Equestria: The Alpha Files "Phobia"

by Lucario247

Rating: teen
Tags: Gore, My Little Pony: Friendship is Magic, Dark, Alternate Universe, Original Character, Adventure, Crossover
Length: 3386

Alpha ponies. Myth or truth?

Alphas. Normal ponies, with extraordinary abilities. They live among us, pretending to live a "normal" life. But they still exist. One in every ten ponies is an Alpha. However, some Alphas have chosen a not so normal life, abusing their abilities and using them for crime. This is where Dr. Omega's team of Alphas comes in.

Kind of a parody/crossover of the Syfy show Alphas. I just randomly thought it would be cool to write something like this. If you havent seen the show, you might as slightly lost as to what the story is about. But, you'll probably get the hang of it. Please enjoy!

Published 2012-08-31 23:34:01 UTC
Last updated 2012-09-11 04:57:00 UTC

Prologue

Equestria: The Alpha Files "Phobia"
By: Lucario247

Prologue

"How can you claim to be an Alpha? How can you even believe in that kind of nonsense?" she said.

"Aw c'mon Creme. You know how good I am at making ponies do what I want. I must be an Alpha!" replied the colt next to her

She scoffed and flipped her mane out of her eyes, "Yeah yeah. You're probably just naturally manipulative."

He jumped in front of Creme and frowned at her in concentration, "In the name of my Alpha ability, I command you to do my bidding!"

She scowled at him before she crossed her eyes, "Yes master Spots! I have no will of my own!" she drawled mockingly

"I command you to, uh..., kiss me!" Spots said triumphantly

"As you wiiiiiish..." she drawled with a smirk as she leaned forward and pecked his lips.

The two were walking back to their inn. It was a cold night in the streets of Manehatten. Both ponies were wearing coats to keep themselves warm. Creme pulled away from Spots and looked at him.

"Seriously though. We need to get back to the room."

He smiled a little, "You're right. I'm freezing my tail off."

They continued to walk down the dimly lit street. After a minute of silence, Spots turned to Creme.

"So, do you think that Alphas really exist? That message that Princess Celestia sent out seemed pretty legit." he asked

She scoffed again, "Please. It's probably just one of her weird and over the top pranks again. Like that "Banana Day" she announced last year."

"I think it'd be pretty cool if anypony we knew was an Alpha. Say... You seem to avoid the subject of Alphas. You aren't an Alpha yourself, are you?!" he asked excitedly

"If I was, I'd have used my ability to kick you out of my house." she teased

They both laughed as they continued walking. They passed an alleyway and stopped.

"We could pass through there. It'd be faster than going around the whole block." said Spots as he trotted towards the alley.

She hesitated, "I'm not so sure. What of there are thugs or kidnappers in there?" she gave a small shiver in fear.

"Don't worry. I'll use my Alpha ability to protect you." he smiled kindly at her.

Creme nervously smiled back as she trotted up next to Spots. The two stepped into the alley. It seemed like the atmosphere in the alley was completely different. It was...thick. And the deeper that Creme went into the alley, the bigger her fear grew.

It didn't seem like there was anything to be afraid of in the alley. Albeit, it was somewhat creepy, but not enough to cause a fear this massive. Creme huddled up next to Spots for comfort. The relief was minimal.

"Although, if Alphas truly exist, there are probably bad ones that misuse their powers." Spots said.

She looked at him. He was afraid to, she could see it.

"I g-guess."

"I'd imagine that an Alpha would most likely be unstable and sadistic."

"Who knows what somepony would do. Theft, kidnapping, maybe even mur-"

She was interrupted when she tripped on something and fell to the ground. She let out a small cry from the sudden action. She clenched her eyes shut as she collided with the ground. After a moment of shock she opened her eyes.

A pony stared back at her. It had an expression of pure terror on its face. Creme's fear began to rise as she realized that the pony was dead. She scrambled to her hooves and rushed to Spots' side. She noticed he was staring in horror at something near the alley wall. She turned to look at what he was looking at.

Another pony lay, slumped against the wall. It's mouth was open mid scream. A gleaming, razor sharp sickle protruded from the pony's forehead, blood seeping from the wound.

The fear from the atmosphere and the new discovery came crashing down on Creme.

And she screamed. For a very long time.

Chapter 1

Chapter 1

He listened. Or he felt. Either one. He listened/felt the sound waves return to him.

"Aero! He's going down Neighberry street!" he shouted into the radio.

"Yeah I see him!" came the staticy reply, "C'mon Chime! We need to catch him!"

