Sonic: Chaos in Equestria

by Snicket

Chapter 1: Prologue

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The sky explodes in a fury of red and orange as a large red space ship soars through it. Sections of it bellow out fire and puffs of black smoke. The large space fighter descends over a plot of dense forest, clipping a large pillar of stone as it clears a path through the trees. It comes to a stop just yards away from a large ravine.

A red light flashes in a large, otherwise dark room, lighting the room every three seconds as an alarm sounds in the distance. A certain blue hedgehog lets out a groan as he stumbles to his feet and gives his head a quick shake. "Is everyone okay?" he asks as he looks around the room.

"OW!" another voice calls out from a few feet away. "I think that crash broke my everything," a familiar orange fox whines as he rubs his forehead and tries to use his other hand to push himself off the floor.

"Remind me not to let you plan the next vacation," a third voice says as a red echidna stumbles to his feet.

"Quit complaining!" a female voice shouts. "If Sonic hadn't done that, we all would be dead!" a pink hedgehog snaps as she jumps to her feet and retrieves a large hammer several feet away.

"Everybody be quiet!" Sonic snaps. "We're not out of the woods yet."

"Oh ho ho ho! How right you are, Sonic," a certain mad doctor's voice states over the ship's intercom.

"What do you want?" Tails demands. "We've already grounded your ship, and attacking us with anything else would only diminish your precious resources." Knuckles lets out an amused grunt. "Maybe the good doctor wants us to do a little renovation," he boasts, smashing his fists together.

"Fine by me!" Amy adds, resting the handle of the large hammer on her right shoulder.

"Give up now and we won't have to put you in a hurt locker!" Sonic states as he crosses his arms and smiles in his trademark fashion.

"How very amusing," the doctor states. "You four think you have the upper hand. Well, think again," Robotnik says as the room suddenly brightens, the sound of a light hum coming from a control module nearby.

"Thanks for turning the lights back on," Sonic begins. "But you still haven't answered Tails' question. What do you want?"

"Never one for semantics, were you Sonic?" the mad doctor states as a large monitor pops up, displaying Robotnik sitting in a large egg chair, surrounded by a large array of computers circling the chair in a ring formation, the only break being behind the chair. "Well then, let's cut to the chase. You have something I want."

The blue hedgehog lets out an amused laugh and crosses his arms behind his head. "I've been getting that a lot, but what could you possibly want from moi?" Sonic asks."You've already got all seven of the Chaos emeralds, what else could you possibly need?"

The doctor grins from behind his control panel. "Well, your life for one, but we'll get to that later. What I'm interested in is this!" Robotnik states as he smashes down a large red button with his fist. Suddenly, the alarms sound again as a series of clear tubes burst from the floor, three of which trapping the blue hedgehog's friends as he leaps out the way of a fourth one.

"Haha, impressive!" the doctor quips. "However, it changes nothing." The blue hedgehog runs to his trapped friends, who are beating on the clear tubes with their fists.

"We've done this song and dance before, Eggman," Sonic says solemnly. "Your beef is with me, let my friends go!"

Robotnik taps on the edge of his control panel with an unamused look. "My name is not 'Eggman'," the doctor states as he leaps from his chair. "It's DR. IVO ROBOTNIK! And you'd best remember that. But what makes you think your friends don't have a role to play in my plan?"

"Enlighten me," an unamused Sonic demands.

"Very well," the doctor replies as he adjusts his glasses. "Since you asked so nicely." Two more tubes rise from the floor, each containing another occupant. "Ever since our little clash on Angel Island some time back, I've been rather intrigued on how the Chaos emeralds surpassed their usual state and became super-charged with power from the master..." Robotnik's rant falls out deaf ears as the blue hedgehog has already run to inspect the new tubes. "HEY, I'M TALKING HERE!" the doctor shouts.

"Blah, blah, blah, emerald fetish, mommy never loved you. I've heard this before," Sonic replies as he steps towards one of the tubes.

