Answer.”
He leaned down and kissed Fluttershy hungrily once again. Once he was finished, he extinguished the lights and left the room, leaving Fluttershy in the dark.

Several hours later, Sombra returned. Fluttershy was still lying there, in her restraints.
Deciding to test how tender her rump was, Sombra poked her with his horn.
A yelp from the mare assured him it was still raw and tender. Perfect.
Sombra climbed atop the table, and positioned himself over Fluttershy.
His stallionhood quickly rose to attention, as he ground up and down Fluttershy's rump, causing her to cringe in pain.
When he was ready, he slowly began to slide into Fluttershy's hind quarters. This evoked an ever so slight moan from the mare.

With the same vigor, stamina, and skill he had shown in the everfree forest, Sombra began to pump.
Fluttershy moaned in both pleasure and pain as he thrust into her raw rump, time and time again.
His masterful hips moved in a well defined rhythm, as he leaned forward and grabbed her ear in his teeth.
Pulling her head back, no holds barred, Sombra began to speed up, giving Fluttershy a ravaging she wouldn't soon forget.

With Fluttershy at his mercy, Sombra decided to bring another part of her personality crumbling down.

“Where are your friends now?”
“They gave you to me. They didn't want you.”
“You were nothing but an object to them.”
“I am all you have. And yet you still recoil from me?”
“You are a terrible pony. Nopony wants you.”
“You're lucky you have a master like me, to pull you out of trouble.”

Sombra continued to thrust, until eventually he couldn't hold on any longer. He shot right up into Fluttershy, and, after finally pulling out, she fell limp. Exhausted once more.
Sombra smirked. His plan was flawless. He had even slipped birth control into Fluttershy's soup the night before. Sombra trotted around to Fluttershy's head, and stared down at her. Straight into her eyes.
She was unable to look away.
Sombra lunged down and began to kiss, once again. This was by no means a loving kiss – It was a display of ownership.

There would be plenty of time to show her love once her mind had been fully remade.

P.O.V. Change – Fluttershy

It can't be true... All my friends abandoned me?
They DID send me in there with him...
Everyone knows Sombra is evil...
But he can't be that evil... He's being so kind...
Nopony has come to help me...
Will Somepony come to help me...?

P.O.V. Change – Third Person

Sombra laid back, a satisfied smile upon his muzzle.
Fluttershy would not be able to hold out against him for long. She had already allowed herself to be taken away so easily.

His eyes droopy, Sombra decided to take a well earned night's sleep. Soon, It would be time to start taking things faster.

Sombra Woke with the sun.
At least, he thought he did. It was difficult to tell, so deep underground.
Once again, he ate quickly. There was a lot of work to be done. Trotting towards Fluttershy's room, Sombra envisioned what he would use on her today...

Sombra decided on one of the magically powered vibrators he kept. He seldom needed to use them, but Fluttershy deserved a reward for her behavior. An act of mercy now could greatly incline her toward him.

Sombra took his time opening the door. Fluttershy was still restrained, anyway. As he entered and turned on the lights, she looked up at him.
Closing the door behind him, he released her bonds, before calling for another bowl of soup.

This time, Lukewarm.

“You've been a good filly. You deserve a treat.”

Fluttershy lapped up the approval. She needed all the positive attention she could get. Taking her in his arms, Sombra held the bowl up to her while she ate. She was beginning to incline herself towards him, but he still needed to chip away at her personality. Once she had finished eating, Sombra grabbed her in an iron grip, and returned her to her restraints.
Her struggles were near useless – She was in no condition to fight against the powerful stallion

Sombra took a look around, and found two decently sized vibrators amoung his wide array of toys.
He decided to test just how resigned Fluttershy was to her fate.
Levitating the two vibrators, Sombra slowly inserted both of them into Fluttershy's rump and marehood, before pouring magic into them.
The Vibrators sprang to life, and Fluttershy moaned loudly.

Sombra then crouched on his haunches atop Fluttershy. He stroked his stallionhood a few times in order to arouse it, and slipped into Fluttershy's mouth. It wasn't long before he was pumping in a steady rhythm.

Sombra stopped when Fluttershy's breath became heavy.
Pulling out both vibrators with magic, He pulled from her mouth as well.

Fluttershy was still extremely aroused, and struggled in her restraints. Struggling for something, anything, to finish her off.

King Sombra laid down, his member just inches away from her desparate marehood.

“Do you deserve it?”

Fluttershy could only stare. She didn't know the answer.

“Have you been a good girl?”
“Y...yes..”
“Good girls don't give one word answers.”
“Yes... I have been a good girl...”
“Yes sir?”
“Yes sir...”
“Stay it in full.”

Fluttershy hesitated.

“Say it in full, Or you won't be allowed to finish.”

Fluttershy gulped, closed her eyes, and whispered;

“Yes sir. I have been a good girl.”

