Kalos Region — Lumiose City
At the very heart of the Kalos region lay its greatest metropolis, Lumiose City—a sprawling urban core and the most populous city in the entire known Pokémon world.
Lumiose was renowned for the iconic Prism Tower and its celebrated Lumiose Museum of Art. Tourism flourished here, supported by countless bustling cafés, restaurants, and shops that drew in both locals and visitors from across the globe.
On the city's outskirts stood the Lysandre Labs, where cutting-edge inventions were unveiled year after year, ostensibly to benefit the people.
To the public, Lysandre was a man of compassion—a philanthropist who lent aid to the poor and downtrodden.
But at this very moment, the man himself sat with a stern expression, eyes fixed on the glowing screen before him.
Satellite images revealed a young man and woman—the very same pair who had just defeated and captured Groudon and Kyogre, riding their Legendary Pokémon at incredible speed, heading straight for Lumiose.
Straight for him.
"…So, I've been found already? What a sharp instincts…" Lysandre muttered.
He had never expected this. His people had stolen away the Rayquaza that Paul was on the verge of capturing, and mere moments later Paul himself was already bearing down on his location without a shred of hesitation.
As if Paul had seen straight through every move he made.
Watching the distance rapidly shrink, even Lysandre felt a flicker of unease.
True, there was no conclusive proof tying him to Rayquaza's abduction. But what if Paul decided not to care about proof? Some people were not interested in reasoning with others. From what Lysandre observed, Paul was the type who liked to dictate reason to others, but despised having it imposed on himself.
And worse… these two outsiders from another world weren't merely carrying one or two Legendary Pokémon.
Just one of their Legendary Pokémon or even that strange "second-rate fool" they had just caught, could flatten the entire research facility. Or destroy Lumiose itself. Even the Pokémon League wouldn't be able to stop it.
His plans had barely taken their first steps, and already he was facing this precarious crisis.
After a long silence, Lysandre sighed. Before Paul could reach Kalos, he opened his communicator and gave the order:
"Release Rayquaza."
"What?! Representative! Rayquaza is far too powerful. If we release it—"
"Release it. At once. Cleanly." Lysandre cut him off coldly.
"…Yes, sir!"
The subordinate hesitated only a moment before obeying.
...
Off the coast of Kalos...
Paul and Akari sped across the skies on their Pokémon when the sea suddenly erupted below.
With a thunderous roar, a green serpentine dragon burst from the ocean depths and soared into the open sky.
Rayquaza, free again, turned sharply. Its eyes blazed, locking on the submarine it had just escaped from. A surge of violet energy swelled in its jaws—
Hyper Beam!
"BOOM!!"
The devastating blast tore through the sea. An instant later, a mushroom cloud of water and flame erupted as the submarine was annihilated, fragments of steel raining across the waves.
"AAAAAHHH!"
Rayquaza bellowed in triumph, delighted both at its escape and its vengeance.
But its victorious roar cut short. Turning its head, it froze midair—its eyes meeting Paul's.
Man and dragon locked eyes, the world itself holding still in that suspended moment.
Then Rayquaza's body flared with radiant light. Without warning, it ascended to its ultimate form: Mega Rayquaza.
In a dazzling surge of emerald brilliance, it launched upward like a living lightsaber, vanishing past the clouds into the upper atmosphere.
Paul barely had time to draw a Poké Ball before releasing Mewtwo, but Rayquaza was already gone.
"…Go after it." Paul said after a beat of silence.
Whether or not he captured Rayquaza wasn't the point. Letting a quarry this close slip away felt too wasteful. With Mewtwo's power, if it caught up and fought again, a victory wasn't impossible.
"I'll try." Mewtwo replied calmly.
Its body gleamed as it assumed its Mega Mewtwo Y form, and in an instant it streaked skyward, leaving the atmosphere behind.
"…Impressive resolve." Akari murmured.
With Mewtwo gone, Paul directed Metagross lower, scanning the wreckage of the destroyed submarine.
"Could it be..." Akari said thoughtfully, "that Rayquaza didn't escape on its own, but was released?"
Paul gave a thin nod. "Most likely. Too coincidental otherwise."
A thorough search turned up no insignias, no corpses, not even blood. Whoever had manned the submarine had already evacuated in smaller escape vessels before Rayquaza destroyed it.
"So… do we still go to that research lab to confront Lysandre? Ugh, this is such a headache… I hate this!" Akari groaned.