"Not once have I ever mentioned my mother to you!" Robotnik shouts over the TV screen.

"But you never said she loved you either," Sonic adds as he wipes away the condensation away from one of the tubes and takes a step back. "What the hell? Eggman, what is this? Why is she here?"

The doctor drums his fingers atop the control panel bearing the same expression as before. "Robotnik, my name is Robotnik. Why can't you understand that?"

"Zip it!" Sonic shouts. "WHY IS CREAM IN THIS TUBE!?" the blue hedgehog demands before running to the other container and wiping away the fog away from it."WHY IS ROUGE HERE?!" Sonic expression fades as he scratches his chin. "Why IS Rouge here?"

Robotnik lets out a sinister laugh as the occupants inside the tubes begin to stir. Cream is the first one to open her eyes and look around at her new surroundings. "Mr. Sonic," she begins. "What is all this, why am I here?" Before the hedgehog can answer, Rouge awakens and begins to immediately bang her fists against the tube's casing.

"LET ME OUT OF THIS INFERNAL TUBE!" The white bat suddenly turns to the blue hedgehog. "Sonic! Thank heavens, get me out of here. I'll get you anything you want. You want jewels? I can get you jewels," the white bat continues. "Gold? I can get you all the gold you could ever want. I'll even give you my hand in marriage. JUST GET ME OUT OF THIS TUBE, I HATE BEING IN SMALL SPACES!"

"Hey!" the pink hedgehog shouts. "Sonic is mine, not yours, you stupid bat!"

"Not really the time, Amy," Tails adds frowning at the events unfolding in front of him.

"You never answered my question, Eggman," Sonic states as he glares at the computer screen."Why are Cream and Rouge here? Neither of these two poses any threat to you."

"HEY!" the white bat shouts as she smashes her fists on the walls of the tube.

The doctor removes his glasses and cleans them on his coat before answering. "Maybe so, but it's the influences they have that poses a threat. Your little rabbit friend over there may not be much on her own, but when she's able to call upon an army of chao (that you and I both know can be a formidable foe). I'd rather not be defeated by a bunch of squishy flying marshmallows."

"And Rouge?"

"Rouge is at most a minor threat, but given her alliance with a certain government group, she's become more than a tiny blip on my radar when I'm faced with a barrage of warships sitting on my door step. Also, her being here helped me procure this," the doctor states as he pushes another button, causing a larger flat steel box to rise out of the floor.

"What is..." Sonic begins, but trails off as the casing of the box slides back, revealing Shadow strapped unconscious to a strange device with a series of tubes and wires attached to his body.

"You see," Robotnik begins, "aside from her military pull and her ability to obtain any jewel, our little bat has captured the heart of a certain 'ultimate life form' here, making his capture mere child's play once we threatened to hurt his little girlfriend here."

Sonic turns towards a blushing Rouge, then to Knuckles, then back to Shadow. "Aw, we've got a love triangle here. Though with my sudden addition to it, it would make it a square now, wouldn't it?"

"Shut up, Sonic!" Knuckles shouts. "You have so many facets to your ever-growing harem that it might as well be a circle."

Everyone gives the echidna a bewildered look at his sudden outburst except for Robotnik, who begins to snicker behind a closed fist. "Aw, the miracle of cross species relationships…" The doctor’s face turns serious. "It sickens me."

"Says the man with mommy issues," Sonic jests, giving the doctor a smirk. Robotnik snarls furiously at the hedgehog.

"Enough!" Robotnik shouts as he slams his fists on the control panel. "I've gathered you all here for one reason. Though you may all be a threat to me and my plan to rules his merger planet, you all have something in common that is of use to me." A crude sketch of Sonic appears on a smaller window on the screen, many graphs and figures surrounding it.

