The Choices We Make

by nightshade745

Rating: teen
Tags: Alternate Universe, Human, Dark, Adventure
Length: 3518

They're back after 3,000 years and they want the throne of Equestria. Celestia and Luna will face an enemy older then they are..

Celestia and Luna narrowly avoid disaster in Canterlot only to find themselves in possession of a changeling with a disturbing horn mutation. He's obviously crazy with all his talk about being "human" and "America", but his appearance has earned him the attention of an ancient and mysterious Order. Each of their members posses strange powers that they plan on using to destroy Equestria and everything it represents!

The changeling, Max, may be the key to uncovering the truth behind the founding of Equestria and the greatest cover-up in history! Not to mention, he is the best chance Equus has to defeat the bad guys' leader, Skull.
—————————————————————————
Things to Know Before You Read:
*Human in Equestria, if you didn't pick that up from the description.
*Takes place just after the Crystal Empire's return. (No alicorn Twilight & Discord is still evil)
*Lots of ancient Equeastrian history

Published 1970-01-01 00:00:00 UTC
Last updated 2013-04-20 16:28:07 UTC

Prologue: Rain

It had been a month since the Crystal Empire's return, and only a little longer since the changeling invasion was thwarted. Equestrians had reason to celebrate, but it didn't feel like it today. The weather patrol had held off the rain for far too long so ponies could enjoy these good times. Now, they had no choice but to leave the big faucet in the sky open. They had to make up for the short drought that was torturing the crops of many hard working farm ponies.

The dark cotton like clouds doused the the city, turning the many narrow streets into raging rivers. Most ponies were driven inside where they'd sit by a warm fire and enjoy warm drinks. Some of the younger ones would throw on raincoats and splash in the massive puddles that had formed in the pot-holes of the streets. The heavy drops of rain sounded like falling stones as they beat mercilessly against the umbrellas the aristocrats wore on their way to important places.

The royal guards were not given the day off and weren't at all prepared for this kind of weather either. The unicorn guards did their best to make shields that protected themselves and their partners from the falling water, but some of the pegasi and earth pony guards didn't have a unicorn around to protect them from the rain. Instead, they had to either deal with the cold drops tapping against their armor, or break code and wear a bright yellow tarp over themselves. Miserable was one way to describe those with stations outside. The indoor guards felt bad for them because of how terrible the weather was, but they felt worse for themselves because they knew that they would have to take their place outside when the shift change occurred.

Many of the stores were closed because there simply were not enough ponies out buying today. Donut Joe was one of the lucky ones; many of the colts and fillies that enjoyed the rain were lining up at his shop with allowance money to spend on his world famous hot chocolate. He did his best to keep up with the high pitched calls and there was always a steaming cup of hot cocoa gliding across his counters. The money Joe was making was phenomenal and he was yet another step closer to expanding his business. Another few days like this and he could open a second shop!

"Rain...it makes a good companion for the helpless soul," a lone unicorn whispered to himself as he gazed aimlessly at the sky.

He had a small build, standing at only 3 and a half feet. His fur was lime green and would have been frizzy if it hadn't been so wet. His mane was a crisp brown that, on a normal day, would have looked good on him. Unfortunately, the relentless downpour had soaked into his hair and left it ugly and ragged. From afar, he was rather depressing to look at, but up close, his eyes were fierce and defiant. His natural eye color was baby blue, but his eyes might as well have been roaring flames right now.

His naked body was crisscrossed in scratches, bruises, and gashes. The majority of his injuries were still fresh and he was loosing blood slowly. Despite this, and his broken leg, he began walking again. He had a mission to complete at Canterlot Castle, or more specifically, in the mines that ran underneath it. He had to reach the dark tunnels today, it couldn't wait for tomorrow or even for him to recover. He knew this would be the single most important act of his life!

Along his way through town, he passed a playground full of laughing foals. He stopped and turned his head to watch them for a moment. About five of them were leaping in the large round puddles and creating small tidal waves. Several others were playing tag as they giggled without a care in the world. It seemed that two colts were daring each other to go down one of the slides and into the lake that was beginning to form at the bottom. The unicorn smiled sadly. He thought about his own childhood, his days wasted having fun and getting into trouble with his friends. He almost felt like running out there to join those innocent little bundles of joy. He probably would have if he wasn't so pressed for time.

