My Little Pokémon

by Amarvax

The Greater Mewtwo

Author's Note:

I've typed and said Mewtwo and Newtwo so much it's all I hear today.

Equestria. Out in the mountains. The Plasma Frigate. Afternoon.

Shadow Mewtwo. A Mewtwo that is obscured from the other two that are facing down with it. The first Mewtwo made by Team Rocket 25 years ago and the second Mewtwo made by Team Plasma more than 8 years ago. Also known as Newtwo as dubbed by Pinkie Pie.

Mewtwo and Newtwo now face down against Shadow Mewtwo. Another one of their species that was once considered a one of a kind species of Pokemon. But it seems that was slowly shifting.

"Another Mewtwo?!" Newtwo gasped.

"The better Mewtwo. Shadow Mewtwo if you will. A Mewtwo that had been born after being possessed by something known as the Shadow Synergy Stone, merging with it. Not only does he have its power but the ability to Mega Evolve as well." Colress explained. "Who needs multiple Pokemon to deal with you when you just need one? Essentially yourself. Now Shadow Mewtwo. You are loyal to Lord Ghetsis and Team Plasma overall. So you know what to do."

"You're just mind-controlling him. We can see it clearly." Mewtwo said, looking at Shadow Mewtwo's glowing eyes. "If anything, this is against his will."

"Right on that." Colress snapped his fingers. "But I'll make sure that doesn't change. As for you two, you'll go well with Lord Ghetsis' future team. Think about. One a Dark Mega Mewtwo X. The other, a Mega Mewtwo Y. And the last one a normal Mewtwo. The only thing missing will be a normal Mega Mega Mewtwo X. But aside from that, it would look matching, wouldn't it?"

"Newtwo. We should take this somewhere else. If all three of us end up battling, the Pokemon living here along with the landscape will be obliterated immediately. We need to find somewhere to deal with this Shadow Mewtwo. At least high above the skies might work.

"I told you not to call me Newtwo. But I don't see anywhere else but the skies. Even passing through the gateway means putting our original world in danger. I don't see any other scenario where we head somewhere else without Pokemon. Even in the skies, we risk the chance of harming the Flying-Type Pokemon. So be careful."

"Of course I'll be careful. It-" But just as Mewtwo was about to finish his sentence, in the blink of an eye, faster than he could usually react, Shadow Mewtwo had appeared right in front of him.

Everything slowed down for a moment. Mewtwo's mind started processing what was going on. It was like Shadow Mewtwo melted into the air, unable to be detected. Shadow Mewtwo went over to grab Mewtwo's face with a Shadow Ball up and ready.

But, thankfully, Mewtwo was eventually able to keep up as he flew back. Right in the nick of time. Shadow Ball had just been unleashed, hitting the walls of the upper deck and causing a black explosion. Colress left the upper deck, leaving everything to Shadow Mewtwo. Newtwo also moved away after the initial explosion.

Shadow Mewtwo then looked up at his cloned variations before raising his arms. By raising his arms, the corrupted and mind-controlled Mewtwo made a radius of pillars erupt from the deck, damaging it in the process. Mewtwo and Newtwo narrowly evaded these pillars as they broke through the clouds.

"We should snap him out of it since he's under mind control!" Newtwo exclaimed while hovering through the air. "How good is your mind control?!"

"I was able to control a Nurse Joy once but that's about it!" Mewtwo replied. Right as he replied, Shadow Mewtwo left the floor of the upper deck, flying straight towards the duo. The corrupted Mewtwo had then used what seemed to be Flamethrower. He had spurt fire from his palm as it had maintained a horizontal movement.

Newtwo had put up a barrier, pushing the flames back. After Flamethrower had been negated, Shadow Mewtwo had then teleported above his clone. Newtwo specifically. Newtwo gasped before surrounding herself with the barrier.

However, Shadow Mewtwo had grabbed the barrier despite Newtwo being inside of it. And like a ball, he had thrown the barrier and Newtwo towards Mewtwo with full force. Newtwo's barrier ended up hitting her fellow Mewtwo as they both crashed into the walls of the upper deck.

After they hit the walls with Newtwo lowering the barrier, Shadow Mewtwo didn't waste any time attacking. The corrupted Mewtwo had then used Psywave but in the shape of a blade. He had absorbs the Psywave itself, converting it into a different shape as he now had a blade. Two of them. Both on each hand as he flew towards his targets.

Mewtwo shoved Newtwo aside to save her as he used Psytrike to try and push Shadow Mewtwo away. Mewtwo created a white force field that expanded rapidly from his body. It was meant to explode on Shadow Mewtwo, but that didn't come to fruition.

Instead, Shadow Mewtwo's Psywaves had cut the Psystrike in half. Mewtwo's own signature move had been overpowered, shocking him as that has never happened. As Mewtwo gasped, he had been slashed by the Psywaves two times. Shadow Mewtwo then kicked his fellow clone into the air as Mewtwo started spinning.

"Mewtwo!" Newtwo gasped, aiming to catch Mewtwo and prevent him from being harmed. However, Shadow Mewtwo acted fast, putting his hand to the side and unleashing Flamethrower. A burst of flames came flying out as Newtwo quickly put up her arms for protection.

The flames had pushed her back, burning the wood of the Plasma Frigate as well. Newtwo's hands felt scorched as she then lowered them. But as soon as she did, those same pillars emerged from the floor, engulfing her. Newtwo cried out while being punished by these pillars. Afterwards, they had erupted with a golden explosion as Mewtwo tumbled on the floor, almost falling off the ship.

