Secrets of the Darkness

by Silent Running

Rating: teen
Tags: Dark, Alternate Universe, Human, Nightmare Moon, Princess Luna, Thriller, My Little Pony: Friendship is Magic, Other, Science Fiction, Violence
Length: 4830

Some things are never meant to be opened, and some places never meant to be explored.

Some things are never meant to be opened, and our insatiable thirst for exploring things we don't quite understand is our gift and curse. This newly discovered universe holds many terrible dark secrets that it never meant to be revealed again. A lone Colonial Guard cruiser is dispatched to investigate one such oddity. As humanity struggles to find a way to make peace and coexist with the ponies of Equestria, what will these new discoveries hold?

This is the first official sidestory of Machine and Might by Kriegor and is independent of the original storyline.

Rated teen for language.

Published 2012-10-20 01:20:02 UTC
Last updated 2012-10-20 01:20:02 UTC

What Lies Beneath

What Lies Beneath

Chapter One: What Lies Beneath--------------------------------------

“So there’s your plan Commander, pretty straight forward if I do say so myself.” Admiral Becker stood at the head of the table, around him only a few souls sat with a look of incredulous uncertainty.

“So let me get this straight sir, you want the Tyrant Sword to probe the surface of a barren moon for something we aren’t even sure is there? Are you sure the sensors are actually fixed?”

Becker smirked, “Commander, have I ever steered you wrong? And why would your CO do something as foolish as deploy one of our best assets on a wild goose chase?” Becker’s deadpan attitude about the entire thing could only garner chuckles from the other people sitting at the table.

“Nice Carson, there you go questioning the Admiral again.” Jack Silverback, a grizzled veteran who had seen far more than his share of operations these past many decades couldn’t help but smirk at the way events were unfolding. Who would have thought the crew of one of the USC’s premier fighting vessels would find itself playing explorers and diplomats far from home and far from any known USC space?

Admiral Becker however was far more composed when dealing with the hotheaded commander who only recently had been given command of the USS Tyrant Sword. Compared to the Vector, the Tyrant Sword is a small assault cruiser amongst many inside the confines of the Vector; remarkable for being completely unremarkable.

“Silverback, that’s enough. You’ll have your moment to shine soon, I promise. Carson, we’ve known each other for how long? Come on, we have work to do, I need you on board for this.” Becker sighed long and deep as he looked out the digital glass window. Below them was this new planet. It was so familiar yet so alien at the same time. Home to the land of “Equestria”, if he remembered correctly, inhabited by sapient quadrupeds who were still in a pre-industrial stage of development.

“Truth be told there are so many unknown variables right now. We are far from anything and we have been out here puttering about looking for something that is not there. Now we are back making small talk with a race of sentient ‘ponies’ who have skills beyond what should be considered logical and acceptable... How long has it been since we made first contact?”

“Six months sir, that sounds right,” a much younger female voice chimed in from the back corner of the table. There a young Squad Commander assigned to the Grid-Omega Raider division who also happened to be a ranking field officer on the Tyrant Sword was sitting. Up until this point she might as well have been completely invisible to the others. The three men who were around her had decades of experience and had served in countless campaigns together. Ultimately it was more than mere chance that had united them all again on the Vector.

“Can someone please remind me why the Raider is here?” Silverback beginning to show serious impatience managed to blurt out. Several eyebrows raised at the sudden angry outburst from Silverback. They were not amused.

“Becausesir, I requested her presence considering she will be leading this whole thing when we do go out there.” Commander Carson who was not afraid to defy the much higher ranking Silverback was now clearly annoyed at his superior’s blatantly cavalier attitude about this meeting. He may have been one to question bizarre operations but he would never act in such a crude and unprofessional manner. Becker had issued some unusual requests before, but he knew the man for decades and had never been steered wrong.

“Jack, that’s enough, I believe your part in this meeting is over. You are dismissed.” Becker was no longer playing around with his second in command. Silverback had been quite irritable lately, however protocol dictated he be present for special operations assignments like these. Without saying a word Silverback exited the room, deliberately knocking shoulder pads with Commander Carson, who made no attempt to retaliate as it would be an ill advised decision.

