Clause

Several months passed.

Fluttershy and Sombra have lived peacefully in the mountains, Away from equestria.
Fluttershy has all but forgotten her history as the element of kindness – she has accepted the new identity Sombra has given her.

But of course, seeing as Sombra exploited Equestrian politics
Raped her,
Kidnapped her,
And turned her into a new mare, the peace was short lived.
It wasn't long before Celestia, Realizing that the Elements of Harmony could not be used without Fluttershy, began a search for the runaways.
Despite what Sombra had lead Fluttershy to believe, her friends were still frantically searching for her.

And they were closing in.

Sombra woke.
Several months had passed, and they had used just about every tool or item in the house as a fetish tool.
It may just be time to move on.
Sombra looked over to Fluttershy, Sound asleep next to him.

Her hair is messier. She hardly bothers grooming herself anymore, unless Sombra forces her to.
Another one of the many new Characteristics Sombra had given her, over months of hard work.
Sombra took a moment to think. He wasn't alone anymore, but something still troubled him.
Life was too tame for his liking.
Slipping out of bed, he trotted to the kitchen, fixing breakfast
Quickly skinning a live bunny and dicing it into teeny tiny pieces with his magic.
Always a great way to start the morning.
Sombra's ears perked as he heard something out of the ordinary above. The mountains were normally very quiet.
It almost sounded like marching.
The sort of marching a line of slaves would partake in.
That or soldiers.
…
…
…
They had been found.
Damnit.

Quickly running into the bedroom, Sombra roused Fluttershy with a slap to the face, no time for subtlety.

“OW! What did you do that for?”
“Soldiers. Army. Talk later. Leave now!”

Fluttershy didn't need to be told twice.
Yet somewhere, deep inside her, a tiny voice squeaked out. Timid, and Gentle.
“They came for me!”

She disregards it, and follows Sombra into the heart of the keep – The fetish room.
He closes and secures the door behind him, before spinning around and blowing the wooden table in the center to smithereens, revealing a tunnel beyond.

Fluttershy groaned. That table had a lot of good memories.

Without hesitatio, Sombra pushed her towards the exposed trapdoor, ushering her into the dark tunnel beyond. Quickly, Sombra closes the trapdoor and casts the illusion of an intact table, before turning and following Fluttershy down the long, winding corridor.

The two silently ran through the dark tunnel, Too terrified to risk lighting any torches, lest they were detected.
All Fluttershy knew was that the soldiers from Equestria were evil ponies, who craved nothing but power and control.
Sombra was, for once, losing his cool.
There was no way he was going to lose Fluttershy to them. Not after all this time.

After what seemed like an eternity, they came to the open end of the tunnel.

They were in the desert.

“We can't waste any time. If they spot us before we can get far enough away from Equestria, We'll be sitting ducks.”
Fluttershy did nothing but nod in agreement, before following her lover into the harsh desert.

P.O.V. Switch

Princess celestia looked on with worry, as Twilight Sparkle and the guards searched frantically, destroying the whole keep. Leaving no corner unchecked. The rest of the mane 6 watched, dismayed.
Eventually, Twilight Solemnly returned to the cave mouth, her head hung low.

“I can't find them anywhere. There was a bunny Corpse in the kitchen, though. I shudder to think what Sombra must be doing to her.”

The rest of the mane 6 grimace as they picture Fluttershy crying over a dead woodland creature
Suddenly, One of the guards came running from a room in the heart of the keep.
“We've found some sort of torture chamber, your highness! There was an illusion cloaking an exit. Sombra must have used it to escape!”

The mane 6 had heard enough. They rocked off to follow their friend through the tunnel. Determined to save her from the evil stallion who had taken her so long ago.

Celestia sent several guards to follow and escort the mane 6, while commanding Shining Armour and his right hoof to aid her in tracking Sombra by air.

P.O.V. Switch – Sombra and Fluttershy

The desert heat was too much for them. Sombra and Fluttershy found a cave and took shelter from the harsh sun.

“Where can we possibly go?”
“The Arctic. They won't be able to search thoroughly through the blizzards.”
“Alright.”

Sombra turned to look at Fluttershy. He considered starting something right there and then, but he knew there would be better times.

“That means, If the desert is in the south... We need to make it straight through equestrian land?”
“Yes.”

The idea didn't sit well with Fluttershy.
For as long as she could remember, Sombra had told her about the evil land of Equestria.
She certainly didn't want to travel through, as Fugitives no less.
But they had no choice.

“We need to move, Before the guards catch up with us.”

And without another word, the lovers began their pilgrimage.

The tunnel hadn't deposited them too deep into the desert.
Within a half hour, they were in the meadows of equestria's southern borders.
“We're out in the open here. We can't stay.”
“Yes. We need to move, and move quickly.”
Fluttershy was confident and focused.
Sombra had truly outdone himself with her.
Running to a grove of trees, Fluttershy and Sombra collapsed and took a silent moment to think about everything happening around them.

