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                      UFO: Equestria                       
                     -by Toxic Spill-                      
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                         Chapter 1                         
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Chapter 1
"Nighttime.  Those gray bastards always seem to hit us at nighttime, when they know they have a visibility advantage over us.  Luna sends us out there to grope around in the dark for aliens, and those bug-eyed freaks would just stand back and pick us off like fish in a barrel." – SGT Moonbeam
Darkness was a thing that the Knightmares had grown accustomed to.  As servants and protectors of a nocturnal goddess, many of their training regimens had involved learning to live and fight blind when the situation demanded.  Yet even now, Sergeant Moonbeam could see that there had been a particularly fatal oversight in their training: it had always assumed that one's opponent would be likewise handicapped by darkness.  That reality was underscored when a bright blue flash pierced the darkness, eliciting a howl of agony from Excelsior.
"Cover!" yelled Moonbeam, quickly diving behind a stone well.  She could hear the deafening cracks of plasma bolts impacting the other side of the well, each shot hot enough to audibly boil the very moisture from the air.  "Spiral, get us some light out there!"  Light Spiral - a white Unicorn stallion who had transferred into ECLIPSE from the Sun Guard – was more than happy to oblige that request.  His horn flared to life for but a moment, and a globe of bright light suddenly appeared over the battlefield.
Now they could see the adversary that had already brought down four of the six ponies who had been sent on this suicide mission; two more would make it official.
"I've got a visual, Sergeant!  It's one of the gray-skinned ones!" yelled Light Spiral, peeking out from behind his cover just long enough to get a look at their enemy.
Moonbeam was all too familiar with their gray-skinned adversaries.  They weren't much taller than a pony, but walked upon their hind-legs in the same fashion as a juvenile dragon.  Their bodies were slender and hairless, covered with a mottled gray skin.  Their heads were almost comically large and bulbous, with two large, soulless black eyes that – if the rumors were to be believed – could snap a pony's mind like so much tinder.  They had proven to be the most numerous of the alien invaders, and while they proved to be the easiest to kill, the weaponry they fielded made them more than a match for any ordinary soldier.
"All right," Moonbeam said, lowering her voice.  "On three, we pop out and shoot it."
Light Spiral was less than enthusiastic about this reckless plan of attack, but could see no alternatives.  He swallowed hard, and nodded his assent to the sergeant.
"One...two...GO!"
Both ponies simultaneously stepped out from behind their cover, and in the split instant that the alien spent trying to decide which pony to shoot, shot at the alien with their shoulder-mounted auto-crossbows.  One bolt whizzed past the alien's head, while the other buried itself dead-center in the alien's torso.  Several agonizing moments passed as the alien simply stood there dumbfounded, before it finally collapsed onto the ground.
"Nice job, Spiral.  That kind of shooting will land you a promotion," Moonbeam said as she readied her auto-crossbow for another shot.  While that might have been a good joke before the aliens invaded, nowadays anypony who managed to bring down an alien was considered a war hero.  "Let's move up and secure the UFO.  It looks pretty small, so I don't think we'll encounter any more resistance."
Steeling themselves, the two Unicorns began to march their way towards the gleaming metal disc sitting amidst a field of grain...
XXXXXXXXXX
The rest of the events from that night had blurred together to create a jumbled mess.  Even now, she wasn't even entirely conscious of her surroundings.  She could vaguely recall securing the interior of the UFO with Light Spiral, which hadn't taken long.  They'd searched the rest of the farmland for any other aliens that might be in hiding, and she could remember Light Spiral getting his first good look at what the alien weapons could do to a pony when they found Private Evening Star's body sprawled out in the grass.
"It was his first time," she said, to nobody in particular.
"And you're positively certain that there weren't any other aliens left there?" asked a disembodied voice.  It was soft and refined, clearly a mare's voice, but deep and with a strong sense of authority about it.
"Positive.  Spiral and I turned over every rock and hay-bale looking for aliens," she replied.  She was gradually becoming more and more aware of her surroundings as the seconds passed.  The room was white and smelled of disinfectant; a hospital in all likelihood.
"That's all, then," the disembodied voice stated.  "Miss Sparkle, please gather your team and prepare to retrieve the UFO once day breaks."