Colress observed everything from his monitor while grinning. He was not worried about Shadow Mewtwo losing. But he was right to be cautious about the mind control being overpowered. However, he had a contingency for that.

"Try as you might...with this indicator, I can tell when Shadow Mewtwo's control is on the verge of being broken." Colress held up a metallic stick that multiple bars on it. "One touch of this and the control will return as if nothing happened."

Meanwhile, Ash and the others looked up to see the scuffle happening above. They witnessed golden lights and constant Psychic waves flying about. The ships had also stopped attacking suddenly, no longer firing their beams.

"What is happening up there?" Rarity wondered as they all squinted their eyes. "Are the Mewtwo okay?"

"Every other ship's stopped all of a sudden." Twilight observed. "Maybe they're all focused on just Mewtwo and Newtwo.

"I'll go and check." Rainbow Dash chose to check up on Mewtwo and Newtwo. But she wouldn't get close to the ships. Instead, she would just stay a far distance while in the air.

"Be careful, Rainbow Dash!" Fluttershy cried out.

"No pr-" Just as Rainbow Dash ascending, a loud explosion came from the ship with a massive wooden floorboard flying through the air. The floorboard almost struck Rainbow Dash as she instinctively managed to move out of the way. "Woah!"

A close call. The floorboard had then crashed into a hill, breaking afterwards. Rainbow Dash had a shocked poker face before gazing up at the location of the explosion. A massive smoke cloud could be seen afterwards.

And out of that smoke was both Mewtwo and Newtwo each. They were still there but they were not having the best of times. Everyone gasped after seeing them hurt. But more than that, they had also seen another Pokemon fly through.

Their first time seeing Shadow Mewtwo.

The corrupted Pokemon flew through the smoke before grabbing both of his clones. By holding their legs, he then tossed them back onto the Plasma Frigate at full force.

"Is that...another Mewtwo?" Spike gawked.

"Yeah but it's different." Ash took out his Pokedex, trying to read the data of this Mewtwo. But he was met with just one response.

"Data not found."

"Data not found? So it's a new kind of Mewtwo!?" Ash looked at the Pokedex before gazing up at the sky once more.

"Pika?!"

Back on the Plasma Frigate, Shadow Mewtwo had flung three shocks of electricity by using Thunder. The three shocks zoomed towards their targets. Newtwo quickly countered by using Aura Sphere to destroy them both.

Mewtwo then got up from the floor, using Shadow Ball. Two of them. He summoned two Shadow Balls, hurling them at Shadow Mewtwo. The corrupted Mewtwo seemed unbothered as he had cut the blobs of shadows with his Psywave blades.

And speaking of Psywave, he had then used Psywave differently. A vortex. Once again Shadow Mewtwo absorbed the Psywave and spun into a tornado of dark energy. This dark tornado started tearing up the floor of the upper deck, even going past that and reaching the other floors as well.

Mewtwo got in front of Newtwo, using Hurricane to retaliate. He put his hands out, summoning a giant gale that had matched the size of the tornado. Both forms of wind had wrapped around each other before cancelling out.

After they had vanished, Shadow Mewtwo dashed midair towards his clones, then drilled downward feet first. Mewtwo quickly used Poison Jab to counteract this incoming attack. He managed to force his clone away after the initial collision as Shadow Mewtwo flew back. Newtwo then followed up by using Aura Sphere, sending multiple shares of Aura upwards.

But, there was a response to that. The corrupt Mewtwo had used those blades again. But this time, in the form of Fire and Ice instead of Psywave. He had absorbed Flamethrower and Ice Punch to make this possible. He then cut the spheres in half as they had separated, crashing into the floor and blowing up.

"Is there nothing he can't do?!" Newtwo gasped.

"He's like us. But much like us and every Pokemon, he's not unstoppable." Mewtwo said before standing upright. Shadow Mewtwo hovered there with those Fire and Ice blades out. Mewtwo and Newtwo started coming up with a plan to deal with their corrupted kin.

They did this telepathically instead of speaking out loud. After going through their plan and with approving nods, both of them enacted their plan. And it started with Newtwo using Mist. By putting her hands together, she formed a thick white mist that had cloaked a majority if not all of the upper deck. Even the skies themselves.

Shadow Mewtwo covered his eyes before using his tornado to blow away the mist. But once he did so, Mewtwo was gone with Newtwo approaching. The corrupted Mewtwo gasped, realizing that Mewtwo was behind him.

Both of the regular Genetic Pokemon had used Thunder Wave in the form of whips. They mimicked what Shadow Mewtwo had done with Psywave, Flamethrower and Ice Punch, altering the natural shapes of this paralyzing Electric-type attack.

Before he could turn around to face Mewtwo, Shadow Mewtwo's arms and legs were restrained by multiple whips of electricity. Once they wrapped around him, they immediately paralyzed the corrupt Pokemon. That would slow him down for a bit as he winced.

After doing so, Newtwo moved in with a Brutal Swing. She had swung her dark-coated hand with darkness, striking the corrupt Mewtwo while he was still restrained. Shadow Mewtwo had finally taken some damage as his eyes widened after the initial hit. Felt like getting slapped by a train to him.