She had learned plenty from Paul during the journey. But now, faced with this dilemma, every option seemed troublesome. With no evidence, accusing Lysandre outright was pointless. Even if they had evidence, would Officer Jenny be able to handle someone like him?
Yet not going… felt suffocating. Unacceptable.
"Since we're here already," Paul said with a cold smile, "why not pay him a visit? Someone should account for our losses."
With that, he urged their Pokémon faster, streaking toward Lysandre Labs.
The sprawling research complex came into view—a fortress of steel and glass, more similar to an industrial park than a lab. Without hesitation, Paul and Akari dove straight in.
"CRASH!!"
Lysandre had just received a word: Rayquaza released, personnel evacuated. He was preparing his next move when the sound of shattering glass filled the room.
Through the ruined skylight, two youths dropped onto the floor, their Pokémon behind them.
"Breaking into another man's property is hardly polite." Lysandre said smoothly, rising to his feet. His face remained calm and composed. "May I ask why you've come?"
"Do Pokémon thieves deserve politeness?" Paul shot back.
"Of course not." Lysandre replied without a twitch. "Such disruptors of peace deserve no courtesy. But… what does that have to do with me?"
Even as he spoke, his voice over the comm soothed his rapidly approaching security forces.
"…Truly worthy of Team Flare's leader." Paul said dryly. "Steady as ever."
"Team Flare?" Lysandre's heart skipped, though his expression betrayed nothing. That name was not yet known to the world.
"…So dishonest. I'll leave this to you." Paul glanced at Akari.
"No problem!"
Akari's hand swept to her belt, releasing Uxie, the Being of Knowledge.
"Uxie, Hypnosis!"
"Wha—?!" Lysandre's eyes widened, then glazed over. Uxie's psychic pulse swept through him, leaving him standing slack and motionless.
"Now speak." Paul said, hands in his pockets, his tone was ice-cold.
"Tell us everything."
Under Uxie's spell, Lysandre had no strength to resist. And so, piece by piece, he began to confess.
"So it really was you!"
Akari had been watching silently for some time. When Lysandre revealed the details of the Z Project including Rayquaza's capture and escape, she almost couldn't believe it.
Sure enough, these shadowy schemers were nothing but master actors—Oscar-worthy, every one of them!
"Where does the Z Project stand now?" Paul asked coldly.
Lysandre replied, his tone level:
"We've already captured Z2 and part of the scattered cells. My researchers are analyzing and attempting to control them. However… since you stole the Giant Rock, our original plan to destroy the world has become difficult to realize. We've decided to initiate the backup: the XY Project."
Paul narrowed his eyes. "And what is this XY Project?"
"Seeking out and capturing the Legendary Pokémon Xerneas or Yveltal. With their power, we can fully activate the Ultimate Weapon and annihilate the world."
"…Where is the Ultimate Weapon now?"
"In the underground base beneath this laboratory. Our researchers are studying, controlling, and preparing to activate it."
"That's enough."
Paul turned slightly. "Uxie… thank you."
"Yuuu~"
Akari recalled the Being of Knowledge into its Poké Ball. Lysandre blinked back to awareness, dazed.
"…What did you do to me?"
He had no memory of what had just happened, but a deep unease told him he had revealed something important. For the first time, Lysandre's composure cracked.
Paul, however, remained calm. He leapt back onto Metagross and before leaving with Akari, left only two sentences behind:
"When faced with humanity's selfish greed, you chose not to resolve problems, but to resolve the world itself."
"I look forward to seeing how far you've gone… next time we meet."
Lysandre stared at the retreating figures, fists clenched tight. In his mind, unbidden memories surfaced: leading Team Flare to aid the poor and suffering.
Yet afterward, those very people became ungrateful—treating his generosity as nothing more than their due.
'Disgusting. Were such people even worth saving? Was this world still worth saving?! No… to destroy and rebuild the world from its ashes, that was the only true solution.'
Lysandre's silence was deafening.
That night, he was jolted awake by subordinates bursting into his quarters. Their reports came in rapid fire:
Z2 and the cells—gone.
The Ultimate Weapon—stolen.
Every piece of illicit research data—deleted.
All laboratory equipment—systems scrambled beyond repair.
In that moment, Lysandre finally understood Paul's parting words.
But that is a tale for later. The true mastermind behind these actions was not in Kalos—indeed, not even on this planet.
...
Outer Space...
Mewtwo soared tirelessly, pursuing its quarry: the escaped Rayquaza.
But space was far too vast. All around were asteroids, planets, and drifting debris—yet no trace of life.
