Sonic groaned as he was flung into the wall again, and again. Damnit, Shadow got a Speed Boost.
Amy helped him up, and he grinned. Shadow's never fought the two of them together before, and it's just his usual attacks right now...
They might have a fighting chance!

And then both the Mare and Shadow vanished. Dangit.

Twilight heard many gasps when Shadow, it had to be Shadow, showed up. It looked like a hedgehog, but with Silver highlights like that emerald Nightmare Moon was holding.
"What are those things!?" someone shrieked.
"Aliens!" someone shouted.
"Monsters!" another screamed. "We're all going to die!"

Applejack and Pinkie Pie were staring in shock, while Rarity, Rainbow and Twi were all normal about this. They had met Sonic and Amy earlier, a third wasn't that strange. Fluttershy was hiding under a table.

She meekly poked her head out, and gasped as Sonic and the... Black Hedgehog clashed.

And then Nightmare Moon and Shadow? Was that Shadow? Possibly. Odd colouring, but it did seem... Powerful. And what was that gem Nightmare was holding? Anyway, they were both gone.

Gone with a poof of smoke, and little trail. Sonic tsked, and kicked the ground. "Dangit. Gone with the Emerald."

"Emerald..." Applejack muttered. "What'in the... What are you!?" she demanded. "Why do ya look so weird?"
"I'm Sonic. Sonic the Hedgehog," Sonic said, the biggest claw on his hand pointed at himself with a cocky grin. "Fastest thing alive."
"I'm Amy Rose. His, uh... Is Soulmate a bit too corny?" Amy giggled, landing next to him.
"Nah, not if it's true~" Sonic teased.

Everyone blinked. And agreed to ignore that. "So, uh... I'm just gonna... Go," Twi said, before dashing out the door.

In the Everfree, Sonic and Amy were moving around, slowly. Slowly, and to the point the others, who haven't even known the two for long, looked worried.

"So, uh... Sugar-cubes. Ya seem... Ancier than a worm in a bird shop." AJ said with a timid look. "And uh... Yer sparkin'?"

Sonic and Amy both sighed, and Sonic rolled his shoulder. "Sorry, Applejack. It's just... We're used to moving fast, but we're slowing down so we'll keep pace with ya. But, my Quills are acting up, and Amy's Tarot is saying' something's coming," he said, and fiddled with a small charm around his neck. "So, we're prepared..."

"Right." Fluttershy nodded. "Be careful." She gave a whimper at a twig snap. "And brave. You'll... You'll help protect us, right?"
Sonic nodded, but then looked around, as something rushed past him with a burst of rainbow colours. He growled. "Amy, watch over them!" He shouted, before rushing after the damn robot.

He caught up in seconds, and Chaos laughed. "Hello~" The Robot sang, before kicking Sonic into a tree, and punched him twice in the chest. Sonic coughed, as he swept the legs of the robot, kicked the chin up, and saw a few sparks of lightning.

"Oh~ Fiesty aren't we~" Chaos sang, before digging his claws into Sonic's arm, and raked them down. Sonic cried out in pain, but punched the eye of the synthetic life-form that he was fighting.

"Damn. You," Sonic growled, before punching twice and headbutting it, before kicking twice, and then Spin-Dashing it into the air, and then using his Homing-Attack.

He groaned, as Chaos spun around with its annoying laugh, and just punched Sonic twice in the face, before kicking him into another tree.
"Ow..." Sonic hissed, before dodging a lethal blow. "Damnit..." he muttered, missing his speed boost the Parado-
SThen he grinned. With malice.

"Oh... Oh I don't like that smile," Chaos said, backing away a little.
"You're powered by a new Paradox Crystal, aren't you~?" Sonic sang.
Chaos took a step back. and another. And then crashed to the floor, with Sonic standing on him. "Time for a power boost!" He laughed, and slammed his hand onto the chest of Chaos.

And absorbed.

Amy winced, hearing a yell of pain, a mix of Sonic... And something not living.
"What in the hay was that?" Applejack asked.
"Something... Sonic is dealing with," Amy said gently. "Come on, let's keep going!" she said, as they had just dealt with that river... Spirit? Dragon? Monster? Whatever it was.

Sonic grinned, as Chaos stared at him, the lights dimming. "Mon- Mons- Monst-" It powered off.
Sonic took it into his arms, and started to run. And run. And run. And Run.

