Shadows in the dark

By MaiaGeesin

86.2K 1.7K 406

This is a mlp fan fiction of Sombra and Twilight sparkle. Sombra returns to Equestria. The Crystal Empire is... More

Chapter 1
Chapter 2
Chapter 3
Chapter 4
Chapter 5
Chapter 6
Chapter 7
Chapter 8
Chapter 9
Chapter 10
Chapter 11
Chapter 12
Chapter 13
Chapter 14
Chapter 16
Chapter 17
Chapter 18
Chapter 19
Chapter 20
Chapter 21
Chapter 22
Chapter 23
Chapter 24
Chapter 25
Chapter 26
Chapter 27
Update
Chapter 28
Chapter 29
Chapter 30
Chapter 31
Chapter 32
Chapter 33
Chapter 34
Chapter 35
Chapter 36
Authors Note
Chapter 37
Chapter 38
Authors note
Chapter 39 (Finale pt 1)
Chapter 40 (Finale 2/2)
Ideas
Sequal

Chapter 15

1.9K 36 2
By MaiaGeesin

Three months later...

Black Fire galloped down the hall leading to the throne room at full speed. His armor clanging against each other as he pumped his legs as fast as he possibly could. Running by guards and receive confused looks until he finally skidded to a halt in front of the throne room doors. Taking moment to catch his breath before stepping inside. The scarlet pegasus felt his face suddenly blaze with embarrassment from the site before him: Twilight was straddled on her king's lap. Arms wrapped around his neck and body pressed close to his chest. Sombra had one hoof on the small of her back while the other was slowly caressing her flank. Twilight pulled away from their kiss to let out a soft moan.

Black Fire felt his legs begin to wobble and he did his best to stand his ground. He cleared his voice loudly. Catching the attention of both ponies. Twilight immediately pulled away from the kiss and her cheeks blazed once she saw the captain standing there. She was about to jump off Sombra's lap before the king gently held her down and pressed their lips against each other once more to finish their kiss. Black Fire looked away slightly. Flattening his ears against his skull. When the two finally broke their kiss, both Twilight and Black Fire were blazing red. If Black Fire wasn't red enough already.

"May we help you, Black Fire?" Sombra asked casually. Acting as though nothing happened. Normally he would've reprimanded the pony for walking in on a moment between him and his queen. This wasn't the first time they'd done this outside of their chambers.

Black Fire swallowed. Shoving the images away before speaking. "W-we've received a message." he said, bringing out the neatly rolled up scroll.

"Oh?" Sombra cocked his "brow" curiously. "From who?"

"The Changeling Queen. Chrysalis."

Twilight suddenly tensed at the name. She bit down on her tongue hard enough not to gasp. Instead she merely remained silent and acted as though she knew nothing about the Queen. But bitter memories of the wedding in Canterlot came rushing back like a storm.

Using his magic, Sombra unrolled the scroll and read what it said silently to himself. Twilight watched her king with a blank expression. Noticing the occasional change of look in his eyes. One minute he looked displeased. The next he looked a bit shocked. After a full five minutes of reading, Sombra suddenly let out a chuckle as he rolled the scroll back up with his magic.

"She wishes to meet with us in the Hayseed Swamps."

"When?" Twilight asked as she tilted her head curiously to the side.

"As soon as we can make it." The dark king chortled to himself as he walked up to his captain and handed the scroll back to him. "Send her a reply." Sombra said, "Tell her my Queen and I will be there this evening."

Black Fire looked hesitant. "But, my liege, are you sure about this? These are Changelings, after all." he said.

"Are you questioning me, Captain?" Sombra asked slowly. Narrowing his crimson eyes towards the red pegasus as green started to replace the white that surrounded the irises. Black Fire gulped and quickly shook his head.

"N-no, my liege."

"Good!" Sombra gave him a smile and patted his head. "That's what I expect from my favorite Sky Captain." he cooed.

Black Fire said nothing. Shuddering at the seemingly caring pats before turning around to leave.

"Ah! Which reminds me." Sombra turned back to his captain, who stopped to look back at him as well. "Are the troops ready for their little "visit" to Dodge Junction?"