"You see, whether you knew it or not, you all have had contact with this blasted hedgehog in one way or another-" a few other crude sketches of the others appear on screen "-resulting in each of you absorbing some Chaos energy. Three of you-" the sketches of Shadow, Tails, and Knuckles change color "-have even been able to obtain super forms of your own."

"Then why is Shadow strapped to that machine and not stuck inside a tube like the rest of us?" Tails asks the doctor, who grins cheerfully behind the computer screen.

"Glad you asked. You see, despite being able to drain the energy from you pests at the drop of a hat, I've never been able to distill it, purify it, use it for my own purposes. Until now." Robotnik points to Shadow. "Thanks to his extensive genetic engineering, he makes the perfect vessel to store all of this raw Chaos energy."

"But why!?" Tails demands. "Why are you doing all this? Is it just to super charge the Chaos emeralds?"

"It makes no sense," Knuckles adds.

The doctor's smug expression fades as he raises an eyebrow to the orange fox. "I've grown tired of trying to explain this to you lesser creatures. You will see soon enough," Robotnik states as he presses another button on his keyboard.

Suddenly, the five tubes begin to sink into floor as their occupants begin to thrash about.

"Get me out of here!" Knuckles shouts.

"Sonic, help me!" Amy pleads as she strikes her tube with her hammer

"Not like this, not like this!" Tails adds, pacing inside the small tube.

"LET ME OUT! LET ME OUT! LET ME OUT!" Rouge shouts as she sinks into the floor.

Cream just lets out a high-pitched scream.

Sonic runs to each of the tubes, trying frantically to free his friends from their cylindrical prisons, only to watch in horror as they vanish into the floor, silence taking over the room.

"EGGMAN!" Sonic shouts as he turns to the computer screen.

The mad doctor stares longingly into a red chaos emerald before acknowledging the hedgehog's cry. "Magnificent aren't they? So beautiful, yet so deadly."

"LET THEM GO!" Sonic demands as he snarls at the doctor.

"In due time, Sonic. In due time." Six smaller images of the doctor's prisoners appear on the screen, replacing the crude sketches and graphs, each of Sonic's friends frantically looking about as a heart monitor beeps from under each image. Robotnik places the red gem into a large case with the others in front of him and places his hand over a blue lever. "Now, on to phase two," he says as he grabs the lever and pulls it down.

Suddenly the images begin to scream out in agony as they're shocked with some sort of strange energy. Even Shadow's eyes burst open as he's forced to hold all this new energy.

"STOP IT, DAMN IT, STOP IT, EGGMAN!" Sonic demands.

"Sorry, can't hear you, over the sound of my plan coming together."


The six images go limp as the heart monitors flat line, filling the quiet room with a long, high-pitched beeeeeeeeeeeeep.

The doctor giggles madly. "Oops. Looks like I killed them. Thought they'd hold out a little longer than that."

Sonic stares blankly at the images of his six dead friends on the screen.

"Oh well," Robotnik muses as he holds his hands up into the air. "I guess I'll just have to do this the hard way," he adds as he pushes another button, causing the six images to disappear from the screen and the steel case to slide into the floor. "They're genetic material will be more than sufficient."

The blue hedgehog balls his fists in rage as he glares at the image of the Doctor before him. "What's this?" Robotnik asks in a mock-worried tone. "Did I hurt your little friends?"

Sonic punches the computer screen, causing it to crack and splinter as the image flickers for a brief moment. "You're dead!"

"Come and get me," the doctor teases.

The blue hedgehog bursts from the room in an explosion of speed and power, charging through the airship at breakneck speed, destroying everything in his pursuit of the doctor. Steel doors burst from there hinges, defense cannons snap from there mounts, and security camera explode as Sonic tears apart the airship, finally arriving at the top of the downed cruiser. Flames destroy the forest around him as the ship smolders in the newly-made trench it's sitting in.

Robotnik frantically zips around the ship’s exterior in his egg mobile, unaware of the hedgehog's arrival. "Fly you infernal machine, fly!" the doctor demands as he solders an exposed wire.