And then he found himself in New York, near Nine's lab. He dumped Chaos on the street, and rushed to Nine. He’d got his power back, and he'd be needing those Regulators.

Amy gasped as they got to the castle. She hadn't needed to do much, but the fact that Sonic was standing there, looking... Calm.

"Hey," he said, waving. "Got an upgrade, and got to punch something. I'm good for now." He grinned.
"That's good," Amy nodded. "Ready for... This." She and Sonic turned to the Ponies. The two, the youngest of the group. Hell, they might be at least four years younger, at least.

And they were the ones ready for this. They were used to this. Sonic and Amy had fought gods and monsters that could destroy reality... A simple pony that got her hands on a Chaos Emerald? That's normal. But... A Shadow without even the slightest hint of a Moral? Without the memory or being able to act with the memory of Maria?
That worried the two hedgehogs. More so than Eggman ever could.

"So, uh... We kinda missed it, but who's this Mare in the Moon?" Sonic asked, as the two had been distracted by Spike's mumbling in his sleep, and then had been distracted by how motherly Twi was with him.

"You're worse than me," Rainbow muttered after a beat. "Evil Mare. Went crazy. Tried to kill Princess Celestia. Has just kidnapped Celestia. Has a weird Magic Gem. You called it an Emerald. Weird dark version of you. Magic like we've never seen," Rainbow rattled off.
"You did listen!" Fluttershy said, her wings and tail fluttering in a happy and loving way, her voice excited. Before she blushed, and curled into herself a little.

"Ignoring the happy couple..." Sonic drawled. "Thanks for the recap. Just uh... Why is she kinda lookin' like Twi?" Sonic asked, confused. Everyone blinked, before looking at Twilight, and seeming to think about how Nightmare Moon looked.

"Uh... You uh... You have a point..." Rarity said meekly. "But... Little detail there darling... No stars."

"Twi's covered in stars. From her coat to her mane," Sonic said, with a slight odd look at everyone, then sighed, and rubbed his eyes. "Dang it. Ok, uh... Amy, can you see it?"
"No."
"Use your Tarot Sight."
"Holy-" Amy gasped. "Now I can."

Everyone blinked. What? Sonic just shook his head. "Never mind. Come on, let's... Let's go fight a goddess." Fluttershy gave an eep, but Rainbow nuzzled her gently, calming her enough that she could walk in, with Rainbow beside her.

Sonic sighed, as he dodged a high speed punch from Shadow.
"Keep going," he ordered, his hand outstretched. He looked at Amy. "You too, Rose." Amy shook her head, balling her fists.
"No," she hissed. "I'm not running."

The Ponies looked worried, and took a step back, while Rainbow Dash took to the air, and both Rarity and Twilight lit up their horns. "Neither are we!" Rainbow Dash declared, and even Fluttershy nodded.

Sonic grinned, and rubbed his nose, turning towards the black and silver Vassel. "Then let's get to it!"

Sonic dodged another punch, as Amy delivered a kick to Shadow's back. As Shadow started to Spin-Dash, Rainbow kicked him into a wall.
As Shadow went after Rainbow, Sonic pulled on the leg, and slammed him to the ground.

As Shadow was prepared to blast with all his power, both Rarity and Twilight sent him flying, allowing Sonic to Spin-Dash into him.

And then Sonic felt something... Brew. His gloves and shoes went from high-tech to a simple white and bright light blue blueprint design.
He grasped a crystal, one of the Prismatic Shards, that came from the Paradox Crystal. The Yellow. Applejack walked next to him. too close.

In a flash of Yellow, the two found themselves on a certain Hill, with a Certain Loop-De-Loop.

"Where in the Hay are we!?" Applejack shouted, as she looked around the sprawling green hills, and checker patterned dirt.
"Green Hill...?" Sonic muttered. "But... This is Shadow's..." He was about to dash, but then paused, looking at his gloves.

Applejack noted they weren't those nice looking techy ones, with white parts covering the main parts of the shoes, giving them a contained and shielded look, glowing light blue parts, made them seem like something from the future you'd read in a comic. The gloves, keeping the simple white, had a nice grey covering, with little lights at the knuckles, and seemed like they could punch something without much trouble.