Black Fire smirked and nodded. "Yes."

"And how is our newly promoted Earth Pony captain feeling about this?"

"He's just as eager as the other stallions. He just wants to get in the action already."

Sombra laughed darkly. "Good, good. Have the unicorns transport them at noon. Remember: just outside of the town. We want to take them all by surprise like last time. By the way. Any word from our little spy?"

"Nothing of importance." Black Fire replied.

Sombra nodded and gestured with his hoof for him to be on his way. Black Fire bowed deeply before trotting out of the throne room with the scroll clenched in his sharp teeth. As soon as the doors slammed shut, Twilight slipped out of her throne and approached her king. Nuzzling his mane.

"I don't trust the Changeling Queen." she murmured.

"Hm? And why is that?"

Twilight pulled away from his mane and her eyes glowed green. "Let's just say we have a...history together."

Ponyvill

The train came to a screeching halt at the Dodge Junction Train Station. Sand and dust trailing behind it and briefly fogging up the platform before it cleared. The doors hissed open and ponies casually trotted out with their luggage. Rarity stepped off the train and stretched her back legs until they cracked.

"Ah!" Applejack jumped out of the train and breathed in the desert air. "Nothing like that fresh, country air!" the Earth Pony said with loud enthusiasm. Spreading her arms out to embrace the warm sunlight bathing the desert town.

"I'll say!" a voice behind them coughed. Trixie stepped out of the train coughing like a mad dog. "I'm not used to being in deserts!"

Rarity and Applejack exchanged annoyed expressions. Trixie had been a pain in the flank during the entire trip. It was a wonder as to why the blue unicorn even volunteered to become a spy for the Royal Guard. AJ merely rolled her eyes before turning to the blue unicorn. "You'll get use to it." she said.

"'You'll get use to it'." Trixie mimicked annoyingly before shooting the Earth Pony a glare. "I didn't go through three month of hellish training to spend another month in some damn, old western town!"

AJ suddenly shot the unicorn a dangerous glare. Lips curled back to reveal pure white teeth as she tightened her jaw. Nostrils flaring, she pressed her face to Trixie's. "What did you just say?" she snapped angrily.

"Oh, sweet Celestia of the damn Sun!" Rarity groaned before shoving herself in the middle and separating the two. "You're both acting like little fillies fighting over candy!"

"Hmph!" Trixie held her head high and marched past them like nobody's business. Only to accidentally trip and land face-first on the ground. It was enough to cause both Rarity and Applejack to snicker as the blue unicorn helped herself up. Cursing Celestia and Equestria while dusting herself.

"So why did Celestia send y'all to Dodge Junction in the first place?" Applejack asked as the trio made their way through the town. Rarity opened her mouth to reply, only to be cut off by Trixie.

"Something about working on our spy skills and stuff."

AJ frowned, but decided not to make a big deal out of it. "Thanks for coming with us to Dodge Junction, by the way." Rarity said.

"Not a problem!" AJ replied proudly. "I needed to get away from the farm anyways."

"How's Strongheart?"

"Doin' great, actually!" Applejack said happily. "Apple Bloom and her little friends even welcomed her to the Cutie Mark Crusaders!"

"Really? Even if she's not a pony?"

"Mm hm!"

"Well that's awfully kind of them."

"Yup! I'm proud of my little sister for doing that. Always welcoming others with open arms. Just like she did with Bab Seed. Speaking of Bab Seed, she's gonna be comin' over real soon for another visit to Ponyville."

"That's wonderful!" Rarity smiled. "Does Apple Bloom and the others know?"

That's when Applejack snickered before giving her friend a mischievous wink. "Nope. I was goin' to surprise them."

Trixie, who clearly showed no interest in what they were talking about, suddenly stopped when she noticed a speck in the sky. She wasn't able to make out its shape, but it was dark. First it was one. Then two. Then three. They were all showing up at frightening pace. The blue unicorn stopped in her tracks as she kept her eyes on the sky. A dark, foreboding feeling suddenly kicking in. Rarity and Applejack stopped when they noticed this and walked up to her.