It took him a moment to force his emotions down so he could continue. He knew he had to focus and that the entrance to the mines was a few minutes outside of town, off on a dirt road to nowhere. There, thanks to the changeling attack, would be guards waiting for him. If Chrysalis hadn't reminded everypony about there existence, the mines probably would have been unguarded and he could complete his mission without any interference. He didn't want to start a fight after all, but there was no way they'd let him through. He groaned, he was going to have to get aggressive.

He picked up his pace, his eagerness to be done with this last act powering his legs forward. A quick rasp of air escaped his lungs as he slipped on the wet stone beneath him. He managed to keep himself from falling, but it caused him to pause and shiver. His temperature was dangerously low and every drop of rain that hit him took some of his precious body heat with it. He hardened his gaze even further and pushed his legs forward once again. This weather was testing his determination, but he could not give up.

Two unicorn guards stood at full attention; each of them had a fragment of a shield dangling over his head that acted like an umbrella. Despite their attempts at not getting wet, a pond was taking shape around their ankles and there was little they could do about it. It was their job to guard the entrance to an old mineshaft just outside of town on a dirt road nopony ever used. It wasn't like anypony was going to use the mines to gain access to the castle. An intruder would have to navigate in complete darkness through miles of tunnels, work around cliffs, and cross numerous underground rivers. Even if they were able to conquer all those obstacles, there was no guarantee that there was anyway from this particular mine shaft to the castle. And if there was they'd also have to go through all the guards that stood at attention inside. So the two guards stood there, both feeling a little like they were wasting their time.

Unexpectedly, a single unicorn came along the path. The road was little more than a mudslide right now and he was clearly struggling to keep his footing. The guards looked straight ahead, almost trying to ignore him despite their curiosity. "What could anypony be doing down here?" they both wondered. Suddenly, the unicorn's horn erupted in green light as he prepared a spell. Both guards didn't even have time to react as the lone unicorn fired a single electric bolt at the puddle they stood in. Their highly conductive gold armor and soaking wet hooves meant they were both feeling the full force of the spell. The lone unicorn quickly found himself with two unconscious Solar Guards.

He made sure they wouldn't drown while they were out before turning his attention to the doorway. It had been a sturdy pine back in the day, but the wood was old and rotten now. He quickly blasted the frail beams out of his way so he could continue. After making a small light with his horn, he began his descent into the earth. He was so close to completing his mission that he could taste it. He could certainly taste the moist moldy air of the cramped tunnel he was in. He never had a particular fear of small spaces or rancid smells, but nopony suffering from claustrophobia would last long in these passages.

A steady stream of rain water was flowing down the tunnel with him. Along the way it gathered up loose mold and smelly mushrooms. The deeper the lone unicorn went, the more disgusting the soup he was forced to tread through became. The stream resembled the polluted river of Manehatten in his eyes. That thought suddenly made him reminisce about his friends that he'd left behind without even a goodbye. It was a shame he couldn't tell them what he was doing, but he couldn't trust anyone but himself. They would have never understood why he was doing this, heck, he barely knew what it was he was doing.

The tight tunnel abruptly opened into a enormous cavern! The room was almost as big as a hoofball stadium, all it needed were some stands. The rocky tunnel floor smoothed considerably and ran a few dozen steps forward before dropping a hundred feet straight down off a jagged cliff. The flows of water ran over the edges like tiny waterfalls in a pathetic attempt at beauty, not seeming to realize it was pitch black here.. In the great expanse below, with an almost heavenly aura shining around it, he saw a great diamond. There were many large crystal rocks that stood like monoliths along the walls, but this one stood out amongst all the rest. It was easily 50 feet tall and it was probably just as wide. The mine was still so full of these goliaths that it made no sense that this place had been abandoned.

The unicorn gave himself a few moments to catch his breath. He wasn't tired, but his injuries were catching up to him. The pain was starting to get to his head and he was on the edge of hypothermia. His rapid shivering and the clouds that appeared whenever he exhaled a clear indication that it was just as cold down here as outside. Taking in a gulp of the freezing air, his horn began to glow and he gathered his magic. A fast pop resounded as he teleported down to a circular clearing where the crystals surrounded him like Stone Henge, the biggest being just a few steps ahead. He looked up at it with an eerie sense of calm. The time was at hand, it was the end of his journey. Now all that remained was the ritual.