Now, they were a simple cloth, and seemed... Classic. There wasn't a single grey part, and it seemed that shadows didn't hit the glove. His shoes lost the grey part on the underside. It... looked like a memory.

"Well, uh... Your'a lookin'... Nice?" she tried. Sonic shrugged, and tapped his shoe onto the ground.
"Eh. It's pretty classic." He grinned, like it was a pun. "But that's not the point... Why this place?"
"Huh?"
"Well, I'd assume maybe me, Amy or Tails having this as our Memory Scape. But Shadow? Shadow was born on The Arc, long story. So... Why here?" he hummed.
Applejack was so confused, but decided to roll with it for now. Then paused. "Uh..." She pointed at... Another Sonic. With the gloves and shoes from before. Not the Future ones. But his Original ones.

"Hey, Shadow~!" The ghostly Sonic said, his voice slightly warbly. "Wanna race?"
Then another. "Yo, Shads! Wanna practise with the Emeralds?"
"Wanna race?"
"Wanna go to a movie?"
"Hey pal! Twitter Takeover time!"
"Hey, Vanilla's making dinner, wanna come?"
"Yo~ Shads! Got-" Sonic shivered.

"Ok, that's... Creepy," she admitted. "What is this?"
"Ghost Hill," Sonic said. "Not Green Hill," he said, and kicked a Checker Patterned bit of dirt. "Scat." He growled, and punched a random rock, and an Emerald popped out. It looked like a Green Version of the one Nightmare Moon had.

"What the..."
"Chaos Emerald," Sonic explained. "The memory of one at least," he said, grabbing it. "Lead us," he ordered, letting it float. He gestured for Applejack to follow, and she nodded.

"So uh... Ghost Hill? Green Hill? Your home is... Nice," she said again, looking around and then pausing. "Wait, is tha-"
"Ignore that... Please," Sonic said, turning away from Amy, who just repeated something about forests, over and over. "It's... Something I'm ashamed of."

Applejack lowered herself, as a bunch of... Weird metal things flared in, in bursts of prismatic light. "Badnik!" Sonic growled, and dashed towards them, smashing them in seconds, and grabbing the Chaos Emerald, as it's called, before a strange device could. "BACK OFF!" He yelled, as a bunch of Sonic appeared, cloaked in blue lightning, and smashed the rest in a second.

"Holy..." She breathed. "Ain't you jus' a lil' powerhouse?"
"Heh." Sonic rubbed his nose, "come on, Shadow's this way," Sonic said, pointing at a large barn looking thing with a giant metal contraption outside it.

"What... What in tarnation is this?" Applejack asked.
"The Tornado. It's a plane. Uh, a plane is-"
"I know what a plane is," Applejack said, breathless. "Bu' not one like this!" She looked all around this, and at the giant two fox tails near the end... "Tails."
"Hmm?" Sonic hummed.
"You mentioned someone called Tails before... Is this... Their plane?" she asked.
"Mhm." Sonic grinned in a proud way. Like Applejack herself with Applebloom. "Little guy's got a good head on his shoulders, and smart as a textbook. But he's not so good with street smarts."

Applejack smiled. "He sounds great," she admitted. "So uh... Why would..."
"Because out of all the places? This place is the only one with damage," Sonic said, pointing at the damaged ground.

Applejack entered with Sonic, holding herself low. Heck, she thought she was strong, but... Those three fighting? It was almost... Monstrous.

Shadow glared at Sonic. "Another, huh? What are you going to say? Hmm?"
"How about, nice ta see ya, old pal?" Sonic grinned. Shadow stared at Sonic in shock, before noticing Applejack. "We're going to help ya."
"I don't need help. Especially from a pony, and never from YOU!" Shadow shouted, before punching Sonic directly in the face, and sending the younger one flying, as Applejack galloped after him.

Applejack gently nudged Sonic, who got up, looking... For once, beat up. He took a beating before, but he didn't look damaged then. "Sonic..." she said, worried.
"He's a friend."
"He hurt you. Friends don' do that!" she growled out.

"He's hurting," Sonic said. "I know what that's like."
"SO!? That doesn't mean-"
"I can take it," Sonic admitted. "I can take it. Shadow... He's had a rough life. He's... He's not... He wasn't born, like you or me. Not in the normal use of the word." Applejack stilled.
"Wha-"
"He was made in a lab, to help a dying girl. To be her cure," Applejack gave a gasp. "And... She died. Not from the disease. But, from... Another living being," Sonic said, balling his fists tight. "She was killed... For little reason. And Shadow was placed into Stasis, for... Fiftyish years? Maybe? probably more like thirty, but..."