The pony nodded to the response and turned to the pony next to him.

"Dr. Omega. This colt is going to Reinington when we catch him, isn't he?" he said

Dr. Omega gave a small sigh, "I'm afraid you're right, Visor. Clay still won't listen to my complaints about the treatment in Reinington."

Visor nodded sadly as he returned his attention to the pony his team was chasing.

Aero was chasing after the perpetrator. Chime was following behind. The perpetrator pony's heart rate was 130 bpm. A little foal dropped her stuffed animal on the ground and a colt stepped on it. Aero nearly collided with a pedestrian. Chime was beginning to slow. A couple was arguing over tea about political issues. A mare grabbed a tourist's wallet. The perp suddenly pushed a standee into Aero's path. A street dancer slipped and landed on his snout. A group of teens laughed immensely as one of them snorted from laughter.

Visor placed his hooves on his temples, "Dammit! Focus! Focus on Aero and the perp! Nothing else." he thought to himself.

He returned his attention once again to the chase.

Aero was pretty angry. Of course, he usually was angry. He was especially angry that the Alpha that his team was investigating ran when they confronted him. He hated it when they ran. He looked behind him and saw his partner, Chime, panting as she tried to keep up with him.

"Chime! Try and circle around and cut him off! I'll either corner him or turn him around!" he shouted behind him.

"Huh, huh... Ok..." she puffed in her tiny voice.

She slowed her pace as Aero returned his gaze to the pony, who was now outrunning him. Aero also hated when they outran him.

Aero gave a small, devilish grin as he felt the blood and adrenalin seep into his legs. The distance between him and the pony he was chasing quickly shrank. Soon, he was neck and neck with the pony.

"Hey..." Aero said as he zoomed next to his target, "Why you running? Only bad ponies run. I know..."

The pony glared at Aero. He kicked an empty bottle, which flew and bounced off a sign. It then broke, causing a stallion that was dragging a cart full of heavy barrels to suddenly stop. A barrel flew out of the cart and sailed towards Aero.

He quickly turned and positioned his hindlegs to buck the barrel. When his hooves connected with the wood, his Alpha strength caused the barrel to explode into thousands of shards. Pickles splattered from the barrel as well. Aero turned and snorted as he noticed the lengthened distance between him and his target.

He sent as much strength as he could to his legs, and took off. Easily breaking 35 mph, Aero weaved his way through the bustling crowd of ponies as he locked his sight on his target. The pony turned into an alley, and Aero nearly laughed at his stupid mistake. The tighter quarters would be easier for cornering him.

Aero skidded around the corner and scanned the area for the pony. He saw him running down towards the other end of the alley. Aero quickly searched for a way to stop him and spotted a trash can. He turned and bucked the metallic cylinder, sending it flying towards his target. It smashed into the pony's back, causing him to fall over. Aero used that opportunity to close the distance.

The pony staggered to his hooves as Aero advanced on him. The pony quickly recovered and aimed a buck at Aero. He gave an abnormal leap and flipped over the pony. When he landed, he turned around and barely dodged a jab from the pony. He countered with a powerful hook to the pony's gut. The force sent the pony up against the wall.

He staggered for a moment before he stepped on a small wooden beam. Aero watched in partial awe as the chain reaction caused a shard of a broken flower pot to fall towards the fire escape step ladder. The pony pushed Aero, in his awe, towards the end of the alley. The next thing he knew, Aero was watching the fire escape ladder fall towards his head.

He quickly used his wings and hind legs to flip himself out of the way. He felt the metal ladder graze his back as he flipped back onto his hooves. Aero looked around and saw the pony already nearing the exit of the alley. He took of as fast as he could towards his target. He realized he wasn't going to be able to intercept the pony, until he saw a figure move in front of the alley.

The pony stopped as he looked at a panting Chime. Aero smiled at his back up.

"Stop...huff...right there...phew." she puffed

The pony snorted at the small mare, "Whatcha gonna do shortie? Make me trip over you?"

Aero's eyes widened as he thought, "Oh crap. He's so dead."

Chime's chest stopped heaving as she slowly looked up at the pony. He recoiled slightly at her piercing glare. Aero quickly fell to the ground and covered his ears as he prepared for what was about to happen.

"You..." Chime said slowly, "Did not, just CALL ME SHORT!!!!!" she screamed

The colt crumpled to the floor as the sound waves emitting from Chime's enhanced vocal chords, assaulted his ears.

"I AM NOT SHORT!!! AAAAAAAH!!!!" she screamed at him.