Standing perfectly straight and breathing deeply, he gathered every last drop of his magic. He closed his eyes and focused solely on his task. An arc of green energy suddenly shot from his horn to one of the crystal stones! After zapping it, the diamond gained a deep inner glow. The unicorn immediately shot another of the diamonds, having an identical result. After he fired off a few more arcs of magic, each of the large stones had gained a faint green glow coming from deep within. All of them except the largest diamond in the center that he had purposefully ignored and would continue to do so for a while longer.

He gave each diamond a second dose of magic. Then he gave each of them a third, and a forth. With each pass he zapped them faster and faster and they turned progressively brighter shades of green. After a few passes, all but the largest diamond were a shining green. The unicorn opened his eyes to make sure they all had identical glows before turning his sights on the largest one. This one he'd have to pour everything he had into if he wanted to complete the spell.

He roared ferociously as his horn erupted in angelic light! He unleashed multiple arcs of pure magic at the massive diamond; his head vibrated and his teeth ground against each other from the sheer effort. His wounds seeped blood due to the pressure that was building within him. He growled like an animal as he felt the limit of his magic coming. No matter what happened to him, he had to complete this ritual. He had to force himself beyond his magic limits...even if it killed him.

The entire cave was engulfed in a bright flash of green as the unicorn's horn exploded! Horn fragments blazed through the air, but it wasn't just his horn that was gone, but the top of his skull as well. His head spurt blood skyward like a demonic fountain and large globs of red rained down on the smooth rocky floor. Slowly, the ground around him was painted a grizzly scarlet. His body began to lean to one side, eventually toppling over over. As his head smacked the stone floor, yet more blood gushed forth.

The hands of death already had him in an icy grip and were pulling him from this world, but they were not without some ounce of mercy. For they allowed him just enough time to be assured that his ritual had succeeded. All of the diamonds were pulsing green in perfect harmony. As his eyes closed and his soul faded from the world, he smiled. He didn't care that he was about to die. "I succeeded," he thought. "I only regret that it couldn't be my hooves that saved Equestria." Seconds later, his eyes pulled themselves shut...

Water ran over the edges of the rooftop and poured into the streets below. There were no guard rails around the edges, but there was a dark metal fire escape on the back of the building that dropped down into the alley. The building was an antique shop that sold old, rare, and valuable items from throughout history. The store was closed due to weather unfortunately. Three ponies were standing on the roof almost in a line, each of them wearing a thick black raincoat. One stood a few steps away from the fire escape, another stood off to the side near the center of the space, and the last stood at the ledge.

The one that stood at the back of the group had his head pointed downward, his golden eyes locked on a the stone floor beneath his hooves. He had his raincoat stretched up over his head as though he were trying to hide his face. His muzzle was a little short and his eyes were rather small. His fur was a dark plum violet and his mane, that dangled out from under his hood, was scorch black. He stood at a decent height of 4'2". He had his hooves huddled together due to the mild wind that was blowing by.

The one standing in the center of the roof top was a unicorn and did not bother trying to conceal his horn or his face. His fur was scarlet red and his wild mane was scorch black as well.  He was 5'2" and his body seemed well built and strong. He had an angular muzzle and his bright magenta eyes were set deep in his skull. He did not quiver in the freezing rain or bone chilling wind that ripped past him and blew the tail of his raincoat about like a fish on a hook. He also wore the deepest scowl planet Equus had ever seen as he watched the third pony intently.

The other unicorn stood at the front of the group and at the very edge of the rooftop, his front hooves only an inch from going over the side. His hood was only barely clinging to his head with his big violet eyes just underneath the lip. His mane was snow white and his fur was sky blue.  Even though it was wet, his short mane pointed outward like porcupine spines. He was the shortest of the three at 3'9", but his horn made him unique from any other unicorn in the world.