Sparkle...Sparkle...Moonbeam knew that name.  It belonged to Twilight Sparkle, one of the Bearers of Harmony and head of research and development at ECLIPSE.  So she'd somehow managed to make it home, and was now in a hospital bed.  Why?  She didn't feel any pain at that moment, but attempts to move her limbs were met with sluggish responses at best; she'd obviously been sedated for some reason.
"And as for you," the disembodied voice continued.  "Cephalopod."
Without warning, the release from hypnosis caused the physical world to suddenly come back into crystal-clear focus for Moonbeam.  While memories of the battlefield quickly began to fade once more, she found that a large number of other things began to make sense.  She was in a hospital bed, and she recognized her surroundings as the ECLIPSE base infirmary.  Likewise, she recognized the form of Dr. Fluttershy quietly tending to the corpses of several ponies, and the form of Princess Luna – the founder and director of ECLIPSE – sitting next to her bed.
"Twilight Sparkle did not jest when she said that you proved difficult to interrogate under hypnosis," the Lunar Princess spoke, offering Moonbeam a warm smile.  "I apologize for any confusion you're feeling right now; it took a great deal of magic to open up your memory enough for us to make sense of what happened."
For several moments, Moonbeam simply sat there trying to take hold on what fleeting memories she could.  When it was clear that her increasing efforts were only giving her an increasingly vicious headache, she decided it prudent to simply ask Luna for an explanation.  "So what did happen, Princess?"
"Your mission was a success," the princess responded, clearly quite excited and cheerful for some reason that Moonbeam didn't understand.
"Six ponies died killing one alien, and you're calling that a success?" she blurted out as she sat upright.  Embarrassment flooded her, however, as she remembered who she was speaking to.  "I, er...forgive my insolence, Princess."  She steeled herself, expecting a stern rebuke from Luna.
The harsh rebuke never came.  Instead, Moonbeam felt Princess Luna's hoof touch her shoulder, and gently push her back into a resting position.  "You're forgiven," the Princess said, rolling her eyes at Moonbeam.  "I understand where you're coming from, but please understand that this is the first time we've managed to be the last ones standing when the shooting stopped.  More importantly, you and Private Light Spiral managed to not only bring back one of the alien weapons, but you were the first to successfully secure an enemy UFO."
The realization ran down her spine like ice water.  If killing a single alien was enough to make a pony into a war hero, then capturing an intact UFO was the sort of thing that would get a pony written into the history books – assuming that there was an Equestria left to write said history books when the war was over.
"Now, Dr. Fluttershy is going to give you a once-over when she finishes with the autopsies.  You stay here and get some rest until she tells you it's time to go," Luna said, her smile fading as her voice took on a more authoritative tone.  "No getting up and wandering around like a lost soul, Sergeant.  Stay put."
Moonbeam had to question which frightened her more: the alien menace, or her own boss?

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                         Chapter 2                         
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Chapter 2
"A state of armed conflict between different nations or states or different groups within a nation or state." – the definition of war, Unabridged New Equestrian Dictionary
Princess Celestia released a mournful sigh as she closed the dictionary that sat upon her private writing desk.  The hefty book before her was one of the few places where a pony could even encounter that particular word, its memory having faded from common vernacular out of simple disuse.  Even the very concept had become so alien to her subjects that she had required several hours to explain it when the authors of said dictionary had sought her counsel in defining the word.
Simply discussing the matter with them had been a painful experience, as the last pony to use the word with any degree of sincerity had been Nightmare Moon.  The shade that had overcome her sister spoke of fortresses and armies, and laying waste to all who opposed her eternal night.  So painful was the memory that she had almost immediately forbade the authors from even scribing the word into their dictionary; only the memory of Princess Luna – her real sister – prevented her from doing so.
"Who art thou, that knowest not thy history?" she had lectured Celestia, time and time again.  As much as Celestia was loathe to admit it, her sister was right; trying to write the concept of war out of Equestria's history would only invite it into Equestria's future.  It was times like that when Celestia was thankful for her sister's tendency to cast her eyes towards the past, even while her own eyes remained fixed upon the horizon.