After hours of searching, Mewtwo encountered only a single Rayquaza—the same one once summoned and thrashed by Hoopa. At the sight of Mewtwo, that dragon bolted like it had seen a ghost.
Though it couldn't escape Mewtwo's grasp, it also couldn't reveal the whereabouts of the particular Rayquaza capable of Mega Evolution.
Time passed. The cold of space gnawed at Mewtwo, forcing it to reinforce its psychic barrier to endure. Then—suddenly, an immense surge of energy rippled across the void.
Mewtwo immediately accelerated toward the disturbance.
There, in the endless dark, a humanoid Deoxys clashed against a Rayquaza.
By all logic, Rayquaza's immense strength should have overwhelmed its foe in moments. Yet the battle was completely one-sided—in Deoxys's favor.
Through seamless Form Changes, it toyed with Rayquaza.
From afar it unleashed Psycho Boost, Thunderbolt, and Ice Beam in relentless barrages. Up close it alternated Ice Punch and Thunder Punch.
Even when it misstepped, Deoxys shifted into Defense Forme, effortlessly absorbing Rayquaza's counterattacks.
Enraged by the humiliation, Rayquaza roared—its body blazing with emerald light. In an instant, it became Mega Rayquaza.
Yes, the very same dragon that had only just returned to space after escaping Paul.
On its home turf, furious from losing the Giant Rock, nearly being captured, and enslaved by humans, Rayquaza vented its wrath. It opened its maw and spewed Hyper Beam wildly across the asteroid field.
But then, one struck asteroid shimmered with strange light… and transformed into another Deoxys.
Rayquaza was in no mood for games. But neither was Deoxys, whose slumber had just been violently interrupted by Rayquaza's rampage.
One furious Legendary met another. They fought.
With Mega Evolution, Rayquaza's power skyrocketed. Every casual strike forced Deoxys onto the defensive. Even its Defense Forme shields buckled beneath the dragon's assaults.
Before long, Deoxys had to resort to Recover, then shifted into Speed Forme to evade and harry its foe.
Outpowered. Outmuscled. Only speed kept it in the fight.
But Rayquaza's fury only deepened. Channeling its might, it conjured a cataclysmic space-storm—an all-encompassing maelstrom that even Deoxys couldn't outrun.
Caught within, Deoxys braced desperately, erecting a psychic shield in Defense Forme as Rayquaza twisted its body and unleashed its signature finisher: Dragon Ascent.
Impact!
In an instant, cracks spiderwebbed across Deoxys's barrier, spreading fast. Its fate seemed sealed—
Until a new figure appeared before it, intercepting the strike with bare psychic force.
Mega Mewtwo Y.
Rayquaza's eyes widened. Mewtwo had pursued it even here, to the edge of space itself.
"Planning to bully the weak? I won't stand by and watch."
Mewtwo's psychic aura exploded outward. It countered with a crushing Psystrike paired with Counter. The combined force hurled Mega Rayquaza backward, smashing through dozens of asteroids before it regained balance.
"RAAAHH!"
Furious yet shaken, Rayquaza hesitated. Outmatched by the two of them, it finally turned and retreated into the void.
Mewtwo gave chase, but the nature of space battles differed greatly from terrestrial combat. Even at full power, it could not decisively defeat Mega Rayquaza. At last, it could only watch as the dragon's silhouette dwindled into the darkness.
"Hm? Why are you still following me?" Mewtwo said, turning.
Behind it, the very Deoxys it had saved lingered silently.
"…Mewtwo. Long time no see."
For the first time, emotion flickered across Deoxys' alien face.
"You are… the Deoxys I met before?" Mewtwo's mind returned to that encounter in Sinnoh's—years ago.
"Yes. After we parted, I traveled the world, growing stronger. In time I returned to space, entered stasis, and absorbed cosmic energy to hone my power. That was when Rayquaza attacked… and I crossed paths with you again."
Deoxys summarized its journey in stark brevity.
"Incredible." Mewtwo admitted. "You've changed so much, even your psychic signature is almost unrecognizable."
The last time they met, Deoxys had only just awoken after being struck by lightning. Now it was strong enough to clash with Mega Rayquaza. The difference was staggering.
Deoxys' eyes glowed softly. "To protect myself… and to catch up to you… I've never stopped working."
"You succeeded."
Mewtwo extended its fist.
Deoxys paused, then twisted one tendril into the shape of a hand and met the gesture.
Their fists touched—two solitary beings, reunited in the endless void.
(End of Chapter)
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