Author's Note

Greetings Gotham, Joker here! Welcome to my Mewtwo in Equestria story! Now, before we get started, I just want to say that THIS IS NOT A DISPLACED STORY IN ANY WAY, SHAPE, OR FORM. The Mewtwo depicted in this work is indeed the real Mewtwo. In any case, I think that about wraps up everything I was going to say. Let us begin!

Chapter 1: A Second Chance

Floating… floating in the blackness… that was all there was to do. That was all he COULD do, even with all his power… he was the brainchild of some of the greatest minds of a generation, whose sole purpose had been to create the world’s most powerful Pokemon.

And they succeeded with flying colors.

But, it seemed not even he, the great Mewtwo, the “son” of Mew, was powerful enough to live forever. Strong enough to manipulate the weather itself in an attempt wipe out all of humanity and Pokemon and replace them with genetically enhanced clones, yes. But powerful enough to cheat death? Apparently not.

The purple and white cat-humanoid Pokemon let out a sigh. Perhaps he’d been hoping to be reunited with Amber. She was the friend he lost so long ago, who he’d been created to try to save, and failed. After all, he was created in a test tube with spliced Mew and human DNA, and had never truly known a mother’s love. Or any love for that matter. All he knew was fear. Fear of his psychic powers. Powers that Giovanni, leader of Team Rocket had wanted to use to bring the world to its knees, all while feeding him lies that they were equal partners.

Mewtwo scoffed. Team Rocket. Teams Magma and Aqua.Team Galactic. Team Plasma. Team Flare. The Aether Foundation. Everywhere he went to try to find some peace and solitude, there always seemed to be some group of power-hungry fools out there trying to seize control of the world or mess with things that shouldn’t be messed with, and he’d been forced to keep moving, even when he thought he found somewhere safe to live in solitude.

Guess it’s true what they say, thought Mewtwo bitterly. Everybody wants to rule the world. Although, I have to admit, that Team Skull had style… unlike those… children.

A small spike of anger and humiliation surge through him at the thought. On three separate occasions, he’d found himself imprisoned inside that accursed Master Ball. But, what those children failed to realize was that he would not bow. So, he played ultimate weapon for them and bided his time. Then, when he had the chance, he purged the memories of his capture from all three of them, as well as their Pokemon. As far as he was concerned, his encounters and subsequent servitude to Red, Gold, and Calem had never happened.Although, truth be told, he’d envied the bond and friendship that they shared with their other Pokemon. Sometimes, he’d wished he had someone to truly call his friend...

Suddenly, a bright flash of light lit up the blackness of Mewtwo’s world. Once the light faded, what was unmistakably another so-called “Legendary” Pokemon floated before him. It somewhat resembled a Furfrou, but was clearly bigger, sleeker, and more powerful. On top of that, it had what seemed to be a yellow ring around its waist.

Mewtwo recognized this entity immediately. The one Pokemon who could possibly be even stronger than he was. Revered by humans and Pokemon alike as God, and creator of their world. “Arceus,” said Mewtwo, in a somewhat formal way.

“Hello, Mewtwo,” said Arceus. “I trust you realize that the Cycle of Life, Death, and Rebirth has begun.”

“What are you talking about?”

“You were not the only one who had their life force drained out of them. Yveltal was on death’s door. I created it with, shall we say, a protocol, that when it dies, it absorbs the life force of all life on the planet to sustain itself before entering its cocoon once more, only to emerge when the time has come for all things to die once more,” explained Arceus. “Now that Yveltal sleeps once more, it is time for the process of Renewal and Rebirth.”

“Starting with you.”

A second figure emerged from the darkness. It seemed to be a green and black humanoid creature of some kind. Every bit of its body seemed to be moving, shifting constantly.

“And you are?” asked Mewtwo.

“We are Zygarde, the Order Pokemon. We maintain the balance between life and death, dark and light. We resurrect what Yveltal has destroyed, and pave the way for Xerneas to create new life,” explained Zygarde.