“I swear Silverback is really starting to become a pain in my ass. He has been on people for petty things lately for as far as I can see no reason. Not to mention he has serious issues with us even talking with the ponies.” Becker sighed, “I’m worried Carson, people are starting to get uneasy on this ship. Atlas has been delivering unsettling news from around the ship too.”

“Forgive me for asking sir, is Atlas your personal eyes and ears?” Carson couldn’t help but ask this time. He had heard rumors from time to time but dismissed them as hearsay amongst a jittery crew with no experience with the augmentees.

“I don’t like to put things in such a way Carson, Atlas is a good man. He isn’t out to get anyone and he has done what I have asked of him without question. He also successfully opened up discussions with the Equestrians. It’s a tremendous risk having him on board, I know. I can only hope his abilities and duty here, now will change their opinions. I also don’t know if he can ever leave the confines of my ship. You know what will happen if the USC proper finds out about him...” Becker had a sobering look on his face as he stared at nothing in particular.

“I’ve got nothing against him sir, I was just light infantry when the augmentees were purged. I knew a couple, had to hide that fact damn well for so long.” Carson spoke up after a moment.

“It doesn’t matter anyways at the moment. Who the hell even knows if we can find our way out of here.” Becker looked grimly at the two other soldiers in the room. “You keep that to yourselves, you understand?”

The two in unison were quick to respond “Sir!”

“Alright then Commander, we have a mission to achieve. While you explore whatever the hell it is we saw on the lunar surface, Atlas and I will continue our discussions with the Equestrians. Oh and Carson, I know how much you love to go all lone wolf with your ship and try and save the world. Please don’t do anything too rash, and please keep me updated more than what is required.”

“I won’t let you down Admiral, we’ll play it by the book.”

“Good! I’ve already ordered the Tyrant Sword prepped for departure to save you the trouble.” Becker smiled in a trusting manner only a ranking officer could achieve.

“Thanks sir, I owe you a drink. One last thing sir, why me?”

“Because you are the only ship commander on this damned vessel I can trust to tell me exactly what I need to know. That’s why I keep you around.”

Carson saluted and the two officers departed the room leaving Becker alone as his gaze once again turned to the planet below them and the moon peeking out from the shadow of the planet.

“What the hell are we getting ourselves into?”

--------------------------------------

“All systems show green sir, we are cleared for departure!” An excited technician happily announced.

The Bridge of the Tyrant Sword was alive with activity. For months the ship had been laid up in drydock undergoing emergency repairs after it took a beating when the Vector made an emergency jump six months ago. Now the updated cruiser was ready for its first major deployment of this new tour of duty. The crew was visibly excited as they had been assigned crude and mundane tasks that were unfitting of a ship's crew during the down time. There was little for them to do onboard the Vector when they weren’t in their own ship after all.

“Alright then Lieutenant, take us out, and keep it clean.”

Commander Carson sat patiently in his helm chair as the massive ship began to disembark from the vast metallic canyon that was the Vector’s primary ship bay. It would take several minutes for the cruiser to maneuver its way through the myriad of other ships assigned to the Vector that at the moment clogged the ship bay.

“Once free, it will only be a few minutes until we reach the satellite. We have been tasked with performing a thorough flyover of the surface and map the entire thing. Admiral Becker still suspects the Vector’s sensors are faulty in some way.” Carson was not talking to anyone in particular as he began to state their initial objectives.

He pulled up a holographic folder marked clearly ‘CLASSIFIED’ and quickly opened it up. Inside the folder was a wealth of information from what little intel had been gathered by the ground teams.

“Mare on the moon, nightmare moon... what does it all mean?” Carson quietly said to himself, he wasn’t exactly sure what he was looking at. He accessed the ship’s central comms system.

“This is Commander Carson, I need the intel officer and ground forces commander to the bridge immediately. That is all.”

Several of the technicians at their posts looked up at him. Carson was quick to notice their quizzical looks at the unusual order.