Sonic opens his mouth to announce his arrival, only to clench his jaw in pain as he hold his hand over a fresh wound on the side of his stomach. Fresh blood runs down his side.

"You bastard! What have you done?!" he snarls at the figure before him.

"I did what had to be done, Sonic," the doctor replies from behind a thick veil of smoke.

"You monster."

The doctor smirks. "That's debatable," he states, pressing a button in his mobile that causes the ship's engines to fire up. "Well it's been real, and it's been fun, but it hasn't been real fun," he adds as the ship start to take off, causing the hedgehog to stumble backwards.

Robotnik lets out an evil laugh as he flips opens a hatch and enters the now functional ship. "Good bye, Sonic the hedgehog."

Large thrusters on the side of the ship flip downward and begin to scorch the already charred earth as the craft begins to lift from the ground. The blue hedgehog clings for dear life to the rear of the ship as it starts to gain altitude and thrust forward.

Inside the ship, the mad doctor leaps out of his egg mobile as he reaches a long corridor and enters a large room as a metal door slides upward.

"This wasn't part of the plan," Robotnik states as he frantically starts pressing numerous buttons. "I have to divert all non-critical power to thrusters to get this tub back to base," he adds as he presses another button, causing a small podium to rise from the floor, holding a large case containing the 7 Chaos emeralds, now with a dark aura around them. "Darn it, I was close. If those pathetic creatures hadn't died then I'd-"

"Those 'pathetic creatures' were my friends," a voice says from behind the doctor, causing him to tense up and slowly turn around.

"S-Sonic, glad you could make it. Great to see you," Robotnik says coyly as he starts to inch towards a console.

"Skip it, I know what you're planning."

Robotnik lets out an amused chuckle as he eyes a green button in the console marked with a lightning bolt over it. "Do you, Sonic?" he asks as he takes a large step towards his target...

"You're planning on recreating the super emeralds, but what I don't understand is why." Sonic states as he watches the Doctor hover over the counsel.

"And that's why you'll never achieve greatness, because your feeble mind will..." Robotnik trails off as he smashed his fist down on the button, causing a large laser to drop down from the ceiling and fire in the hedgehog's direction, only to strike the pedestal holding the emeralds, causing the case to begin to crack.

The Doctor stares in bewilderment at the fact that he missed, only to turn to his right and see Sonic, who instantly grabs his arm and begins to twist it.

"W-what are you doing?" Robotnik demands as his arm start to bend in an unnatural direction.

The hedgehog gives the arm one final twist, letting out a loud snap, causing the doctor to collapse to his knees and grab his broken arm. "Taking away you're tools of destruction."

Robotnik lets out an amused chuckle as he sways to his feet, still gripping his broken arm. "You've progressed nicely. Too bad it took the death of your-"

"Did I say you could stand up?" Sonic asks quietly as he kicks the Doctor in the knee, resulting in it snapping in the wrong direction. The mad doctor winces in pain as he falls to the ground again.

"Muahahaha!" Robotnik breaks into a fit of insane laugher. "Yes, keep at it! Let the hate consume you. Relish in the feeling, because you will be feeling it for a long-"

Sonic grabs the doctor by the collar of his jacket and jerks him up to eye level. "Did I say you could talk?" He asks, to which Robotnik shakes his head.

The black-tinted emeralds on the pedestal begin to vibrate, cracking the already damaged case.

The blue hedgehog releases his grip on the doctor and lets him hit the ground with a hard thud, then holds his right shoe over his gut. "Give me one reason. Give me one damn reason why I shouldn't kill you right now."

Robotnik smirks. "Because I'm all you have left. Everyone you ever cared about is dead. You're all alone without me."

Sonic removes his foot from the doctor's stomach and takes a step back. "That's all you got?" the hedgehog asks. "THAT'S ALL YOU HAVE TO SAY?"