She had, of course, hoped that the very notion of war had been banished from Equestria's future along with Nightmare Moon.  "Such a foolish thing to believe," Celestia said to nopony in particular as she turned and walked out onto the balcony of her tower.  All of Equestria sprawled out before her gaze, but her attention immediately fell upon the skyscrapers of Manehattan.  Glistening spires of glass and steel that once rivaled the towers of ancient Canterlot had been scorched and gutted by flames, and a haze of smoke hung low over the still-burning city.  The fires had been burning for almost a week now, but even the firefighters had evacuated the city when the aliens came.
Even Celestia herself wasn't sure where the invaders had come from, save that they had come from beyond the stars.  The arrival of their flying machines over Manehattan had been sudden, and their attack had come without warning.  The city's contingent of guardsponies was unable to fend off the invaders, who bore weapons that could reduce even an armored pony to little more than ashen bones.  Worse, the aliens seemed to be completely immune to any magical spells that the Unicorns among the guard had tried.  In the end, they had been reduced to literally throwing rocks at the aliens.
Seeing no other recourse at the time, she had ordered the evacuation of Manehattan and summoned the bearers of the Elements of Harmony to purge the invaders from Equestria using the strongest magic known to ponykind – the kind of power that even the princesses themselves could not bring to bear.  After outfitting the bearers with the finest equipment and supplies to be found anywhere within the palace, Celestia had sent the bearers to Manehattan with the future of Equestria riding on their shoulders.
Minutes spent waiting for their return turned into agonizingly long hours, and Celestia remained within the throne room even while Princess Luna held evening court for her petitioners.  For all the faith that Celestia had in both her students and the Elements of Harmony, she could not help but imagine the horrible fates that might befall them on their mission against these otherworldly horrors.  It was true that they had survived through countless hardships during their time as the bearers, but this was something that none of them – not even the princesses – could have ever conceived of.
If the anticipation had been unbearable, what followed was even worse.  She remembered the sudden rush of both terror and hope that had come when a member of Luna's Knightmares had burst into the middle of evening court and interrupted several dignitaries to deliver a report on the status of the bearers, and a message to the princesses from Twilight Sparkle.
"The Elements of Harmony had no effect whatsoever upon the alien invaders."
Her entire world might have collapsed right then and there, had it not been for her sister.  While Celestia sat dumbstruck upon her throne, Luna hurriedly dismissed the court and left her throne to pull Celestia into a tight embrace.  Through the shock, Celestia could remember her beloved little sister assuring her that she had a plan and that everything would be all right.  All Celestia needed to do was take some time to rest and recover her composure, and continue to assure the ponies of Equestria that the alien threat was being dealt with when the morning came.
Celestia shook her head to clear away the memories of that fateful night, and turned to gaze towards the Everfree Forest, not far from Ponyville.  She had all but guessed the entirety of Luna's plans for stopping the aliens when she announced her intention to clean out one of Nightmare Moon's many underground fortresses, and quietly given her sister her blessing to carry on with the work.
While she wasn't sure where Luna was getting the money or the horsepower to do so, she had managed to turn a derelict bunker from Equestria's past into the best hope for its future.  Soldiers, engineers, sages and scientists, materials of almost every kind...there was an almost nonstop flow of these things into the Everfree.  Into her sister's plan.  Into ECLIPSE.  Once again, ponies found themselves heeding a call to war from her younger sister.
And helpless as she was, all Celestia could do was lie down on her balcony and weep for her world.
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It had occurred to Princess Luna that use of the Elements of Harmony – being magical in nature – would probably not prove particularly effective against an enemy that had proven to be surprisingly resistant to magical interference thus far.  When her older sister announced her intention to send her prized students on what amounted to a suicide mission, she knew that it was time to start taking some drastic measures to prevent her sister's short-sighted sacrifice from becoming a long-term disaster to Equestria's future.
The aliens were bad enough.  If the bearers died and the power of the Elements dwindled, it was entirely probable that Discord would be freed from his stone prison.  No, Luna preferred to take her world-threatening cataclysms one at a time, please and thank you.  Fortunately for Luna, Twilight Sparkle could see the logic in Luna's approach, and was willing to help convince the other bearers that it was in their best interest to visit the Everfree Forest instead of Manehattan.  Once her own guards had taken over for the evening, it was a simple enough matter to fabricate a report of failure from Twilight Sparkle and get Celestia out of the picture.