“You see, Mewtwo, I have seen your thoughts, wishes, hopes, and desires. You crave to know true friendship. You want to know what it’s like to love and be loved back rather than feared. To be admired rather than hated. To be an equal rather than a slave, pawn, or weapon. In short, you want to be a hero rather than a villain. Zygarde and I intend to give that to you. Wipe the slate clean and start over in a new world. In a new form,” said Arceus.

“A new world? A new… form?” asked Mewtwo, confused.

“Yes. My creation is now a barren and lifeless wasteland, and will remain that way for many centuries. And even if it wasn’t, being a genetically engineered super-clone, the molecules of your original body became unstable. What was left after Yveltal’s purge has since degraded into dust,” explained Arceus. “Moreover, there is a catch to your clean slate.”

“And this catch is?” asked Mewtwo.

“I take it you’ve wiped the memories of those Trainers who’ve captured you? Well, now it will be your memories that are wiped. You will have no recollection of past events. You will, however, maintain knowledge of your name, mastery of your powers, and your talent for the sciences. Otherwise your past will be a complete and utter blank.”

“I see…” said Mewtwo thoughtfully. “Very well then. I will make the best of this… opportunity.”

“Good,” said Arceus, before turning to Zygarde. “Shall we?”

“Yes… we shall,” replied Zygarde.

The two legendary Pokemon began to focus their energies and chant in a language unknown to Mewtwo, before firing a combined blast that caused him to lose consciousness.

…

A group of five pony-human crossbreed women all of whom looked to be in their early 20s,were walking along the path leading to a town called Ponyville, although they had a decent ways to go yet.

Two of the woman had the horns of a unicorn on their foreheads, two who could’ve easily passed as powerfully built normal women had it not been for the pony ears and tails, and one with the wings of a pegasus

"Come on, girls, if we can get back to the library, I have a book that I just know will give us a clue!" said one of the horned women, who, unlike her friends who were currently the same shade of gray as a rock, had a dark blue mane and tail, both of which had a magenta stripe in them, and wore a purple jacket with a magenta starburst on it, underneath which was a white shirt, black pants, and magenta and purple sneakers. This was Twilight Sparkle, and no sooner said this than she was trampled by a gang of bunnies with unusually long legs.

Recognizing one of the bunnies, the winged woman, Fluttershy, who was usually seen with a light pink mane and tail wearing a leaf green sweater, blue jeans, and pink sandals, called out, "Good boy, Angel! Mama's so proud!"

Meanwhile, the other horned woman, who usually had a beautiful purple mane and tail wearing a black dress with a belt and black and blue heels, who went by the name Rarity, and the two strong-looking women, were arguing and bickering over the large boulder Rarity was dragging along with her, which for some bizarre reason she seemed to think was a diamond.

One of the well-built women was normally tan from working on her farm in the sun all day and had a blonde mane and tail wearing a brown stetson hat, a green long-sleeved work shirt, a brown belt, blue jeans, and brown cowboy boots. Her name was Applejack. The second woman normally had a bushy pink mane and tail wearing a yellow t-shirt, a blue skirt, and orange sandals. Her name was Pinkie Pie.

"Ah'm tellin' ya, Rarity, Ah distinctly heard Pinkie Pie plannin' ta steal that there diamond right out from under yer nose," said Applejack with a southern drawl, her left eye twitching as she spoke.

"Oh, sure! Like YOU weren't planning on doing the same thing when Rarity fell asleep!" snapped Pinkie Pie.

"Both of you, STAY AWAY FROM MY DIAMOND!" yelled Rarity.

The sounds of their bickering reached Twilight's ears, and she gave a huge sigh. The sooner they got to Ponyville, got the Elements, and stopped Discord, the farther away she could get from those four irritating women.

…

Meanwhile, in a forest just outside of Ponyville, a young man in his early twenties began to stir. He had chalk white hair that had two cowlicks that seemed to resemble cat ears, a long purple tail sticking through holes in his clothes just at the base of his spine, and two tubes of some kind, which were in actuality two separate cerebral cortexes that fused into one inside his body. He wore a sleek white coat with a lavender shirt underneath, black pants, white formal shoes, and white gloves. This was Mewtwo.