Sombra decided that this was a better time. They both needed stress relief, anyhow. It would only be quick.
Sombra moved over, and positioned himself over Fluttershy.
The two kissed in that same, hungry fashion. Thrusting into each others muzzles.
Sombra knew he had to make this quick. There was no time for Fetish play, not right now.
Slowly and gently, Sombra slipped into Fluttershy, as he had done so many times before.
His powerful, Masterful hips began pumping rhythmically.
With each thrust, Fluttershy let out a small moan. The one thing he hadn't changed was her passive, submissive, and helpless composure during sex.
He liked that control over her.
Sombra continued pumpiung, His hooves trailing over Fluttershy's hips, back, and rump.
Fluttershy wrapped herself around Sombra as he pumped.
After some hushed moans, They two finished. Almost dripping with sweat from the desert heat, combined with their own, the two searched for somewhere to clean up.
As if their luck had finally turned, they happened upon a small forest spring.
The two decided to rest a short while, and plan their hike through equestria.
Meanwhile...

P.O.V. Change – The mane 6

Rushing through the tunnel, the mane 6 came to the edge of the mountain range.
Face to face with the harsh heat of the desert.
“Which way did they go?”
“Can't be sure.”
“Ugh. First dust and now sand? It's like hes TRYING to ruin my hair!”
Completely lost, the mane 6 decided to head back to Ponyville. They could make contact with Celestia there, and go from there.

P.O.V. Change – Shining Armour, a young guard, and Princess Celestia

The three flew via Pegasus wagon, scanning the area below for any signs of the runaways.
“Have either of you found anything yet?”
“No, Your highness.”
“They're lost to me.”
This prompted a swift hoof to the back of the head.
“Have some composure when speaking to the Princess, Soldier! My apologies, Your highness.”
“It is quite alright. They can't have gone far. I would have been able to sense any form of magic used by King Sombra.”
“So that means they're travelling by foot, right?”
THWACK!

P.O.V Change – Sombra and Fluttershy

The lovers found themselves unable to come up with any viable plans.
“My magic is very distinct. Celestia will sniff us out like a wolf if I use any. That's probably how she found the keep.”
Fluttershy looked concerned, then thoughtful.
Without magic, They had few options. Neither of them were smart, Or easy to pull off.

Sombra stood up, and walked around. Looking for something.

“What are you doing?”
“I have an idea. You probably won't like it, though.”

The words didn't sit right with Fluttershy, and she would soon discover why.
Finding a decently sized rock, Sombra pushed it into Fluttershy's hooves.
He then lowered his horn onto another rock, and looked up at Fluttershy Expectantly.
Her eyes widened as she realised what he wanted her to do.
“Don't ask. Just do it. I'll be fine.”
“But I can't...!”
“DO IT.”
The booming voice reminded Fluttershy of something. But she couldn't quite figure out what.
“DO IT NOW.
Looking away, Fluttershy brought the rock down with a sickening CRACK
“RRGH!”
Sombra clutched the remnants of his horn, poking at its stump tenderly. It was a lucky break that unicorn horns don't get blood circulation. He would be fine. He'd just have a headache.

“Now. Call down one of those birds.”
“What? How?”
“It's your special talent. Just let your instincts do the work.”

Fluttershy walked towards the nearest tree, and saw a decently sized bluebird lazing amoung the topmost branches.
Looking up to it, a voice suddenly burst out from the depths of her mind.

“Please come down, My friend. I need your help with something, I won't hurt you at all!”

Surprised at the sudden outburst, one that she certainly hadn't been aware of, she hardly realised the bluebird fly down and perch on a rock nearby.
Wasting no time, sombra took a few ferns from the nearby bushes, and tied his horn to the bluebird.
“NOW. FLY.”
The bluebird, Frightened by Sombra's booming voice, took off at top speed.
Just before his horn left his sight, Sombra channeled all of his will into having it cast a single spell; one that caused dark crystals to drop wherever the bird flew.

“What did you just do?”
Fluttershy was completely bewildered.
“Those crystals will distract Celestia. Spreading like the plague, and giving off a magical signature identical to my own.
Fluttershy nodded slowly
“That means it'll be harder for her to search for us?”

“Yes. Well worth the sacrifice.”

Sombra once again lifted a hoof to his tender stump of a horn.
He had lost it before. It could be restored eventually.
“Come now. We need to get moving. Do you know where we could possibly get clothes to obscure out identities, without entering any settlements?”
“The everfree forest.”
“Pardon?”
“There's a zebra who lives there. I can't remember her name. She wear's dark hoods. We can steal some.”
Fluttershy was taken aback by the memories that she didn't even know she had.
“That'll work. Let's get moving.”