"What's wrong, Trix?" Applejack asked, "Trix?" The Earth Pony waved her hoof in front of the unicorns eyes; only to receive no reaction whatsoever. "Hey! I'm talking to you here! I've just had about enough of your bullshit today!"

"AJ..." Rarity suddenly had her eyes on the sky as well. Tugging her friend's shoulder as she snapped insults and curses in Trixie's face.

"What?"

Trixie pointed a shaky hoof to the sky in front of them. Eyes widened with a terror she's never seen in the blue unicorn before. Not since the incident with Ursa Minor. Applejack looked around and noticed that everypony else was looking up at the sky as well. Some with horror. Others with confusion.

"What in Equestria's name are those?" the Earth Pony murmured to herself.

"TAKE COVER!" somepony suddenly screamed.

"Huh?" Applejack barely had time to react when she suddenly felt Rarity grab hold of her hoof and pulled her away from one of the buildings she was standing by. In a split second, a stampede of frightened ponies came rushing out as the building was engulfed in flames. The armored Pegasi above them were dropping live torches like bombs all around the place.

"We have to hide!" Trixie screeched. Her dark grayish violet eyes widening with pure fear.

The trio frantically looked around for any sort of structure that wasn't on fire. "There!" Rarity yelled, pointing a hoof to a lonely shack underneath a dead tree. "Hurry!" AJ yelled before the trio frantically galloped over to the shack. Pumping their legs as fast as they could while keep their heads down to avoid getting hit by any debris. Rarity was the first to make it; quickly opening the door and jumping in. Followed by AJ. Trixie was the last to enter. Jumping in and crashing into Applejack's arms and causing the both of them to fall against the back wall.

"Celestia damn it, Trixie!" Applejack hissed as she pushed the unicorn off.

"Well sor-ry." Trixie hissed back as she dusted herself.

"Ssh!" Rarity hushed the both of them as she peeked out a small hole on the door. Watching the destruction take place.

"What's goin' on?" Applejack asked as she leaned forward to get a peek herself.

Rarity swallowed. "C-chaos. And not the Discord kind." she said.

"W-what are we going to do?" Trixie asked in full panic mode. Breathing rapidly as she huddled herself in the corner. "W-we have to get out of here! W-we have to teleport back to Canterlot and alert the princesses!"

"And leave AJ here?" Rarity said. Narrowing her eyes at the blue unicorn. "We're not strong enough to teleport any pony with us. We can't just leave AJ here for dead! And besides." Rarity suddenly pressed her face against Trixie's and spoke in a low, serious voice. "Remember what Celestia told us."

Trixie blinked before frowning when she remembered their mission. "Oh. Right." she sighed.

Applejack, who was unaware of their real reason for coming to Dodge Junction, cocked her head to the left curiously. "Watcha both talkin' 'bout over there? Don't leave me in the dark, here!"

Rarity turned back to her friend and opened her mouth to say something, only to snap it shut when she realized something wasn't right. "Do you guys hear that?" she asked. The three ponies remained silent before Trixie gave the other unicorn an annoyed frown.

"I don't hear shit." she said.

Rarity nodded. "That's the point." she said ominously, "Silence. Pure. Dead. Silence." There was no screaming. No burning wood. Just nothing but the sound of their beating hearts and the gentle wind outside. The trio then jumped in surprise when they heard a shout coming from outside. Breaking the brief silence.

Applejack slowly lowered her head down to peek out hole herself. "Looks like them Pegasi are gone." she said, "But now there's a bunch of armored Earth Ponies and Unicorns."

"What are they doing?" Rarity asked.

"Looks like they're- wait a minute." Applejack lifted her head up and backed away from the door.

"What? What's wrong?" Trixie squeaked as she felt a burning sense of fear inside her. Pressing her body even deeper into the corner until she was all cramped up.

"Three of 'em is coming this way." Applejack said shakely. "We need to crouch down and stay quiet so they won't have to check in here."