The pony screamed and writhed on the ground. A small bag of rainbow colored tablets slipped out of his coat pocket. Chime gave one last hyper shriek, and a window from the side of the building shattered.

Aero quickly jumped up from his spot and pounced on the stunned colt. He tried to struggle, but Aero raised a hoof and slammed it into the ground next to the pony's head. He looked in shock and fear at the cracks in the concrete that were created during Aero's stomp.

"Struggle some more, and your skull will look like that." Aero said devilishly. The pony gulped and nodded

"Lookat wha we gah ere." Chime said as she held up the bag filled with the chromatic pills.

"Ah, possession of Chroma! That there is illegal, mister." Aero taunted the pony.

"Dr. Omega. We've got him." Chime said into the radio she carried

"Good. Me and Visor'll be right there."

When Aero saw Dr. Omega and Visor round the corner into the alley, he stepped off of the pony.

"Twitch, and I scream." Chime said coldly. He understood.

Dr. Omega watched as Aero, Chime, and Visor apprehended the Alpha pony. It was sad that somepony with such an amazing talent would use it for such horrible reasons.

He was interrupted from his melancholy thoughts as he heard his radio crackle. He pulled it out of his coat with his magic and clicked the button.

"Yes?"

"Dr. Omega," it was Psyche, "Chamille has left again."

He sighed. This was the fourth or fifth time.

"I tried to stop her from leaving but, well you know her. She has a way of blending into places. And I lost her." Psyche said

"That is fine. She's probably at the nearest club." Dr. Omega replied.

"I'd go and get her, but I'm busy filling out the Pie incident report."

"Just send Mr. Nightfall."

"Shutter isn't even here yet. He's probably off sneaking into some royal facility or-EEEEK!"

Dr. Omega jumped at Psyche's sudden cry.

"Psyche! Are you alright?"

"Holy Celestia, Shutter! You scared the living day lights out of me!"

"Sorry." came the quiet reply

"Urgh. Dr. Omega wants you to go find Chamille and bring her back here."

"...Fine."

Dr. Omega sighed again. He'd sighed a lot today. Right now his priority was to get the rogue Alpha back to the office for interrogation. But he still couldn't shake the feeling of worry for his team.

Shutter weaved his way through the bustling crowds. He was heading towards the Sloppy Stallion, a cheap club that was down the street from his office. On his way there, he spotted Chamille walking into the club. He decided that it didn't concern him, so he carried on. But now, it did concern him.

He walked up to the entrance, but was blocked by two bulky stallions.

"Where's your invitation?" bellowed one.

Shutter looked up at him, "My friend is in there."

"That blows." said the other colt with fake sympathy

"Look kid, we don't wanna make a scene with you, but if you don't scram, we'll scram you into a dumpster." said the first

"...I'd honestly like to see you try." Shutter replied casually

"H-huh? Why you-!" the colt lunged at Shutter

He easily sidestepped and melded with a small group of tourists that were strolling by. He then began to vibrate his body, causing his body to become invisible.

After the crowd passed, the two colts were looking around in confusion, "Where did 'e go?!" shouted the second.

Shutter quietly stepped past the colts and into the bar. The music was loud, as were the sounds of ponies chatting and laughing. The smell of alcohol wafted into the air. Shutter guessed that the door ponies were occupied with finding the vanishing pony outside, so he uncloaked.

"I gotta find Chamille." he thought to himself, "But she could be disguised as any of these ponies around here. I need to find her cutie mark."

He began to observe the cutie marks of any female ponies he came across. He slowly made his way across the dance floor, checking each mare's flank for the familiar multi colored heart cutie mark.

One mare noticed his staring, "Hey! What the hay are you doing?!"

He slowly straightened up, "I'm looking for someone."

"Pfft. I've heard that one before." the mare said as she pulled her hoof back for a punch.

Shutter backed up so that the punch missed him. However, he accidentally bumped into a waitress who dropped her tray full of hard cider shots. The shattering of he glasses and the clanging of the tray was somewhat louder than the music.

Shutter, not trying to attract attention, quickly cloaked and weaved his way through the crowd of drunk, dancing ponies. He stopped moving and uncloaked near the bar. Letting out a silent sigh of relief, Shutter resumed his search for Chamille's cutie mark.

He didn't have to look far. A mare with an indigo tail and mane and bright green coat with dull yellow eyes was sitting at the bar, chatting up an obviously intoxicated colt. Shutter understood Chamille's tactics, she was probably schmoozing the colt into buying her, possibly another, beer. The bartender brought out two glasses as the two guffawed at some joke the colt said.