Satisfied, Sombra plunged into Fluttershy. His masterful hips working magic. Fluttershy moaned, louder and louder, Until she reached Orgasm.

“What do you say?”

Fluttershy, still breathing heavily, looked at King Sombra once again.

“What do you say?”
“Thank you.”
“Thank you MASTER.”
“Thank you master.”
Sombra once again leaned in for a savage, hungry kiss, before climbing from the table.

He didn't finish, but he didn't mind. He had made good progress.
This time, he allowed Fluttershy a dim light before leaving the room and locking the door.

P.O.V. Change – Fluttershy

How Many days have I been here?
Or has it been months?
Years?
I don't see the sun down here.
Is anypony coming to help me?
They're taking a long time...
Will they come to help me?
Or is what he said true...?
They've abandoned me?
Maybe he's right.
Maybe he's the only one I can trust...
Maybe he is my Master...

P.O.V. Change – Third person

Sombra once again laid in bed, Contemplating his progress with Fluttershy.

More and more of her personality was coming crumbling down. She'd be his soon.

Sombra closed his eyes and drifted off to sleep. Guided by those thoughts...

The thoughts of not being alone anymore.

Sombra woke once more.
He went through his basic morning routine, eating quickly, and heading for Fluttershy's cell
This time however, he entered slowly and silently; It was time for a Psyche Evaluation.
How far had he gotten with reshaping her identity? He knew how to find out.

He silently trotted down to where Fluttershy's head was resting, and woke her slowly.
Staring down into her eyes, he noticed. The fear that had once overtaken her at the mere sight of him had all but faded. She had broken. And now, she was his to remould.

“Who Is your master?”
“You are my master.”
Good. The basics have been firmly established.
“Who can you trust?”
“Nobody. Except my master.”
Good progress.
“Why are you here?”
“My friends gave me away. They abandoned me.”
A smile playing across his face, Sombra deduced that he was closer than ever. Now that she was broken, he had to remould her.

Sombra paused to think; Just how should he do that?

Sombra decided on obedience training. It was tamer than what he had been doing before. He might even be able to let Fluttershy out of her cell, If she proves obedient enough.

Cautiously, Sombra released Fluttershy's restraints.
Slowly, she sat up, rubbing her hooves where they had been rubbed raw.
Slowly, she made her way off of the table, but collapsed when she tried to stand.

In a moment of impulse, Sombra rushed to her. Holding her from a painful collision on the stone brick floor.

She felt frail, and weak in his arms.
She was far too weak to do anything like this today.

And it was all his fault.

Taking her back to his room, Sombra gently lay her down on the bed.

Flashing his horn, he commanded the shadowy clouds around the keep to bring soup.

Hot, this time. With warm bread.

He watched as she ate and drank, before falling asleep right where she lay. She was like a blank slate, now. He would be able to mold her into a new pony after a nights rest.

P.O.V. Change – Fluttershy

Was that a dream?
Sombra taking me out of here, Giving me food, Helping me recover...
I'm still here in the cell, though. Did that ever happen?
I don't know what is real anymore.
I'm still here.
Nopony has come to save me. Is Sombra really my master?

P.O.V. Change – Third person

Sombra woke once again.
He had returned Fluttershy to her cell once he was sure she would be alright. He couldn't risk such an act of kindness. Not just yet.
Eating, Trotting to Fluttershy's cell, just like every other day.
Opening the door, Sombra locked eyes with her immediately.
She didn't seem to react at all. Her eyes were misty and blank.
It was time to beat a new personality into this mare.
“Hello, Fluttershy.”
“Hello, Master.”
“Who are you?”

Fluttershy was taken aback by the question.
She tried her best to remember. Just who was she?
The time before her imprisonment in this cell seemed like a dream. It wasn't real to her.

“I don't know, Master.”
“Would you like me to tell you?”

Fluttershy perked up, just slightly.

“Yes! Yes please!”
“Yes please MASTER.”
“Yes please Master!”
“Very well. You are mine.”

Fluttershy registered. That made sense. He was the only pony she knew, after all.

“Who is it that you trust?”
“You, and only you, Master.”

Excellent. She hadn't regained even the slightest bit of her original identity.

“Who is it that you love?”

Fluttershy paused, and thought. King Sombra, Despite himself, found himself holding his breath.

“I love my Master.”
“Who is your Master?”
“King Sombra.”

Satisfied, sombra released the restraints on Fluttershy.

“When your master tells you do to something, What is it that you do?”
“Whatever it is that master told me to do.”

Excellent. This was going very well.

“Where do you live?
“Wherever master lives.”

Excellent. She was ready.
Leading Fluttershy towards the door, Sombra paused. Just for a moment.
“You don't need to call me master anymore.”
“What May I call you?”
“By my name. Sombra.”