Both Rarity and Applejack quickly retreated into the darkest spot they could find in the small shack. Trixie quickly joined them and the two huddled up in one big pile. Breathing in through their noses as quietly as they could to prevent getting any attention from the approaching stallions. Trixie slapped both of her hooves over her muzzle to keep herself from whimpering loudly. Tightened her jaw nervously while Applejack bit down on her lip. The sound of armored hooves grew closer along with the eerie clanging of armor. The trio felt their bodies tense when the noises grew closer and closer.

Trixie closed her eyes tightly and whimpered softly against her hooves while Rarity swallowed her's down. Applejack felt sweat start to roll down her face as she kept her eyes on the door. Just one noise and it would be all over for them. Something suddenly covered the hole on the door. They were just outside the shack.

"Should we check inside?" a gruff voice asked. "There could be some inside."

A snort was heard. "For what? Who in their right mind would want to risk hiding in this old piece of shit." the stallion kicked the wall of the shack. Causing the trio inside to tense even tighter than before.

"Maybe they want us to think they're hiding in there? You may never know, Night Knight." the first voice growled.

"Stop trying to sound like a smartass, Buck Wood." Night Knight huffed back. Grinning wickedly at the Appleloosa Earth Pony.

"Enough!" a third, familiar voice barked. Sounding more serious and authoritative than the other two that was heard. The stallion stomped his hoof on the ground and narrowed his eyes at the two. Night Knight merely yawned casually.

"Lighten up, Captain." the blue Crystal Pony mumbled to himself. There was a sudden gasp of shock before he was suddenly slammed against the wall by the other stallion. Armored hoof pressing tightly against his exposed neck as he struggled to breathe.

"You got something to say, Night Knight?" the captain asked in a slow, menacing voice. Eyes blazing with hate and anger.

"N-no, sir." the Crystal Pony whimpered before he was released.

Meanwhile inside, Trixie suddenly felt a tickling sensation in her nose. She frantically fought back the urge to sneeze while Applejack and Rarity gave her panicked looks. Without warning, she suddenly let out a sneeze that sounded more like a mouse squeak. The voices outside suddenly fell silent and both Rarity and Applejack shot Trixie a glare.

"Sorry!" the blue unicorn mouthed. Glaring back at them.

There was a full minute of long, agonizing silence. Both Applejack and Rarity knew that they were still outside of the shack. Probably preparing to surprise them by kicking down the door and snatching them up. Applejack boldly crawled forward and stood in front of the door; preparing to pounce on anypony who was about to enter. As soon as the shack door suddenly swung open, tackled the stallion to the ground. Night Knight and Buck Wood were about to go aid their captain before they were shot with a deadly glare.

"Forget me! Go in and bring out any others!" he snapped coldly as he wrestled with Applejack on the ground.

It wasn't long until AJ heard Trixie screaming as Buck Wood dragged her out of the shack after clamping the chains around her neck while Night Knight dragged out a resisting Rarity. "These chains do NOT look good on me!" she snapped as she was dragged along.

"Aaaack!" Applejack grunted when she was kicked off and crashed against the dead tree. She groaned in pain while narrowing her eyes at the battle-ready stallion as he stood in a fighting stance. Nostrils flaring with dangerous hate and anger. Applejack ignored the pain at her side and stood in a fighting pose as well. The two made eye contact as they glared at one another. A tumbleweed gently floated in the open space between them. "Hyaaaaaaaaa!" Applejack screamed when she suddenly rammed herself into the stallion.

The captain grunted in surprise as he fell to the ground. His helmet slipped off, revealing brilliant gamboge locks with amber highlights, and fell beside him. The stallion stood with his back facing AJ. He coughed out some dirt and blood before slowly turning his head over to the young mare. Wiping a streak of blood off the corner of his mouth as he narrowed his blazing, once brilliant, pistachio eyes at her.

It felt as though time itself came to a complete halt as soon as Applejack saw the face behind the helmet. Her heart dropped to her stomach while her legs began to wobble. Tears brimming her eyes as she struggled to say a name she hasn't said since the incident in Appleloosa.

"B-Braeburn?"

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