“I’ll explain everything as soon as they get here. We have a lot to go over before operations formally kick off. In the meantime, keep your heads on. I know it has been awhile since we last got to take the ol’ girl out for a proper spin.”

The Tyrant Sword began to accelerate away from the Vector’s protective gravity shield and began its brief trek towards the planet’s only natural satellite. They would first need to establish a ranged orbital evaluation of the moon before coming in much closer to perform a thorough study of the surface. Commander Carson was busily going through the digital pile of intelligence documents only half listening to his crew enamored with the unusual nature of the documents.

“Sir we are ready to approach the.... uh.... oh my.”

Carson stopped what he was doing and looked up at the massive panoramic monitors in front of them. There as they began their initial ranged pass of the moon, a massive structure began to appear as they rounded the satellite. Carson dismissed the documents and walked closer to the virtual windows. The two officers he called for entered the room with no one taking notice.

“What in the hell are we looking at?” Carson was stunned at what they were seeing.

There emblazoned on the vast surface of the moon was the start of a structure of some kind “Are we seeing this right? Is this a joke?”

“No joke sir, this is what we have been trying to learn about from what little time our ground teams have had in Canterlot. Everyone er.. ahem.. everypony down there who is supposedly ‘in the know’ seems to have little information about the lunar surface. The ignorance on these geographic oddities is astounding... almost deliberate.”

The intelligence officer, Captain Halidon, was now standing next to him looking at the massive structure that jutted out from the moon’s barren surface. Carson chuckled.

“Becker was right, the old man has still got it. Alright everyone back to your posts, we still have a job to do.”

The Tyrant Sword found itself eclipsed in the shadow of the moon as the crew looked on with uncertainty at the ancient structure they had just stumbled upon. Commander Carson looked around and noticed the bridge crew was still standing focused on the image before them. He sighed and smiled.

“Who knows what lies beneath. Only one way to find out.”

“It is a little unsettling sir.” Halidon finally said after a long bout of calm.

“What do you mean? It’s not THAT far fetched from our past operations.”

“That’s just it sir, I mean, these are fully completed structures... on a barren moon. There is nothing natural that could even hope to stand a chance out here. The radiation, the cold, the goddamned vacuum of space.” Halidon shuddered at the thought.

“So maybe we need to suspend our belief of what we know. What I’m trying to say is, maybe whatever built these is not natural...”

“What are you implying sir?”

“I have no idea. Lieutenant, take us in for a closer look. Everyone back to posts, the mission begins now.” Carson sat back in his chair as the ship’s interior lighting switched to combat status.

As the Tyrant Sword began its slow descent towards the lunar surface, they could see the ruins truly massive proportions shrouded vast areas in complete darkness. Beyond their visual range, and beyond their sensors range. The darkness however has always been home to mystery and uncertainty. Why was this darkness so unnatural and unsettling? Commander Carson planned to find out. The vast lunar surface dominated their view as the operation began in earnest.

With my sincerest thanks to: KriegorMenelaus RedzSembrBrony217

Where No Mortals Dare

Chapter Two: Where No Mortals Dare-----------------------------------------

The magnificent brilliance of the night sky Luna had so painstakingly perfected was beginning to overshadow the lands of Equestria with its restful darkness. The world was changing in ways none of the ponies could have ever imagined. But here now at least for this moment, it was calm and peaceful. The distant sound of grasshoppers and other creatures of the night created a silent symphony as few lights went on in the stilled city. It wasn’t always like this however, these were dark times with little reason to have hope.

“Dad, why does it have to be so dark now? I never used to be able to see so much above!”

Hopeful Dawn stared from the small nightwalk of their home on the edge of the city. Her father however did not see things in such a way.

“Well look at it this way Hope, have you ever been able to look up and see so much of Luna’s night sky?”

She had to think about it for a second. Why did her dad always have to be so right about these things? She looked all around, almost falling on her back as the stars shined with such brilliance and intensity. Almost as if to remind those doomed to their fates in Trottingham that their regal princesses, and more importantly, Equestria had not abandoned them. Above all the stars though, the moon in all of its splendor, dominated the night. Casting a longing gaze down on a land in turmoil, trying desperately to reach out and embrace the world.