After being hit by Brutal Swing, Newtwo did it again, this time coating her tail in darkness and whipping Shadow Mewtwo. Following up from that, Mewtwo had then tossed Shadow Mewtwo into the air with the whips of Thunder Wave.

Shadow Mewtwo struggled to use his natural speed due to paralysis as the two Mewtwo then chased after their kin. It was their turn to overwhelm him. Both of them used Psycho Cut at the same time, covering their arms in Psychic energy. After doing so, they started giving Shadow Mewtwo a flurry of Psychic hits by repeatedly walloping his stomach.

Shadow Mewtwo growled as his stomach was taking more punishment than usual. In response, the corrupt Mewtwo had then used Reflect in a split second, summoning a giant reflective screen in front of him. When the next hit from the duo came, the screen reflected them, forcing the two Mewtwo to a lower level.

Afterwards, Shadow Mewtwo amped things up with his destructive capabilities. He raised both his arms before crossing them in a swiping motion. Shadow Mewtwo had used Psystrike. Not once. Not twice. But three times. Two gigantic fields of Psychic energy exuded out of his body as they rapidly travelled with volatile destructive power.

Colress realized this as he had put a shield around the Frigate for protection. Everyone else on each ship did the same to try and nullify the damage. The Psystrike had struck both Mewtwo as they had put their hands out to try and stop it with their Psystrike. Only for Shadow Mewtwo's to easily overpower them.

As the Psystrike expanded, it was reaching the lower lands. Ash and the others quickly realized the approaching destructive field. They all made the smart and conscious decision to run for it. The hills and mountains were being obliterated this gigantic field as the shields on the ships would not nullify something this powerful. But the Frigate would.

Mewtwo and Newtwo realized that the Pokemon onboard were in danger of being obliterated. Not only that but the Pokemon on land even the sky as well if something wasn't done. So, they dug deep, exuding more Psychic power to try and prevent that from happening. Both of their eyes glowed purple as they had just barely destroyed the barrier of Psystrike. But at the cost of harming themselves.

The duo had crashed into the ground after stopping Psytrike. A large dust cloud formed after their crash landing which was right near Ash and the others. Craters had also been formed.

"Mewtwo! Newtwo!" Ash ran over, seeing how they were both on the ground.

"Pika-Pikachu?!"

"A-Ash. Pikachu." Mewtwo groaned before looking up at Ash and Pikachu. He had scratchers and tatters on him which was rare for a Pokemon like Mewtwo. Ash and Pikachu had never seen him or Newtwo like this before. "Get the Pokemon off the ships. As long as they're there, we both can't perform at our best. Even if you can't save them all."

"Yeah. I gotcha." Ash helped Mewtwo up as everyone else nodded, knowing what they needed to do. But as Mewtwo was helped up, descending to the ground with his own fearsome crash landing was Shadow Mewtwo.

He made a pressuring entrance with his landing as everyone's hair had been blown in the wind. Shadow Mewtwo was finally on the ground level. They had bared witness to Shadow Mewtwo at their level. And it was safe to say that he was here for them as well.

"Pika...!" Pikachu's red sacs started giving off electricity as he wasn't scared of this corrupted Mewtwo.

"Don't, Pikachu." But Ash stopped him. "Let's focus on getting all the Pokemon out of there."

"I keep a Travel Sphere just in case," said Twilight. "We can try and use that to send them through to the other world for safety. But there are so many ships to try and use it."

"Do it. We'll provide a way for you to send them all through." Newtwo stood up, wiping the dust off of her. She could see that Shadow Mewtwo by himself was enough for two Mewtwo. So, to get the upper hand, Newtwo had finally used her Mega Stone.

The Mewtwonite Y.

Since it was within her, she didn't need a second stone to activate it. She did it by will. The red and gold lights of Mega Evolution wrapped around the Genetic Pokemon as everyone witnessed the emerge of Mega Mewtwo Y.

But, Shadow Mewtwo had the same thing in-store. He tapped into both the Synergy Stone and Mewtwonite X within his body. After doing so, his energy started warping the area itself. With his amazing power, Mewtwo had formed a mysterious subspace rift that started turning the floor into what seemed to be crystals.

Everyone looked around them, seeing the area being altered. These crystals were actually all Synergy Stone Shards instead of random crystals as mountains of them were being made, replacing the already existing mountains in this landscape. The lake had been covered by this new area, blocking off the water. The sky was suddenly black with cosmic vortexes flowing around.

Shadow Mewtwo did not replace this land. Instead, he had brought everyone else somewhere different.

"What is this?!" Ash looked around at this subspace that had a dark and foreboding sense to it. Everyone else believed that Mewtwo had replaced everything.

"Did he change it all?!" Starlight gasped. "Is all of Equestria-"

"No. He sent us to another dimension." Mewtwo and Newtwo were able to tell immediately. "This is his subspace. We're in his world now."

Shadow Mewtwo then stepped forward as the Mewtwonite X and Synergy Stone had wrapped around him. As he walked forward, the subspace was trembling with shards rising from Shadow Mewtwo's growing power. And in a flash, he had Mega Evolved into Mega Mewtwo X.

He had a seemingly broader posture and a more muscular appearance. However, orange shards of the Shadow Synergy Stone were now shoved up all across Shadow Mewtwo's body as orange veins coursed along his body, arms and legs. Purple energy and black accents now surrounded Shadow Mewtwo, while the outline of him occasionally pulsated a cyan colour.

