The League quickly discovered that the location emitting the Legendary Pokémon energy fluctuations was Manaphy's residence.
Because Manaphy is a lawful Mythical Pokémon with an agreement with the League, the location had been recorded in their database, and the League had even sent a fragment of the Giant Rock to Manaphy in the past.
The giant Milotic's existence was also documented by the League.
However, four distinct energy from Legendary Pokemon had appeared at the time—besides Manaphy and the giant Milotic, where did the other two come from?
At this point, the League was unaware that Zapdos had settled on a nearby island.
The League immediately dispatched personnel to investigate Manaphy's residence, with Champion Steven personally leading the team.
When they arrived, they were confronted with the aftermath of a fierce battle involving three Legendary Pokémon and a Level 100 Pokémon. The ocean was in chaos, and countless innocent Pokémon had been caught in the crossfire. It was during this investigation that they learned of Zapdos's presence.
Relieved to find out that Zapdos was on friendly terms with Manaphy and its companions, Steven breathed a sigh of relief.
Zapdos was also a lawful Legendary Pokémon under an agreement with the League. However, this did not refer to all Zapdos, but specifically to the "God of Thunder" residing in the Orange Archipelago—the most revered Zapdos among them all.
No one knows exactly how many Articuno, Zapdos, and Moltres exist in the Pokémon world. Most of them are neutral or amicable toward humans, but there are exceptions—some are hostile to humanity.
The League promptly negotiated with Manaphy. Due to the Giant Rock fragment gifted by the League, Manaphy had a favorable attitude toward them and informed Steven and the others about Mewtwo's attack.
Manaphy had neither seen Mewtwo before nor heard of it. However, when it described Mewtwo's appearance, Steven and his team immediately deduced its identity.
This artificial Legendary Pokémon that defected from Team Rocket was not a secret among the League's upper echelons. Steven, of course, knew about it. But why had Mewtwo attacked Manaphy?
As far as the League knew, Mewtwo had kept a low profile since its escape from Team Rocket, rarely revealing itself and never causing trouble. It had generally been a well-behaved existence.
Steven posed this question to Manaphy, but Manaphy avoided answering directly and brushed off the matter with vague responses.
It did not want to disclose that it had found another fragment of the Giant Rock. When the League distributed fragments to various lawful Legendary Pokémon, Manaphy had received a piece as well.
However, with so many Legendary Pokémon to accommodate, each received only a small shard. Since Manaphy was neither a Tier 1 Legendary nor a special Mythical Pokémon like Mew, its share was even smaller—insignificant compared to the fragment it had found.
The small fragment given by the League had been handed over to the giant Milotic and Zapdos. For the giant Milotic, which wasn't a Legendary Pokémon, the fragment's effects weren't as pronounced as they were for Zapdos. As a result, that smaller fragment was now being safeguarded by Zapdos.
Knowing the value of the Giant Rock fragments, Manaphy was unwilling to reveal the existence of the larger fragment in its possession, fearing it would attract powerful entities vying for it—Mewtwo had clearly come for this very reason.
Unaware that he had been misled by Manaphy, Steven assumed that Manaphy was also in the dark about the reason for the attack. Left with no other choice, he led his team to investigate further on their own.
Meanwhile, countless wild Pokémon in the area were injured and urgently needed treatment. The League needed to dispatch personnel to aid them, and all of this required Steven, as Champion, to make arrangements.
Overwhelmed with responsibilities, Steven once again entertained the thought of resigning from his position as Champion.
Two days later, the League specially obtained Max Revive from the Joy family and rushed to deliver them to the giant Milotic and Zapdos.
Both had suffered significant injuries at Mewtwo's hands, and their natural recovery rate was too slow. The League worried that if Mewtwo launched another attack, the injured Zapdos and giant Milotic wouldn't be able to handle it.
Although Max Revive were exorbitantly expensive, using them on Zapdos and the giant Milotic was considered worthwhile.
The League's fears were soon validated. A few days later, Mewtwo reappeared above the island.
While Mewtwo had sustained injuries during Manaphy's ambush, they were far less severe than those of Zapdos and the giant Milotic.
This time, Manaphy and its companions were prepared. The moment Mewtwo appeared, they sensed its presence. Manaphy and the giant Milotic surfaced from the water, while Zapdos shot out from within the island.
Seeing the four Pokémon squaring off, Steven knew he couldn't intervene in their battle. He immediately sent a distress signal to the Hoenn League headquarters.
If the four Pokémon were allowed to fight unchecked, the entire marine area would be devastated. Wild Pokémon would not only suffer heavy casualties but also lose their homes.
The first to attack, unsurprisingly, was Mewtwo, the instigator of this confrontation. Its target was the Giant Rock fragment in Manaphy's possession, so it launched its initial assault against Manaphy.