"My goddess..." Applejack breathed. "He's..."
"And when he woke up, it wasn't peaceful. He learned that his friend had died. That everyone on our planet, just forgot the person that meant the most to him. That his home was covered in dust. And... Then he saw me," Sonic laughed bitterly.

"Ya do look a bit alike, bu' not that much..."
"He thought I was made after him. That I was, "The new and Improved", like I was Project Sonic, to his Project Shadow," Sonic explained. Applejack flinched.
"Ah. Replacement." Sonic shook his head, meaning it wasn't the case, but was the thought process. "... We need to calm him down... Any idea?"
"Nope." Sonic shook his head, but grinned. "But I've done it before, what's stopping me now?"
"Nothin'," Applejack agreed, grinning. "After all', ya ain't friends, ya ain't clones, ya family," she stated, and felt good, as Sonic grinned right back.
"That's a fact," he grinned, and the two took off running.

Sonic gasped as he lost the yellow crystal, and his gloves returned to the New York design. He took a step back, as the Silver burst off Shadow, revealing not the usual red, but a bright Orange, making Sonic smile.
"Welcome back, Shads." He said, extending a hand, and Shadow took it, with a scowl. But it was softer than normal.

"Where are we, Sonic?" he growled out, and Amy sighed.
"Of course, straight to the action. Come on, we've got a Nightmare to fight." Shadow tilted his head, but grinned. As did Sonic, and then Amy did as well.
"Ready~" the three said in unison.

They took off running, with the others following behind, the three fastest things alive, keeping to a slow pace.

As they entered the room, they saw the Mare destroy some rocks, and glance back. "You're too late! I have destroyed the Elements of Harmony! This... Chaos, Emerald! Yes, this Emerald is more powerful than any of those Phooey Elements!" she declared.

Sonic grinned, as he rushed around the room, jumping towards the Emerald, before getting smacked down by a rock golem that was destroyed by a good buck from Applejack. "On yer feet!"
Pinkie distracted another, with her confetti cannon, which... Ok. Fluttershy dived out of the way of one attacking her, letting Rainbow Dash wreck it with a good high speed kick.

"How is this possible!?" Nightmare shrieked. She looked very, very scared and confused. Then she looked at Twilight. "Ah. So she reproduced. Of course she did. Good that you took after my colours and powers." She declared, and grabbed Twilight in her magic. "Come here, my little niece."

"I'M NOT YOUR NIECE YOU CRAZY PSYCHO!" Twilight shouted, before she vanished, appearing behind the mare, with her coat now pure white, and her mane being a raging fire. "I AM TWILIGHT SPARKLE, AND YOU'RE ABOUT TO GET A BIG Ol' CAN OF WHOOP FLANK!" she shouted, before bucking the mare in the chin.

Sonic grabbed the Emerald that fell from the Magic grip, and... It felt WRONG to him. It wasn't his Emerald. It wasn't anyone's. It was mainly to increase the power of the one going Super. That's why anyone could use it, and it was often the last one to be found.

"So uh..." Sonic gestured to Twilight's new form. "This normal, or..."
"It's normal," Twilight nodded. Sonic grinned, and nodded.
"Good to know. Hey, kiddo." He bent down, and whispered something in her ear.

After the giant beam of Rainbow Light, he's pretty sure Skittles would try and sue over if they both, A) Existed in Equestria, or B) Sonic actually cared about copyright, there was a teenage pony with both wings and a horn, and looked... Kinda cute?

She was mainly a dark blue, like Sonic's Werehog form, with a light starry blue mane. Her little mark was that of a giant splotch of black, with a Crescent Moon in the center.

"She's... So young," Amy whispered, looking at her. Shadow gave a hum of agreement. Sonic felt something coming from Teleportation, in a different room. Judging from Twilight's ears perking up, she knew the giant pony.

"What the..." The young pony looked around, before her eyes landed on Twilight. "My sister reproduced?" She asked with shock. "When? How? Who?" Twilight blinked, her coat and mane returning to normal. "... What in our mother's power? Why do you look like you could be my daughter?"