"Another Mega Evolution?" Spike gaped. "W-Which one is that?"

"I wasn't aware that there was a second one. So this was the Mega Mewtwo X Colress mentioned."

"Wait! How are we gonna get out of here?!" Pinkie Pie squealed.

"With this." Mewtwo held his hand out, covering Ash and everyone in Psychic energy. He could send them out of this dimension and back to reality. "Go. And save the rest of the Pokemon. At least in here, we can't worry about harming anyone else."

"Alright. Good luck, you two!" Ash said before he and the others were sent back to reality. Now it was just the three Mewtwo. One was not Mega Evolved while two were.

Shadow Mewtwo then stopped walking before standing face to face with what he would consider his lesser kin. But of course, he wasn't in his right mind thanks to Colress.

"Follow my lead, Mewtwo. You don't want to lag behind us Mega Pokemon, do you?"

"Hmph. Don't get cocky because you have Mega Evolution. I'm capable enough on my own." Mewtwo gave a snarky retort as the two of them then challenged Shadow Mewtwo in this lone subspace.

---

Reality.

Meanwhile, after being sent out to reality, Ash and the others were dropped off near a hill. Right out of Team Plasma's sight. Team Plasma and Colress were shocked to see that Shadow Mewtwo and the others had vanished. But they were unaware of Ash and company returning.

"Okay. Leave everything to Mewtwo and Newtwo. Let's find a way to get all the Pokemon from those ships free." Ash said.

"But how? I mean, that's 51 ships in total." Starlight asked. "We only have one Travel Sphere too."

"Let's just get some more." Rainbow Dash suggested. "We'll make a bunch of gateways then get all of the Pokemon through and deck some ships in the process."

"Or you know...let's just leave it to the Mewtwo." Trixie shuddered as everypony faced her. "They're strong enough right?"

"Not strong enough if just one Mewtwo can give them trouble. And after we struggled with one months ago." Twilight pointed her hoof at herself before thinking of a plan. "There's another way. Princess Celestia has some extra Travel Spheres just in case. Plus, there's also Reshiram and Zekrom."

"Oh yeah. What happened with those two? I don't see them around Canterlot anymore." Spike asked.

"Reshiram and Zekrom were sent to help the other universes stop the Empress' forces. They've been busy moving around from world to world."

"So they're occupied. Great." Applejack sighed.

"Not entirely. All they need is a word from Princess Celestia." Twilight cleared her throat as she now had a proper plan for this situation while the Mewtwo take care of the hard part. "Having extra support doesn't help either. As long as we can get them to leave while having the Pokemon safe, then it'll be fine. Trixie."

"What?" Trixie shot up with another gasp as she was still processing the situation she was in.

"Can you help with your illusion one more time?"

"Well..." Trixie bit her hoof before thinking about it. "Despite how intimidated she looked in this situation, this wasn't too overwhelming for her. After all, she had experienced an invasion. However, Trixie did want to boost her reputation so that her students would find her amazing and have more ponies come to her Great and Powerful School. Plus, she'd also be a great friend in front of Starlight. A grin graced her face. "Sure. Why not? I'm already an honorary hero after that invasion."

"Good. Pinkie Pie. I'll need you and Mew to help Trixie with this."

"You got it!" Pinkie Pie saluted.

"Mew-Mew!"

---

Shadow Mewtwo's Subspace. The Dark Colosseum.

Currently, even with the power of Mega Evolution on their side, both Mewtwo were still struggling against Shadow Mewtwo in his Mega Evolved state.

All three were clashing with giant spheres of Psychic energy surrounding them. Their spheres clashed like swords, destroying the landscape around them with the number of pulses coming out. However, Shadow Mewtwo had expanded his to be larger than theirs, overpowering the duo.

Mewtwo and Newtwo had both crashed into hills of Synergy Stones after a rough attack from Shadow Mewtwo. The hills had broken with shards falling afterwards. Both of them groaned as Shadow Mewtwo proved to be relentless.

The corrupt Mewtwo immediately zoomed forward, covering himself in Psychic energy as he tackled Mewtwo while was still up against the hill. By tackling him, he sent his fellow clone through the hills with a massive hole left behind. Newtwo gasped as Mewtwo was being carried through the air and smashed through multiple hills with little time to breathe.

But he could break free. The Genetic Pokemon had used Psytrike to force Shadow Mewtwo back, allowing himself to breathe. Mewtwo then followed up with Stone Edge, summoning multiple glowing crystals that orbited him. The regular Mewtwo then sent the array of rocks towards Shadow Mewtwo, only for them to be crushed by his telekinetic hold.

Newtwo came flying in, attempting a sneak attack. However, Shadow Mewtwo seemed to be swift enough to notice her. Both Mewtwo's had clashed, locking hands with each other with shockwaves emitting from their collision.

"I-If I can just use Hypnosis at the right time...!" Newtwo growled while trying to overpower Shadow Mewtwo. However, she couldn't as they were seemingly equal in strength. At least for now. Shadow Mewtwo was starting to overpower her.

Now that she was up close and personal with him, using Hypnosis was now. Her eyes started glowing blue as the goal was to try and break Shadow Mewtwo's mind control. And with her eyes making contact with his, she started affecting him.

"!" Shadow Mewtwo snarled for a bit as Newtwo's Hypnosis was doing its job, getting into Shadow Mewtwo's head. The corrupt Mewtwo closed his eyes as Colress' control was being combated by Newtwo's Hypnosis. In response, Shadow Mewtwo had used Zen Headbutt.