“What do you think it’s like there?” Hopeful Dawn looked at the moon, and then stared into her father’s eyes.

“On the moon? Well I certainly wouldn’t want to be there. Only bad things happen on the moon.”

That last statement really puzzled her now.

“What do you mean?”

“I guess you were too young to tell to, the tale of Nightmare Moon. Do you know the reason why we go and get you treats on Nightmare Night?”

She could only shake her head no, why did they go and get all that awesome candy anyways?

“Nightmare Moon tried to bring about darkness forever. And for her punishment, she was sent to the moon. A thousand years she spent there, with no one else. Our dear Princess Luna trapped with her on that desolate tomb. As the legend goes, only darkness lives in the light of the moon.”

“Well what is that supposed to be mean?”

Blinking Stars had to think about that now too, what does it mean to have darkness in the light?

“I wish I knew the answer to that Hope. The stars are certainly magnificent tonight. Luna still watches over us, I know it.”

A sense of calm had at last overtaken the bridge of the Tyrant Sword. The numerous technicians and specialists assigned had resumed their tasks as an eerie red glow from the combat lighting enveloped the bridge. Commander Carson however remained transfixed on the quick approaching lunar ruins. The ruins represented something that could only serve to capture the Commander’s imagination like never before. Decades of combat operations had left his sense of adventure he once had for the Colonial Guard muted and shuttered as he moved on with mechanical enthusiasm from one assignment to the next. The Tyrant Sword as he originally viewed it was just another assignment patrolling sectors and defending the behemoth Vector from would be attackers.

Now though things were different. He had finally gotten the mission he was so desperate to receive. Exploratory operations were so rare and unusual that they were typically handled by a very select group of specialists on board even the super massive carriers. The enthusiasm that had vanished so long ago was beginning to reassert itself. What was it about these ruins though that had so captured him? He was lost in the intricacies of it, like something out of a story. Something about the ruins was beckoning him, pulling him in further.

“Sir... Sir... Commander Carson?”

“Huh? What’s up Lieutenant? “ Carson suddenly snapped back to reality. What in the world had he been thinking? Losing concentration on an operation was not only a huge no-no but something he personally never did. He looked around and the entire crew was now staring at him including Captain Halidon.

“Are you alright Commander? It’s not like you to stare off into space, literally.” Halidon chimed in with a hint of concern in his voice.

“My apologies, it’s been awhile since something captured my thoughts like this operation.” Carson weakly chuckled and caught a sigh under his breath. He had a nagging suspicion it was going to be one of those days.

“Sir, we are ready to deploy the MAPSTAR system on your command.”

“Granted, activate MAPSTAR and begin operations.”

Several screens pulled up and a green light began to pulsate as the advanced MAPSTAR array deployed from underneath the ship. Phase one of the operations were now moving ahead as the Tyrant Sword began the routine operation of comprehensively ground mapping a new terrestrial body.

“Maintain visual scanning, this shouldn’t take long. I know we haven’t done one of these in awhile but everything should go smoothly.”

“Speaking of smoothly sir, something isn’t right. Look at these readings, they are completely negative!” An alarmed technician quickly chimed in and immediately pulled the oddities up on the primaries.

“Sir, these readings can’t at all be right, they are completely missing parts of the... surface... right by the ruins...”

“Why on earth would the ruins throw off MAPSTAR, this can’t be right at all. Standby to halt mapping operations and put us right over the last coordinates that were coming up normal.”

The Tyrant Sword immediately began to shift around to backtrace to the last normative coordinates the mapping showed. Barren moons and large planetoids were typically very easy to map because of fairly common characteristics and a distinct lack of unique surface features such as water, vegetation, or angry locals depending on where they were on that particular mission.