Mewtwo’s eyes flew open, he sat up, gasping for breath as he looked wildly around. He didn’t recognize the forest he was in at all. In fact, all he seemed to remember was his name, how his psychic powers worked, and his intricate knowledge of genetics and science in general. Other than that, his past was a complete and utter blank. But, Mewtwo couldn’t dwell on that right now. He sensed something… very, very powerful… seven very, very powerful somethings in fact.

I should go investigate. Perhaps it has something to do with why I can’t remember my past, thought Mewtwo, before he teleported to a location near the source of the powerful energies, so he could approach them undetected.

However, when Mewtwo was able to take a good look around, he began to wonder if whatever had caused his memory loss hadn’t also affected his mind in other ways.

Mewtwo felt his jaw drop as he looked around. Nothing around him made sense. Strange Tauros-like creatures doing ballet? Sentient bells talking like idiots? The sun and moon rising and setting every few seconds? As Mewtwo gazed around his unusual surroundings, he sensed the powerful energy spike drastically before it came crashing down back to its normal levels. Following the energy, Mewtwo caught site of a group of strange human-like creatures with the ears of horses, two of which had horns on their foreheads while one had wings, two others didn’t seem to have anything special about them, outside of a strong build, while the sixth looked to be only a year or two younger than the others, and looked to be something of a cross between a human and a reptile. They were facing down a man with a black hair and a white goatee with two different wings, one a feathered bird wing, the other, a leathery bat wing, poking out of his back and a deer antler and a goat horn on his head, and who was clad in a brown suit. From what Mewtwo sensed, they seemed to be the source of the powerful energy.

Interesting… thought Mewtwo as he took cover behind a rock and quickly read the minds of those he was watching, learning everything about them.

...

"What's going on?" asked Twilight, confused and worried.

"Mah Element's workin' just fine. There must be somethin' wrong with yours," said Applejack.

"I hate the Elements of Harmony!" snapped Pinkie Pie.

Fluttershy then removed her Element of Kindness and tossed it over her shoulder. "Garbage!" she said.

No sooner had Fluttershy's Element had hit the ground than did Rarity dive for it with a scream of, "MINE!"

Knowing a lost cause when he saw one, Spike, Twilight’s faithful assistant who had small purple leathery wings, green hair, and claws wearing a purple hoodie with a black shirt underneath, blue jeans, and purple and white sneakers, removed the Element of Loyalty, placed it on the ground, and began to slowly back away. "Well, that didn't work. I'd better get inside the library and clean up in there," he said before he broke into a run. "Good luck with all th- OOF!" Spike said as he tripped over Fluttershy's outstretched leg.

"Whoopsie! Sorry, 'Rainbow Crash,'" snickered Fluttershy as Spike picked himself up and ran back to the library.

Discord, who was a draconequus with sleek black hair, a white goatee, a deer antler and a goat horn on his head, a bat wing and bird wing on his back wearing a brown suit,meanwhile, was applauding. " Bravo, ladies! Bravo! Harmony in Equestria is now officially dead! Discord now rules over all! I've beaten Celestia!" he said, laughing as he skated away on the soap roads.

"Welp, Ah'd better get outta here! Ah got new, BETTER friends waitin' fer me at the farm," said Applejack.

"Me too!" said the other three grayscale ponies, before they each went their separate ways.

Twilight growled in frustration. "Fine! Go! With friends like you, who needs..." said Twilight before she gave a heavy sigh. "...enemies."

On the word "enemies," Twilight Sparkle turned the same shade of gray that her former friends had been. A gloomy and depressed look on her face, and a cotton candy cloud pouring chocolate milk rain over her head, Twilight shuffled off through the chaotic landscape, forever alone.

…

Discord was lounging on his throne, enjoying a chocolate milk of glass, thinking about how else to spread chaos throughout the world when appeared to be a young man in his early twenties approached him. However, it certainly didn’t seem to be any kind of human that was native to Equestria. It seemed to resemble a cat somehow.

“Hmm, that’s strange,” said Discord, pulling out a laptop of some kind from seemingly nowhere. “I thought that The Sinestro Joker was going to be sticking with his Zoom story as far as Displaced as concerned.”