After taking a long swig of her drink, Chamille sat the glass down and stood up with a drunken grin. She gave a wobbly gesture to the colt, suggesting he follow her. He stood up and followed her as she led them through a back door. Shutter, going into his espionage instincts, cloaked and slowly pursued.

Chamille led the colt through a series of hallways until she turned and pulled him into another room, with a series of giggles. Shutter was curious as to what they were doing. But knowing his partner, he could probably guess. He silently trotted to the room and entered.

Chamille was passionately kissing the colt, who was kissing back in his intoxication. Shutter stepped further into the room and uncloaked. Chamille parted from the embrace and placed her head on his shoulder. He began to kiss her neck. She noticed that Shutter was there and her eyes flashed open. She gasped and backed up.

"Baby! What's wrong?" the colt said as Chamille pointed at Shutter, "Who the hay are you?!" he shouted at Shutter.

He ignored him and looked at her, "Chamille. We need to go back to the office. Now."

She gave him a glare, "H-he's my ex-coltfriend! He's crazy! Don't let him get me!" she said to the colt in a facade of fear.

He turned to Shutter, "If you want her you gotta go through me!"

The colt charged at Shutter. He had to repress a smirk as he sidestepped the colt and cloaked. The colt looked around in bewilderment. Shutter crossed behind him and yanked on his tail. The colt yelped and wheeled around. Shutter tripped the ponies hindlegs so he was sitting. The colt looked back, and Shutter uncloaked. The pony returned his gaze in front of him and saw Shutter's raised hoof.

"Tell the hospital ponies you lost a bar fight." he said as he stomped on the colts head.

He fell to the ground, unconscious. Shutter turned to face Chamille. She at first looked in shock at the crumpled form of the colt. Then she glared at Shutter.

"What the hell are you doing?!" she yelled as her coat and mane began to change into a blood-like crimson, "Can I not get a freaking break?!"

Shutter nearly faltered as her eyes began to shine with fire, literally. Her irises began to shift between a dark red and bright yellow. She flared her wings which also became red.

"...Dr. Omega wants you back at the office." he said

"I quit." she said bluntly

"You know you can't quit."

"Why not? I have a right to do what I want."

"It's not like that. We need you."

She scoffed and tossed her now brown mane out of her eyes, "No. You "need" my ability. If I didn't have my ability, I'd just be another face in the magazines."

"I don't think you'd even be a model if you didn't have your ability."

"Of course not! I'm to beautiful to pass over." her coat shifted to a deep purple

Shutter shook his head, "Look, we can talk about your career later. Right now, let's just get back to the office."

"I already told you! I'm not going back! My ability isn't even worth very much to you anyways."

He looked at Chamille, "You're my partner. We're the espionage team. Don't you ever say your ability is worthless."

He placed his hooves on her shoulders. She turned her head away.

"Do you know how many times you saved my tail with your ability?" he said as he gently pushed her face to look at his

"Pfft, at least twenty times." she smirked

"Exactly thirty two times."

She was obviously surprised.

"Don't say your ability is worthless. If it weren't for you, I'd probably be in as bad a situation as imprisonment in a diamond dog den to maybe even death."

Her eyes changed into a light blue. She nodded her head slowly as she and Shutter slowly turned to leave. He stepped over the body if the unconscious colt and strode back into the club, with Chamille at his side. They past the waitress who was still cleaning the mess off the floor. She gave Shutter a funny look as they passed.

As they passed through the entrance, Shutter turned to look at the two doorstallions. They looked at him in confusion and shock as he nodded to them.

"Afternoon, Gentlecolts."

The two gawked as he and Chamille walked back towards their office.

Hello. If you're confused about the characters' Alpha ability, personality, color scheme, etc. I will be releasing little character bios that will explain the character more thouroughly.

Hope you enjoyed!

Character Bio: Aero

Character Bio: Aero

Name: Aero Dynamic
Race: Pegasus
Sex: Male
Coat: Mint green
Mane: White
Eye: Blue
Age: 17
Height: (did not answer) "Wouldn't you like to know?"
Weight: (did not answer) "Piss off!"
Cutie Mark: Horseshoes with wings

Ability: increased leg strength, heightened agility, abnormal jumping
Downside: Strong anger issues
Team Assignment: Offensive

Personal notes: from Fillydelphia, uses ability to "roof run" and perform parkour, works as amateur "messenger", energetic and haughty