During her descent into the madness that was Nightmare Moon, Princess Luna had constructed a number of underground bases away from her sister's prying eyes.  Her tendency to have her own personal spies monitoring the affairs of Equestria's nobility had paid off in spades, as evidence of corruption, sexual deviancy, and every other bit of dirt she could find had been enough to force the heads of over a dozen noble houses to finance the construction of these facilities in exchange for her continued silence.  A thousand years later, the same practices had once again ensured that ECLIPSE had no shortage of money, materials, or horsepower.
She knew that she wouldn't be able to blackmail the nobility forever; eventually they would dispose of all the crucial evidence linking them to their misdoings, and Luna's hold over them would become progressively weaker.  Of course, by the time they reached that point, Luna would be able to present them with tangible evidence of their successes against the alien threat, and they would continue to fulfill Luna's every need out of fear for their own worthless hides.
Well, almost every need.  One particular need would have to wait until after she'd dealt with the alien invasion and put Celestia back on her pedestal.
"...Princess?" asked a voice from her side, calling her back to reality.  Luna opened her eyes once more, and found herself seated in the ECLIPSE command center.
"My apologies, Spike.  I have not slept much these past few days, and I fear that fatigue is setting in," she told the worried little dragon.  "I seem to have forgotten what we were speaking about.  Could you remind me?"
While Spike was initially skeptical of Luna's claims of forgetfulness, his skepticism couldn't hold against the caring smile that Luna offered him.  "You wanted me to send a progress report to Canterlot," he reminded her.
"Right!  I need you to inform the council of nobles about our recent success in capturing one of the alien flying machines," she patiently explained to Spike.  "Tell them that we're going to begin taking it apart and see if there isn't something we can use to level the playing field a bit.  Oh, and I'd also appreciate it if you made sure that a copy of said report reached my dear sister; she's been beside herself with worry, and some good news should improve her mood considerably."
There was nothing outwardly wrong with Luna's request, but something about the Princess was making Spike more than just a little uncomfortable.  "Is there anything else you need me to do, Princess Luna?" he asked her.
"Yes, actually, there is," she told him, a sudden realization happening upon her.  "You should probably check in with Twilight Sparkle and see if she has any progress to add to your report.  For that matter, you should probably check in with all your friends here; I'm sure they could use a friendly face among all these strange ponies."
This addition to Luna's request brought a smile to Spike's face, and he saluted the princess sharply before hurriedly leaving her to set about his appointed tasks.  She pondered whether or not she was abusing the little dragon's naivete regarding the nature of ECLIPSE, but decided that it didn't really matter – the little guy had never bothered to ask about it, after all.  Like the bearers that had brought him here, he had simply accepted ECLIPSE as a necessary solution to a very dire problem.  And like the other bearers, he had readily accepted his position in her system and continued to give it his 110%.
In short, he was the perfect choice for a personal aide.  Loyal and brave, but not particularly inquisitive.
It was much easier to keep the bearers themselves from putting their muzzles where they didn't belong, given that each had been given a demanding set of duties that rarely placed them in any position to notice the amount of shady behavior involved in running ECLIPSE on a daily basis.  Twilight Sparkle herself was the most likely to notice such things, but as the head of ECLIPSE R&D, she currently had her hooves full with that recently-recovered UFO.  Applejack had been tasked with the monumental duty of keeping ECLIPSE well-fed and its pantries full.  Rarity was currently ensuring that the ECLIPSE armory was producing armor, weaponry, and other war materials in a timely fashion.  Fluttershy was keeping the soldiers physically healthy, and Pinkie Pie was keeping the war from breaking the soldiers mentally.  Rainbow Dash, meanwhile, had taken on a role as the eyes and ears of ECLIPSE.  She would coordinate the large numbers of Pegasus scouts that fanned out across Equestria to monitor UFO activity.
With a few exceptions here and there, everything was running in a smooth, orderly fashion.  "It's good to be the one in charge for a change," Luna thought to herself as she closed her eyes once more.