Mewtwo said nothing, but rather charged up a black ball of energy that he then fired at Discord. The Shadow Ball attack scored a direct hit on Discord, punching a clean hole in his chest.

“Well, that was uncalled for. I can tell you’re going to be no fun at all,” said Discord, snapping his fingers and repairing the hole in his chest, just before he found himself in a telekinetic chokehold and lifted into the air.

You think this is a game, Discord? said Mewtwo’s voice inside Discord’s mind as his eyes turned a solid, glowing, blue. That is your name, is it not? Discord, the Master of Chaos and Disharmony? It’s all here in your mind. Hmph. You’re no god. You’re just an overgrown child with reality-bending powers.

On that note, Mewtwo threw Discord around like a ragdoll, slamming him into the ground and into oddly-colored and sentient trees, none of which were too happy about having some guy rammed into them, before finally tossing him into a house of cards the size of a Victorian mansion.

Discord coughed as he pulled himself off of the ground, a livid look on his face as he glared at Mewtwo. “Of course, you do realize that this means war,” he said.

That’s a war that you will not win, Mewtwo said via telepathy.

“We’ll see.”

With a snap of his fingers, Discord swapped out his brown suit for an outfit that would not seem out of place on a karate student, with a black belt wrapped around a second black belt which was wrapped around his waist as he struck an exaggerated fighter’s pose while Mewtwo took his own fighter’s stance.

”READY...GO!” boomed and unseen voice from the heavens.

Discord snapped his fingers and summoned a huge cannon that was aimed directly at Mewtwo before firing a Banzai Bill from the Super Mario franchise at him at much faster speeds than it normally would have travelled, only for Mewtwo to grab the projectile at the very last second and throw it back at Discord and his cannon several times as hard and fast.

“Whuh-oh!” yelled Discord, pulling an umbrella out of his coat and taking cover behind it just as the Banzai Bill crashed into the cannon and detonated in a large explosion that forced Mewtwo to put up a psychic barrier to avoid getting hurt from the shockwave that leveled several card houses as well as some actual houses.

Discord emerged from behind his umbrella, completely unharmed apart from some soot that had gotten onto his suit.

“How disappointing. Not only are you a party pooper, but you’re destroying my lovely Chaos Capital of The World, and that simply won’t do. Perhaps we should take this fight elsewhere…” said Discord before he rose into the air, supported by his mismatched wings. “Catch me if you can!”

With that, Discord sped off from Mewtwo faster than a fighter jet. Mewtwo closed his eyes and channeled his psychic energy, which lifted him into the air. Opening his eyes to reveal them to be glowing a solid blue, Mewtwo took off after Discord and easily caught up with him.

“Hmm, so he can fly without wings and is real fast while doing so…” muttered Discord as he looked back to see Mewtwo hot on his tail. “Time to call in some backup, I think.”

Discord pulled out what was unmistakably a Rebel pilot helmet and put it on. ”Chaos Squadron, this is Chaos Leader. I’ve got one on my tail, can you deal with it?” Discord said into the helmet’s microphone as he snapped his fingers once again, causing three space fighters, an A-Wing, a Y-Wing, and an X-Wing, to materialize into existence and come flying at Mewtwo, laser cannons blasting at him.

Hmph. Child’s play, thought Mewtwo as he telekinetically grabbed the the A-Wing fighter, crushed it into a flaming, smoking ball of metal, and threw it into the Y-Wing, destroying both spacecraft, before he grabbed the X-Wing in his psychic grip and tossed it at Discord, knocking the draconequus out of the sky and causing him to crash land in front of what appeared to be his throne. As Mewtwo landed in front of Discord, the Chaos God began to cower in fear of the approaching being.

“Wait! Please, stop! I give up! I promise I won’t be so bad anymore! If you just let me go, I- I’ll turn over a new leaf, I swear! HURK!” said Discord as he was lifted into the air, clutching as his throat as he was strangled Captain Needa-style.

Should’ve thought of that earlier. Now, only an act of God can save you from me now, Mewtwo telepathically told Discord just before he felt something tap on his shoulder.