It resembled a lightning rod more than it did a horn, at 3 feet in length! At the moment, he was holding the long and fragile looking thing at a slight angle towards Canterlot Castle. His eyes remained closed as he ignored the pounding of rain, the cracks of thunder, and the roar of the wind while his horn shone with magic. The air around him was filled with static and any nearby radios would have gone haywire. He was using a spell that released and received various signals, with his horn acting like an antenna.

The long horned unicorn suddenly opened his eyes as his concentration was shattered. "Skull...Space Shift just died," he reported with a young voice. He was just out of his teenage years it seemed.

The red unicorn went wide eyed, but still looked mad. "Cause of death?" he demanded, his voice sounding more rough and middle aged.

The unicorn tried to refocus and began using the same magic again. "Wait...sir I'm getting some strange inference."

"What kind of power could possibly block your horn?" Skull asked while walking up beside him.

"I just sensed Space's death, but his magic signature is still there. I don't understand how that's possible." He began twisting and tilting his head as he tried to confirm what he was detecting.

Skull inhaled slowly as he tried to control his anger. "Alright, you don't sense his mental functions anymore?"

"No sir, his brain is definitely dead," he suddenly stopped tilting his head as he got good reception.

"Has his magic been attached to something, is it an enchantment?" A crack of lightning punctuated his sentence needlessly.

"No sir. It almost feels like his magic has...come alive? And is acting on its own. It's......growing." He sounded confused and unsure.

Skull grumbled, that shouldn't have been possible. "What did Space Shift do down there?" he mumbled himself.

The unicorn with the long horn stopped focusing and turned to Skull beside him. "Orders sir?"

The red unicorn met his gaze, "orders? Resonance, I want you to send a message to all operatives: return to Hibernation Phase." He promptly began to turn away.

The unicorn, Resonance, choked at the answer. "B-but sir! We just left Hibernation Phase," he stammered. "We were just about to-"

"I KNOW THAT RESONANCE!" he roared back. "But we have no choice. One of our kind is dead and I don't know why. Not only that," he stepped up into Resonance's face. "But we've been compromised. Canterlot Castle is, at most, an hour away from switching to high alert status, or did you forget about the two guards you yourself told me Space Shift attacked!?" he screamed at Resonance. He stepped away from Resonance before continuing, "now do as I ordered. And put your horn away before a commoner sees," he hissed.

As he turned and began to walk away, Resonance went cross-eyed as he looked up at the tip of his spear like horn. Strangely, his horn began to collapse in on itself and shrink. Tiny clicks were heard as the end of his horn came closer and closer to his forehead. His contracting horn looked like a spyglass being put away, and sounded like one too.

"Shade Stalker, you and me-" he stopped talking when the pony in the back didn't look up. "SHADE STALKER!" he boomed.

The pony's head jumped up as he at attention.

The red unicorn stepped up to him and put his muzzle only an inch in front of Shade Stalker's. "Tell me you are aware of what has just taken place," he commanded.

"Space Shift has betrayed us sir," he recited with a dark dry tone. Resonance thought that might be the wrong term. It was more like Space Shift had abandoned them then actually betrayed them.

"And?" he raised an eyebrow angrily. It was clear Shade Stalker hadn't heard anything that had just been discussed.

"Resonance is tracking his movements sir." Skull shook his head in a dissapointed fashion as he walked around and stood behind Shade Stalker.

"You and I are going to investigate Space Shift's last act. Whatever it may have been, I want to know. If we confirm his death, then-"

"Space Shift is dead!?" Stalker blurted out, interrupting him.

"Yes," the unicorn hissed. "One of our kind has died and I'd appreciate it if you...PAID ATTENTION!!" he raged into Stalker's right ear.

Shade Stalker reflexively stepped away, but held his tongue. Resonance idly watched Skull berate Shade Stalker on his short attention span for a moment.

Skull eventually made his way to the fire escape at the back of the roof as he spoke. "We will have to delay our plans yet again. You and I need to investigate and determine what Space Shift did before we can do anything else." He looked back to find that Shade Stalker had not moved and Resonance was respectively waiting for them to leave first. "Are you coming Shade Stalker?" he asked threaningly.

"Am I to assume you need my...'talents'?"

"Yes," Skull hissed.

"Coming sir."

Resonance watched them leave before looking up at the castle. His best friend had left without even a goodbye and now he was dead. "Why?" Resonance asked himself. "What did you do?"