“Alright, engines to easy Lieutenant, look’s like we’re coming up on the last coordinates... No, that still can’t be right! There is no way in hell MAPSTAR is malfunctioning just over the ruins. Run full diagnostics on the system and we’re going for another pass. In the meantime, get us away from the site until we run the checks.”

The crew quickly nodded and the Sword pulled away from the site with urgency.

“What do you think it could be sir? I have a nagging suspicion that MAPSTAR isn’t malfuncti-”

“No Halidon, don’t even finish that statement. MAPSTAR has run with 100% efficiency on every operation we have ever used it on. The idea that there is anything out here that could potentially interfere with it is absurd on it’s face. We have no idea what could have malfunctioned, and I plan on keeping it that way until diagnostics are completed.”

Captain Halidon wasn’t entirely surprised with the by-the-book reply from the Commander.

“Understood sir, I’ll keep that in mind.”

The main screens meanwhile were now flashing DIAGNOSTICS COMPLETE after several tense minutes of waiting.

“Run the report Lieutenant.” Carson quickly snapped. A hint of irritation now in his voice.

“MAPSTAR diagnostics check. Primary sensors, nominal. Secondary sensors, nominal. Data monitoring boom, nominal. Auxiliary camera unit, nominal. Atmospheric sampler, nominal. Power input, 100%.... All systems at nominal efficiency, no errors to report.” The report ended and the look of surprise on their faces told the tale. Something isn’t right.

Carson angrily sighed at this turn of events. “Oh you have got to be kidding me!” after a brief moment of collecting his thoughts he spoke again.

“It doesn’t matter anyways, we’re going for a second pass. As soon as it’s completed we move on to phase two.” Carson quickly pulled up his communications network and accessed the tab marked HANGAR BAY.

“This is Commander Carson, Away Teams Alpha and Bravo prepare to drop. We are now in a full first contact scenario, appropriate ground forces will be applied. I want dropships on the launch pads in 0-5 minutes. Carson out.”

“Sir we are ready to redeploy MAPSTAR at your command.”

Carson nodded and the MAPSTAR system once again launched from the belly of the ship. They were now rapidly closing in on the site. Everyone was on edge as they came closer and closer to the area where the system failed the first time.

“C’mon, please work.” Carson muttered under his breath, however everyone else on the bridge was far too consumed with the data readings to hear his plea.

“On target in 3... 2... 1... On target sir.”

As the Tyrant Sword passed over the location everything began functioning normally. The crew let out its collective breath as they began to comb the site.

“Everything is functioning sir, however there is still something well, off about the data. I still don’t think it’s reading the depth layers correctly.”

“Until we go down there to check, assume they are, I don’t want anymore issues with MAPSTAR. We are behind schedule as it is and need to get a move on.”

As the mapping operation began to wind down, Captain Halidon thought it to be an ideal time to probe the Commander for more answers.

“Expecting trouble down there sir?”

Carson looked over and raised an eyebrow at the upfront question. Had it been anyone else, and had he not been as laid back about these things in the safety of his ship; that question may have not ended so well.

“No Halidon, I’m not, however that being said this is an ideal opportunity to give the first contact teams a workout. They don’t get to do this job much so who better then to deploy.”

He stared grimly at the ruins, the feeling that something was watching him enveloped his mind again. A chill ran down his spine at the thought.

“And if something does go wrong, Commander Spechart will be able to figure things out. I trust her a great deal. She has gotten her forces out of jams before, this should be a walk in the park in comparison.”

Halidon could only nod in reply and continued to watch as the surface came into better view.

In the central hangar bay, several stalls were alive with activity as flight crews raced to get the dropships ready. A ground crew boss walked over to Commander Spechart, a tall and built Raider who had worked closely with Commander Carson for years. She had only found herself in charge of all of the Tyrant Sword’s infantry forces when Carson had been promoted to Commander of the ship. He was quick to gather his favorites and brought them all on board with him.

“Sir, everything checks out ok on these dropships. Commander Carson specifically granted us access to these assault dropships for this assignment. Not sure why though, they are designed to handle a lot more shit than anything that a bunch of moon rocks are capable of.” He chuckled.