He covered his head in Psychic energy, smashing it forward and giving Newtwo a devastating headbutt. Newtwo cried out as her grip had been weakened, allowing Shadow Mewtwo to go on the offensive. Shadow Mewtwo summoned blue energy in the shape of a punch, hitting Newtwo's stomach.

After giving her a hard hit, he then kicked her away as if she was little on the street. And for a finishing blow, he then flew after her to unleash a purple tornado. Mewtwo flew in the way to protect Newtwo, using Solar Beam after gathering enough energy in this subspace that had no sun. A large green beam of solar energy came flying out of Mewtwo's hands afterwards.

Shadow Mewtwo had used the purple-coloured tornado on the Solar Beam instead. And it was certainly larger than it. So large that not only did it consume Mewtwo, but also Newtwo. Both of them had been hit, flying through the air once more.

And it didn't stop there. As they flew through the air, Shadow Mewtwo instantly transported to their location via teleportation. Newtwo gasped as the corrupted Mewtwo had grabbed her face. Newtwo tried to pull his hand off her face, only for Shadow Mewtwo to use Flamethrower. The flames scorched her face as Shadow Mewtwo then flew downwards.

Newtwo was powerless to stop it, causing Shadow Mewtwo to smash her into the ground. The ground had both shattered and torched by the flames. Shadow Mewtwo kept his hand there for a moment, not letting Newtwo break free.

But Mewtwo would deal with that. The regular Mewtwo came flying in, using Poison Jab to force Shadow Mewtwo off of Newtwo. He also added Psystrike into it for a further knockback. And it worked. Shadow Mewtwo was forced off of Newtwo, sliding back.

"Are you okay?" Mewtwo helped Newtwo up.

"I'm fine." Newtwo held her face after feeling the heat of Shadow Mewtwo's crushing Flamethrower. "But I just need to use Hypnosis without him breaking my focus. I saw that it was working with how he started wincing. If I can just get some more time and-"

"You don't have to do it alone. If we combined both our Hypnosis', we can break his mind control." He suggested. Newtwo could get behind that. Combined forces are always a plus.

Shadow Mewtwo stood upright as his body kept pulsating a cyan colour, showing that his strength was rising and overflowing her in this subspace.

This time, it was Mewtwo and Newtwo that went towards Shadow Mewtwo first. Together, they both used Poison Jab and Brutal Swing in unison. Shadow Mewtwo summoned those same Fire and Ice blades by absorbing Flamethrower and Ice Punch.

The three of them made eye contact with Poison Jab and Brutal Swing meeting with those two blades. They started pushing Shadow Mewtwo back by forcing their strength onto the blades. Shadow Mewtwo attempted to grab them with his tail, only for Newtwo to use her own tail to stop it.

The trio separated as Shadow Mewtwo spun around in the air, creating those golden pillars of light in the same radius once more. Multiple of them. Each for both Mewtwo.

But the Mewtwo were ready for this as well. They had zoomed and navigated their way around the pillars, evading them narrowly. After evading them, Newtwo went up to Shadow Mewtwo with Aura Sphere. She put her hand, expecting Shadow Mewtwo to react with a predictable move.

And he did. He had made an orb of Psychic to simply counteract the FIghting-Type move. But that's what Newtwo wanted. She then tossed the Aura Sphere. But not at Shadow Mewtwo. Instead, the sphere of Aura had passed the corrupt Mewtwo.

And right behind him via teleportation was the regular Mewtwo. Mewtwo had used his own Aura Sphere, adding it onto Newtwo's. By merging the spheres, a massive Aura Sphere had been made as Mewtwo used his tail to launch it.

Shadow Mewtwo soon realized this before turning around. Too late to do anything about it as the gigantic Aura Sphere had struck him. The corrupted Mega Shadow Mewtwo X went through many Syngery Stone hills, obliterating them as the Aura Sphere destroyed more with its expansive size.

However, after being carried by the sphere for a while, Shadow Mewtwo had then kicked it away. Aura Sphere went into the air, blowing up afterwards s the azure explosion of it complimented Shadow Mewtwo's menacing stare with his eyes glowing purple.

Shadow Mewtwo's Synergy Stone kept pulsating as he had then exuded a larger aura than before. He went straight for Newtwo, faster than before. Newtwo was met with a Gatling kick made of blue energy upward. However, she had used Substitute, causing a giant doll to take the hits.

Shadow Mewtwo quickly realized the doll as it had been destroyed. Right as the doll was crushed by the force of these kicks, Mewtwo and Newtwo caught Shadow Mewtwo off guard. Together, they had used Aura Sphere in unison. They put their hands together before flying at the corrupted Mega Evolution.

They then thrust their hands right in front of Shadow Mewtwo, releasing it as a combined burst of the aforementioned dual Aura. Shadow Mewtwo stood there in awe as he didn't have enough time to do something about this. Before he knew it, he was consumed by the giant sphere of Aura as a blue gale had emerged.

The ground below was obliterated by this combination as the entire subspace trembled. The duo shoved there, seeing how a gigantic bottomless pit had been formed from the destruction.

As the dust was settling and the smoke fading away, Shadow Mewtwo could be seen floating there. The Aura Sphere had almost knocked the wind out of him as he felt befuddled.