"STOP SAYING THAT!" Twilight yelled. "I have a mother! And she isn't-"
"Isn't me," Celestia said, calmly walking in. "Twilight is just a student I took in, Luna."
"But sister, her coat and mane!"
"I know," Celestia sighed. "She gained them with her Cutie Mark. But no one but us can see it."

"The butt tattoo?" Sonic asked, causing both Amy and Shadow to do a spit take at the blunt way it was asked. "I was wondering about those things."
"Ha!" Fluttershy giggled at Rainbow's loud outburst.
"I did say that when we were younger, didn't I?" Fluttershy giggled.

"... Mobians? Here?" The teenage Alicorn asked. "Did you use the portal? No... You would have become a pony otherwise... How?"
"Ch-" Shadow was cut off by Sonic's hand.
"Accident with some teleportation magic, you know how it is."
"Mhm." The mare who raised the moon nodded. "I do quite know that. I am Luna. Luna of the royal Alicorns."
"Sonic The Hedgehog. I may or may not have a middle name. No one really knows." He grinned.

"Amy Rose. Also a hedgehog," Amy said simply. "It's lovely to meet you, Princess."
"Shadow the Hedgehog."
"Edgehog," Sonic coughed.
"Shut up," Shadow growled.
"Skates."
"Their Air Shoes!"
"Skates. I know skates when I see them."
"Ok, that's it!" Shadow rushed at Sonic, who grinned, and was suddenly on the other side of the room, with an after image in his place. "... I hate you."

"I... Perhaps we have some catching up to do," Luna muttered, watching the interaction. "I was not aware that hedgehogs could be that fast?"
"No, Sonic's weird like that." Amy said. "I'm also fast, but... I usually use my pi- my weapon, or my strength," she explained. "And it slows me down."
"I need my Air Shoes to go fast," Shadow muttered. "Sonic's weird."

"I'm uh... Twilight Sparkle. I'm not related to M- Princess Celestia." Sonic snorted. Great save there kiddo. "My mother is Twilight Velvet and my father is Night Light. And my brother is Shining Armour. Not that I'm sure I can call him a brother, or them family anymore..." she finished muttering.

Celestia gave her a gentle nudge, and nuzzled her gently, before placing a wing around her. "Little Star..." Sonic raised an eyebrow at Twilight.

"Not your mother my flank," Luna muttered. "To ignore that, who are the rest of you?"
"Ahm Applejack," AJ said simply.
"I am Rarity, your highness." Rarity said, with a bow.
"I'm Pinkie Pie!" Pinkie bounced around.
"I'm... I'm... I'm Fluttershy..." Fluttershy said meekly.

"I'm Rainbow Dash," Rainbow said, flapping her wings slightly. Sonic tapped his foot. The two looked at each other. "Race?"
"Sure. I'm Game," Sonic shrugged. "See y'all in a minute." And the two took off from the window, and then came back.
"WHO WON!?" They asked excitedly.
"... Tie," Amy said. "Just a tie."

"..." Both looked at each other, and nodded in respect.
"I-" Luna shook her head. "I wish to go home, and sleep, if you would be so kind sister?"
"Of course, little moon," Celestia said gently. "Twilight, I must get Luna settled in, may one of your new friends offer you a place to stay, and I shall be back tomorrow?" she asked, looking around.

"Homeless," Sonic, Amy and Shadow said together, holding up a hand.
"Ah uh... I could take ‘er?" Applejack shrugged. "We do have a bi' o' room at the farm. You three are also welcome!"
"Thanks, AJ, but I'll stay in the library," Twilight said, smiling.
"We'll take you up on that offer, thanks, AJ," Sonic said with a smile.

Celestia and Luna smiled, seeing all the friends getting along. Then Luna turned to Celestia. "I still think she's yours."
"She is, just... not by birth," Celestia said, before the two flashed out in a flare of magic.

Author's Note

Facts:
Amy and Sonic have a special sight. Amy has Tarot Sight, which is how she's able to choose Tarot cards. Sonic's a bit different, but it's how I headcanon he's able to do his Homing-Attack.

The Ghosts in Ghost Hill, don't look different to the Characters in canon, they only look like that to us.

Applejack's whole thing of, "I'm the Honesty one", kinda sucked. Here's a new one.