“Well I generally don’t like to second guess the Commander, so I suppose we’ll just have to use these flying tanks.”

She continued her walkaround of the dropships and also watched as numerous pieces of equipment were loaded onto one of them. Everything imaginable for an exploratory operation was being stowed away on the third dropship of the group. Right on cue two lines of extremely well equipped infantry marched into the hanger and waited at carefully designated spots for their next orders. They were a mixed bag of troops that brought everything imaginable to the table.

“TheSword’s finest indeed. Alright gather around, we’re going to go over this quickly as we’re fast approaching the launch time.”

The group of soldiers gathered around the raider as she pulled up a large holographic display courtesy of the MAPSTAR system.

“Listen up, Command suspects that the mapping system isn’t telling us the whole truth and we’re being sent down to find out what exactly is the truth. You all know this is a slightly different first contact scenario from normal. There should not be anything living down there, but there are buildings. I have no idea what to expect, so we’re bringing everything in mind. The gravity is exactly like that of Terra’s moon. So set your stabilizers accordingly. When we get down to the surface assume standard formation and wait for me. Let’s get to it soldiers!”

The massive hangar doors began to open revealing for the first time to their own eyes the lunar surface. It looked just like Terra’s moon, just like old times.

“TWO MINUTES UNTIL DEPLOYMENT, ALL DROPSHIPS STANDBY” boomed the voice of the intercom system.

The flight crews quickly scrambled to positions as the cargo doors on the three dropships sealed shut.

“This is Commander Carson, we are ready to begin phase two of operations, to our forces going down to the surface, good luck and stay frosty.”

Commander Spechart looked around at her anxious forces. They were ready for something new and this was exactly the remedy they were looking for.

“Prepare to launch. Dropship November 1-5-7, you are clear to launch. Good luck 1-5-7.”

The engines whirred to life as the three dropships of the away team began to maneuver their way to the large open hangar doors. With engines at full blast they darted out of the Tyrant Sword, away from the safetynet the ship provided, and out into the unknown.

“Fast and low pilot, don’t need anymore attention than we already have.” She quickly thought to herself, why did I give that order? There’s nothing out there.

The pilot nodded as the lead dropship began its diving approach to the lunar surface. The ruins they were all so anxious to get to quickly came into sight as the dropships established a low flight pattern to get them there as quickly as possible.

“Sir we’re approaching the LZ, command picked us out a nice spot to land right at the mouth of this thing.”

“Excellent, I’m headed back to get the troops ready, take us in!”

Spechart exited the cockpit and returned to the watchful stares of her soldiers. They had a passionate look in their eyes, the look of determination. This mission was not anything out of the ordinary, but they could feel it now, with everything else that had happened. This mission was special. She walked to the back of the dropship and right up to the ramp, she was going out first. Her second-in-command gave her an odd look.

“Sir what are you doing?’

She gave him a wicked smile.

“First in, last out!”

He could only smile back and put his helmet on. They all quickly followed and performed the final run through of their armor. The suits they wore should have no issues operating in the cold dead of space. Designed for extended operations in the most brutal and unforgiving of environments, they were ready to drop.

The dropships began to lurch and shake as they closed within feet of their designated landing zones.

“DOORS OPENING IN TWO!” shouted the dropship pilot over the intercom. The dim red glow of the cabin quickly began to fade as the ramp began to open up. Commander Spechart braced herself as the shaking stopped and the dropships hit their landing sites.

“Go! Go! Go!” she screamed as they stormed out of the dropships assuming positions. She hadn’t been able to take point on a deployment in ages it seemed like. Immediately they began kicking up lunar dust as their equipment and sensors compensated for this barren environment.

The dust however soon found itself giving way to the hard surface of something that had no earthly right to be on a barren moon. Polished floors. Spechart slowly began to walk forward on the paved surfaces and looked up at the site before her. She nearly dropped her rifle as the scale of the structure sunk in.

“Commander Carson isn’t going to like this one bit.”

With my sincerest thanks to:KriegorMenelaus RedzSembrBrony217