Next thing Mewtwo knew, he found himself on the receiving end of a left hook from a second Discord, whose hand had been transformed into a giant Orange-Flavored Tootsie-Pop. Mewtwo went flying through the air as though he’d been hit with a cannonball, and smashed his head on a rock, rendering him unconscious as a text bubble appeared in front of the Discord clone.

Discord used Sucker Punch! It’s Super Effective! the text bubble read.

The real Discord gasped and panted for breath once Mewtwo’s psychic chokehold had been broken. “You… you know,” gasped Discord as he massaged his throat. “For a being so powerful, you really aren’t all that durable. Truly, good sir, you are a man of glass.”

“Discord!”

Discord turned around to find Twilight Sparkle, Rarity Belle, Fluttershy, Applejack, Pinkie Pie, and Rainbow Dash, who had rainbow-colored hair that wouldn't look out of place on a punk and had sky-blue wings growing out of her back, and wore a black t-shirt with a white undershirt bearing the image of a rainbow-colored lightning bolt on the front, blue jeans, and blue-and-white sneakers. All of them were fully colored, not to mentioned pissed off at Discord.

"Well, now I see you've decided to try again with the whole 'Blast-Him-With-The-Elements' thing... very well, I suppose I could humor you with one more try. But, you'd better make it quick. Because of that irritating little toerag, I've missed all sorts of wonderful chaos," he grumbled.

"Okay, just remember, you asked for it! Ladies! Formation!" said Twilight.

On Twilight’s command, Rarity, Rainbow, Fluttershy, and Applejack assumed the same formation they'd used earlier against Discord.

“Wait!” called out Pinkie, who was standing underneath what looked like a cotton candy cloud, drinking up the chocolate milk that was falling from it. Once she had her fill, Pinkie skipped merrily over to the other girls, and let out an animalistic growl.

Just as before, the six Elements of Harmony glowed with a bright light as the Mane 6 were lifted into the air, their eyes closed.

Discord didn't really seem all that concerned about this. At least, not until the Elements began to emit waves of magical energy, followed swiftly by small energy discharges. "What's this?" he said, raising an eyebrow.

A rainbow began to flow out of Twilight Sparkle's tiara jewel, which began to connect to all the other Elements. At the sight of the rainbow, fear crept its way into Discord's eyes. "No... no, no, no, no, no," he said.

Twilight's eyes flew open, revealing nothing but a pure white glow of energy, and in that same moment, a huge rainbow-colored blast nailed Discord, who slowly began to turn to stone as he screamed.

Within moments, the petrified Discord fell over with a thud. In that same instant, a bright flash of light emanated from Ponyville, and perhaps all over Equestria, as the twisted and chaotic landscape returned to its original state with lush green hills, cobalt blue lakes, and so on.

With the land restored to its natural state, Twilight and the others turned their attention to the unconscious form of Mewtwo.

“Ah don’t think this feller’s from around here,” said Applejack as she looked over Mewtwo’s form.

“Whatever he is and wherever he came from, I must say he certainly has a keen fashion sense,” said Rarity, looking at Mewtwo’s outfit appraisingly. “Just look at those colors… Idea!”

“Ooh, ooh! I can’t wait until he wakes up! I’ll throw him the bestest party he’s ever seen! That Ponyville’s ever seen! That I’VE EVER SEEN!” cried Pinkie Pie, bouncing up and down on the spot with glee.

“I wasn’t the only one who saw him trying to strangle Discord without even touching him, right? How do we know for sure he’s on our side? Maybe he was just trying to take out Discord so he could take over Equestria himself!” said Rainbow Dash, eyeing Mewtwo’s motionless form with suspicion.

“Well, whatever he is, we’ll have to wait until he wakes up to get some answers. In the meantime, though, let’s take him back to the library. I’ll run some tests there and see if we can’t narrow down who or what he is exactly,” said Twilight. “Applejack, Rainbow Dash, can you carry him?”

Applejack and Rainbow nodded, before the two of them lifted Mewtwo off the ground, and together, the six women made their way to what looked like a large oak tree that had been converted into someone’s home. As they walked Twilight couldn’t help but look at Mewtwo’s form.

Who are you? she asked Mewtwo inside her mind.