"Now!" Mewtwo cried out as they both flew towards their fellow clone. Shadow Mewtwo quickly regained consciousness, only to be met with two hands grabbing his arm. The corrupted Mewtwo had been restrained by his kin, pinned against a Synergy Stone hill.

The aim was to use a Double Hypnosis. Shadow Mewtwo tried forcing them off with Psytrike, only for both Mewtwo to use coat themselves in a protective Psychic aura. Psystrike had obliterated the hill behind them into nothing but dust. However, they would not let go.

Together, they had used Hypnosis with their eyes glowing blue. They made contact with Shadow Mewtwo's mind, controlling it. Shadow Mewtwo groaned as he realized that he could not keep himself in this subspace for long.

Despite his amazing power, Shadow Mewtwo does have a limit. And the Shadow Synergy Stone is to blame for it. After all, he was trying to hold it back. He winced, trying to allow the other Mewtwo to remove the brainwashing so that he could be freed.

But over in the real world, Colress' indicator had gone off, giving him the alert. He smirked, knowing that he would completely ruin the chances of Shadow Mewtwo being freed.

"I don't think so." He said before clicking the device. With just a click, an electromagnetic pulse had been sent through Shadow Mewtwo's brain.

Once that pulse came through, Shadow Mewtwo's brain had rapidly changed cells. His eyes flashed as he had then unleashed a gallant Psychic wave from his body in response to the Dual Hypnosis. Mewtwo and Newtwo were blown back by this pulse along with every hill in this area.

The subspace was practically almost obliterated with nothing left. A bottomless pit and an endless void all around as the duo of Mewtwo managed to save themselves by holding onto the last remaining pieces of rubble. They used their Psychic powers to keep the rubble afloat.

"It didn't work?!" Newtwo gasped with one eye closed.

"It was working! Something came up and changed it, however!" Mewtwo replied.

Shadow Mewtwo then hovered over with his body trembling. Clearly, he was reaching his limit. He aimed to end this as soon as he could or else the Shadow Synergy Stone will end him. He was ready to face down Mewtwo and Newtwo one last time.

---

Reality. The Plasma Frigate.

Colress knew that his little action had succeeded as the indicator was no longer going off. Shadow Mewtwo was still under the control of Team Plasma. But aside from that, Colress was wondering about Ash and the others. He had seen them enter the subspace that Shadow Mewtwo had made and had not heard from them since. To Colress, he believed that they were still in there.

"If Shadow Mewtwo ends up destroying them, then there's one major problem out of Lord Ghetsis' hair," said Colress. "Even if he still aims to harness the Magic of Friendship for himself."

"Colress. Sir." A Team Plasma grunt came in.

"Yes?"

"Should we leave? Ash Ketchum and the others haven't returned yet. Perhaps we should maybe wait for Shadow Mewtwo to bring them out?"

"Shadow Mewtwo has a limit to how long it can maintain itself along with the subspace. Eventually, it will return. And the chances of Ash Ketchum and the others defeating Shadow Mewtwo is considerably low. But then again, they have proven to wedge themselves out of difficult situations." Colress thought for a moment.

"So then we wait, right?"

"Wait for Shadow Mewtwo to return. Don't go anywhere." Colress ordered. "When it-"

Just as he continued speaking, his words were cut off immediately once he had witnessed a portal open up. His attention was drawn towards it. Out of that portal, Shadow Mewtwo had emerged. Along with Mewtwo and Newtwo plus Ash, Twilight, Fluttershy, Starlight, Applejack, Rainbow Dash, but noticeable not everyone else. Some were missing. They had all fallen to the ground with Shadow Mewtwo holding them up with Psychic.

"Oh. Nevermind." Colress said. "Right where we want them. But it seems not all of them were able to return safely."

"Should we capture them or let Mewtwo handle them?"

"The two Mewtwo are coming with us. Lord Ghetsis still wants Twilight Sparkle and the others. Even though they are all not here. Some reserves would work either way."

"Return to the base and refill on Infinity Energy. A few of us will take things from here."

"Yes sir." The grunt saluted before heading off. Multiple gateways had opened just for some of the ships. The Plasma Frigate and a few others would stay behind.

Shadow Mewtwo flew over towards the Plasma Frigate with some grunts there to pick up Ash and the others. Colress was ready to leave through the gateway as well.

"What are we gonna tell Lord Ghetsis when some of them have been destroyed?" A grunt asked. He still wants all 6 of them for power."

"Meh. We'll just say Shadow Mewtwo destroyed them by accident. Did you, Mewtwo?" Another grunt asked.

Shadow Mewtwo didn't respond as he then casually tossed Newtwo over to the grunts letting them catch her. And the grunts would with open arms. At least, that seemed to be the case.

As the grunt went to grab the Genetic Pokemon, they suddenly crashed onto the floor, feeling something heavy go down on him. "Oof! H-Heavy! Are Mewtwo's this heavy?!"

"No, but Audino is." The voice of Ash suddenly spoke, causing the grunts to gasp. They then looked over at the unconscious Ash Ketchum. Except, that wasn't actually Ash. With a head turn, a grin had faced the fake Ash Ketchum. It was instead one of Trixie's Zorua.

"Teehee!" The Tricky Fox Pokemon had revealed himself. The grunts then looked over at Twilight and the others and they turned out to be Zorua's as well.

"Zorua?! T-Then...!"