An explosion erupts from behind the hedgehog as the case containing the emeralds shatters and frees the gems, which encircle the now infuriated Sonic.

"You set up a coup to overthrow our king-" Sonic's voice starts to change "-nearly conquering this world-" the hedgehog's teeth grow jagged "-destroyed my home-" his blue quills start to bend and turn yellow "-and now, YOU'VE KILLED MY FRIENDS-" Sonic's once emerald green eyes turn red and distort into small spirals "-ALL JUST SO YOU CAN POWER UP AN ALMOST INFINITE POWER SOURCE?" Electricity crackles around the now deranged hedgehog as spikes of yellow light pulsate from the body of the once blue hero.

"You have to understand, Sonic," Robotnik pleads as he inches towards the wall behind him. "I was only acting with the people of Mobius's best interests in mind," he adds as he slides his left hand along the wall and stops as it reaches a small lever.

The Chaotic energy encasing the hedgehog becomes amplified tenfold as computer monitors and windows shatter with the raw energy of the emeralds. "THEIR BEST INTERESTS?" Sonic questions as his mouth twists into a jagged scowl. "YOU ONLY ACTED IN YOUR OWN BEST INTRESTS."

Clenching the lever in his left hand, Robotnik smirks at the super-charged hedgehog's claims. "You know me all too well, Sonic," he states as he gives the lever a jerk and disappears as a chunk of the floor slides away, revealing an escape tunnel.

Sliding down the long dark "path to freedom", the mad doctor manages to smack either his injured leg or arm on every bend in the tunnel, finally landing in a waiting egg mobile at the bottom of it. Wiping a bead of sweat from his brow, the doctor starts to frantically press buttons on the craft's small control panel with his one good hand.

However, the doctor’s relief is smashed as an explosion erupts from overhead. Fire and sparks shoot from the tunnels exit. The now fully deranged hedgehog bursting from the flames unscathed as he begins smashing the egg mobile, sending the doctor tumbling out across the steel floor.

"Where do you think you're going?" the yellow hedgehog asks. "I didn't say you could leave."

Sliding away from his sudden entrance, Robotnik looks on in horror at the creature he created before him, only to be picked up by a single gloved hand and slammed into a steel bulkhead several feet away. "Don't do this, Sonic," the doctor desperately pleads. "This isn't you."

The hedgehog's expression twists into a sinister sneer. "You're correct… this is not like 'Sonic' in the least. Maybe that's because... I'm not Sonic."

The doctor's eyes widen.

"You said it yourself: Sonic has nothing left. Everyone Sonic ever cared for is dead."

The hedgehog raises his gloved hand as a set of long claws burst from the glove's fingertips. "What's one more life to the millions you've taken already?"

Robotnik frantically scans the room for anything to stop the super-charged hedgehog. Spotting a red blinking light with a symbol of a skull and cross bones over it, he shouts, "Lethargy Lazar, fire!"

A large cannon emerges from one of the bay doors and fires at the unsuspecting hedgehog, causing him to lose his grip on the doctor. The doctor plummets down, striking the steel floor with a dead thud. Robotnik stares, awestruck as a portal starts to close from where deranged hedgehog flew. The doctor lets out an amused laugh, only to wince in pain and immediately start coughing, spitting up a large portion of blood.

"I win!" the doctor states as he continues to glance in the direction of where the portal once appeared. His breathing starts to get shallow.

In a land unknown, a rift opens and a yellow hedgehog flies through it, tumbling and turning he smashes into a heavily wooded forests and across a large field, finally coming to rest as he strikes a small wooded building, causing its feathered occupants to frantically flee from the sudden arrival.

Author's Notes:

The start of my current running MLP x Sonic series.

All characters belong to there respective owners, let me know what you think in the comment section below.

Next Chapter: All Quiet on the Western Front Estimated time remaining: 11 Hours, 16 Minutes
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