Shadow Mewtwo smirked. Except it wasn't Shadow Mewtwo. It was Mew. "Mew-Mew!" But, he wasn't the true cause of all of these fake outs. Zoroark was. She had used her amazing illusionary abilities to disguise everyone else as fakes. Obviously, Trixie didn't have enough Zorua or Zoroark for disguises. But Zoroark's illusions were able to compensate for that.

Audino was truly Audino and that was indeed the full weight of an Audino on Colress. And with that weight, he was not getting off no matter what.

"Why you tricky little...! Get off!" The grunt grunted, unable to remove Audino from him.

"Ssshh..." Starlight suddenly hushed before having Hatterene use Hypnosis on them all. "Go to sleep."

"Hatterene." Hatterene had put the scientist to sleep with hypnotic spiralling waves. Just like that, the grunts had been put to sleep. Except for Colress as he had already made his getaway by entering the inside.

And this was where Celestia's assistance came in as she couldn't refuse a scenario such as this. However, Celestia assisted without anyone seeing her coming. Zoroark's illusion went past just disguising everyone.

The ships were going the wrong way, surprisingly. They believed that they were entering the gateway back to their base. But instead, Celestia had used her magic to interfere with the gateway, shifting its original position somewhere else. Zoroark had just given the illusion of it being there still.

The ships ended up crashing into something. Everyone onboard believed that they had crashed into a gateway. But not at all. Instead, they had crashed into Reshiram and Zekrom. Zoroark's illusions were still being kept up.

"What did we hit?!" Colress gasped as the Plasma Frigate started trembling. "Is there another ship on the other side?!"

With Zoroark's illusion still active, Reshiram and Zekrom took the time to deal with the weapons. Each of the ships had cannons on them. It was self-explanatory. Destroy the cannons. And so they did.

Reshiram and Zekrom flew at blistering speeds as they simultaneously used Steel Wing. By using Steel Wing, they slashed the cannons off of the airships, causing them to fall. Their goal was to save the Pokemon so no Fire and Lightning for this one.

With the assistance of Luxray, they could have a clear view of the Pokemon inside. Since all of the airships were aligned in a straight line thanks to the gateway. And since all of the airships were built the same, thanks to Luxray's X-Ray vision, he could see where all the Pokemon were. On the back of Reshiram and Zekrom were Ash and the rest of them.

"Luxray!"

"Awesome find, Luxray." Rainbow Dash said. "Now we know where to hit 'em.

And that someone was Passion.

"Now, Passion! Plasma Bolt!" Celestia ordered.

"Garde...!" Passion put her hands out, combining Mystical Fire and Thunderbolt into one attack. But minimized as to not fully obliterate everything. Zoroark's illusion was starting to fade away.

"Hurry! Zoroark's illusion is dropping!" Trixie gasped.

"Now!"

"Voir!" Passion unleashed Plasma Bolt. She struck the back of the first ship, piercing through it. Afterwards, the bolt travelled rapidly at great speeds, breaking through the other ships as if it was a domino effect.

The ships were already damaged due to crashing into Reshiram and Zekrom earlier and this just added to it. With clear precision and accuracy, Passion had pierced holes through almost every ship in her line of sight. Unfortunately, she could not hit them all but she got a considerable amount.

The ships had been damaged further with alerts going off. It was just then that Zoroark's illusion had ended. With the illusion fading away.

"Now, Pikachu! Overload it with Thunderbolt!" Ash yelled.

"Pika...chu...!" This was Pikachu's time to shine. He had used Thunderbolt on the closest ship, sending 100,000 volts right through it. But he was assisted by others.

"Luxray, Discharge!"

"Passion, Thunderbolt!"

Luxray and Passion had assisted, adding their electricity into the mix. And this time, Zekrom could actually do something. He could use his electricity without destroying the ships. A total of 800,000 volts had been sent towards the first ship.

And that was enough. Not only did it overload the systems within the ship, causing something on par with an EMP minus the deactivation, but it acted as chain lightning, springing onto the next ship with greater speeds. Like a parasite.

The ship's electronics had been overloaded, causing the restrains on the Pokemon to be removed. Now that they were free, the Pokemon could run amok. Except, that wasn't going to happen.

It was soon revealed where Celestia had placed the gateway. The same holes that Passion had blasted throughout the ships. Slurpuff had used Sweet Scent to draw the Pokemon in, swaying them away from a potential rampage.

"A diversion!" Colress gasped, looking at the monitor and outside. "Those accursed Zoroark and Zorua..." Just as he growled, Ghetsis' came into view as Colress contacted him. "Lord Ghetsis!"

"Colress. I'd better hear some good news."

"We have a problem! Ash Ketchum and the others have tricked us with Zoroark's illusions! Most of our ships are undergoing electrical problems as well as missing cannons! I'm not sure where Shadow Mewtwo is now and-"

"Are you telling me that you've lost Shadow Mewtwo?" Ghetsis' tone changed with narrowed eyes. Colress shuddered at Ghetsis' crimson stare.

He quickly tried picking up on Shadow Mewtwo's signatures. He could do so even when Shadow Mewtwo was in its subspace world. After searching, he found it. "Ah! It's still in its subspace! Seems that it's still dealing with the two Mewtwo!"

"Retreat," Ghetsis ordered with words that Colress never thought he would hear him say.

"I beg your pardon, Lord Ghetsis?"

"Don't try and fight this. They've already brought upon a large sneak attack on you. Your weapons have been damaged too as well as Shadow Mewtwo being occupied. "It's pointless to try and stop this as you'll risk everything we have on board of the ship, do you understand?"

"Y-Yes. But how am I to return Shadow Mewtwo if it's still in subspace?"

"Do I have to do everything myself?" Ghetsis sighed as he put his hand out. By doing so, he had opened a gateway that had connected to the Plasma Frigate. His hand had stuck out as he could now interact with this universe. Ghetsis had then covered his hand in darkness. By doing so, Ghetsis had managed to interact with Mewtwo from afar.

He clenched his hand as Mewtwo within subspace felt his head twitch. He immediately ceased his attacks on Mewtwo and Newtwo. But then again, he wasn't attacking them anymore. He had defeated them both. Shadow Mewtwo held Mewtwo and Newtwo by their necks, emerging as the victor.

The corrupt Mewtwo could hear Ghetsis calling for him. He also couldn't stay here much longer without rest. The Shadow Synergy Stone was getting to him. With that, the subspace had vanished as it had also reached its limit.

With Ghetsis' command and influence upon the Genetic Pokemon, Shadow Mewtwo had returned to reality, inside of the ship. Mewtwo and Newtwo were on the ground, barely able to move. They were still conscious but badly damaged.

Shadow Mewtwo hovered back to the ship, holding his head as he had deformed out of Mega Mewtwo X. The same went for Newtwo as she reverted to normal.

Colress had given the order for them all to retreat. Ghetsis' word was final. Because of this, they had ignored Ash and the others, much to their chagrin. Ash and everyone were ready for a Pokemon Battle, only to find out that wasn't happening.

"Wait. How come they're leaving?" Spike noticed while on Salamence's back.

"They're retreating," Celestia said. "I didn't see that coming at all."

"Hah! We got 'em scared!" Rainbow Dash chuckled, pointing her hoof out as everyone else remaining on the ship had gotten off, taking a ride of Reshiram and Zekrom's backs.

"I wouldn't say scared," Twilight replied. "With how things are, I can see why they'd leave. So is that our cue as well?"

"Mhm." Celestia nodded. "Our work here is done. We may not have been able to stop them all, but they'll certainly remember this."

The ships had all retreated with Colress opening up a new gateway with his Travel Sphere. As for the Pokemon, Sweet Scent did its job. However, since not all the ships had holes pierced through them, there were still some Pokemon remaining and they had unfortunately passed through the gateway that Colress had made.

Colress looked at the distance, growling as he slammed his fist on the table. This was a confirmed loss. One that he would have to live with.

"Curse you all...I'll get you back for this one day! You'll never outsmart someone like me ever again!"

---

"Mewtwo! Newtwo!" Ash cried out as all of the ships had left. They approached Mewtwo and Newtwo who were sitting on the ground, exhausted. "Are you okay?! You two look really beat up."

"Pika!"

"We're fine. But unfortunately, we lost." Mewtwo lowered his head. "We were so close to breaking the mind control."

"That Shadow Mewtwo was something else. I've never struggled so much before. And to think, Ghetsis and Team Plasma will be using someone like that."

"Well, good news. We managed to save the Pokemon like you wanted. They're safe over at Viridian Forest if that's good enough."

"It is." Mewtwo and Newtwo smiled as Audino went up to heal them with Heal Pulse. "We knew we could count on you all. Thank you for protecting them."

"What are you two gonna do now?" Rainbow Dash asked.

"I now can no longer underestimate Team Plasma. They are too dangerous to ignore. Especially with Shadow Mewtwo on their side. I promised myself I wouldn't get out there too often but...I might have to make an exception."

"I've already decided. I wanted to stop Team Plasma in the beginning when they made me. This is my second chance to make it a reality. But I can't do it alone. Mewtwo. Will you help me?"

"I already thought the same thing as you. But I'm afraid just as two won't be enough with Shadow Mewtwo. However, I can certainly count on you. Ash. Pikachu. And all of you to an extent."

"Yeah. If they come by next time, we'll do what we can." Ash replied.

"I should get going now." Mewtwo stood up. "I've left the Pokemon alone for too long. Newtwo. Will you come with me?"

"I told you not to call me that. And well...Maybe next time. I need to find a way to become stronger. But I'll certainly come to when I need help."

"Hm. And here I thought the one with the Mega Stone didn't need help." Mewtwo started acting playful.

"Oh, don't you start." Newtwo nudged him as the others started laughing. The two Genetic Pokemon went their separate ways, bidding farewell to Ash and the others.

As for Ash and company, it was time for them to leave as well. This Jirachi plan turned upside down for them after all and was a bust. But it was still a work in progress. Meanwhile, Trixie would definitely head back to brag about this to her students. How she got to ride on two Legendary Dragons, encounter three Mewtwo and take on Team Plasma.

This wouldn't be the last they would see of Shadow Mewtwo. Truly a terrifying force. But one that could not control himself because of the Shadow Synergy Stone and Team Plasma as the journey continues.

Chapter 555 End.

Comments

[Rider09]

theres a comic dub series in youtube called mew and mewtwo,
where ash finds and takes care of an injured mewtwo!
its an awesome series to watch!

[Grahf]

I was able to control a Nurse Joy once but that's about it!

and rewrite the memories of at least 7-9 humans and all their pokemon so like 4-6 each so at about 40 individual minds while making a building/castle disappear and using it's mind to also allow all the cloned pokemon to fly with it to a new home