A massive Aura Sphere, the size of a human head, shot straight at Manaphy. Manaphy quickly dove into the water to dodge, and the Aura Sphere exploded on the surface, sending water spraying everywhere.
"Milotic~"
The giant Milotic let out a resounding cry, summoning dark clouds over the island. In an instant, torrential rain began to pour.
Boom!
Thunder and lightning roared in the sky. Zapdos folded its wings tightly and shot into the storm like an arrow, summoning bolts of lightning through the downpour to strike Mewtwo.
Mewtwo glanced up at the descending lightning and raised one arm overhead. A semi-circular shield materialized above it.
The lightning struck the shield, with most of the energy deflected. Only a small portion reached Mewtwo's body, but it didn't even flinch. Instead, Mewtwo extended its other hand toward Zapdos, and in the next moment, Zapdos found itself paralyzed and unable to move.
Bang!
With a tremendous force, Mewtwo used Psychic to slam Zapdos onto the beach, causing the Legendary Bird to let out a sharp cry of pain.
"Milotic~"
"Manaphy~"
The giant Milotic charged forward with Hydro Pump, while Manaphy followed up with Surf. The two attacks were aimed directly at Mewtwo.
Mewtwo suddenly accelerated, shooting high into the sky. The attacks missed, crashing into the ocean and triggering another massive tsunami.
From a distance, Steven wiped the rain off his face, anxiety gripping him. While reporting the battle situation between the four Pokémon to the League, he fervently prayed for reinforcements to arrive as quickly as possible.
This Mewtwo was entirely different from the one under Team Rocket's control. Its strength was on a whole other level. Its current power even surpassed that of ordinary Tier 1 Legendary Pokémon. Despite being attacked by Manaphy, Zapdos, and the giant Milotic in unison, it showed no signs of struggling.
Steven even suspected that Mewtwo's power now exceeded that of Groudon and Kyogre, rivaling that of Rayquaza.
"Hurry up! Rescue the Pokémon caught in the crossfire!" Steven shouted at his subordinates.
Mewtwo disappeared into the dark clouds overhead. Suddenly, a deafening roar shattered the sky, and the clouds exploded outward. The torrential rain abruptly stopped as sunlight broke through the dissipating clouds.
Dispersing the Drizzle effect caused by the giant Milotic, Mewtwo appeared above Manaphy in the next instant, grabbing it firmly. Manaphy tried to struggle, but under Mewtwo's terrifying psychic suppression, it was completely immobilized.
Mewtwo's goal had always been clear: to seize the Giant Rock fragment from Manaphy. It pressed on relentlessly.
Manaphy gritted its teeth and resisted, unwilling to surrender the megalith fragment.
"Melotic~"
"Zapdos~"
Seeing Manaphy captured, the giant Milotic and Zapdos erupted in anger. One launched a powerful Aqua Tail at Mewtwo, while the other manipulated lightning to strike it.
Mewtwo swiftly vanished, dodging the Aqua Tail, which struck the sea surface instead, stirring massive waves. Countless wild Pokémon were swept into the chaos, struggling for survival in the surging waters.
It was truly a clash of titans, leaving the weaker beings to suffer.
Evading the Aqua Tail, Mewtwo flung Manaphy directly into the incoming lightning. The Water-type Manaphy, vulnerable to Electric-type moves, was struck unconscious.
Charred black, Manaphy plummeted into the sea but immediately enveloped itself in an Aqua Ring and vanished beneath the surface.
Time passed second by second. Manaphy, Zapdos, and the giant Milotic were clearly no match for Mewtwo. Their injuries grew more severe, leaving Steven Stone anxiously distressed.
When a flying craft appeared in Steven's sightline, his eyes lit up. He immediately mounted Metagross and hurried toward it.
As the hatch of the craft opened, an elderly man stepped out.
"Mr. Kuni'o, you're here!"
Seeing Mr. Kuni'o arrive, Steven breathed a sigh of relief. Thankfully, the League had prepared ahead of time; otherwise, Mr. Kuni'o, who was stationed in Mauville City, might not have made it in time.
Mr. Kuni'o nodded at Steven and glanced at the four battling Pokémon in the distance. Releasing a Tropius, he mounted it and took off toward the battlefield.
If Yuga were present, he would instantly recognize this Tropius, as he frequently saw it at Mr. Kuni'o. This was a Master-level Pokémon.
Riding Tropius, Mr. Kuni'o headed straight for the fray. Steven hastily followed suit.
At this point, Zapdos was on the brink of collapse. While Manaphy had Aqua Ring and the giant Milotic had Recover to heal themselves, Zapdos lacked any such recovery moves. Its injuries had grown severe.
Of course, Mewtwo wasn't entirely unscathed, but its injuries were negligible compared to those of Manaphy, the giant Milotic, and Zapdos. Mewtwo was merely consuming energy at a faster rate.
Just as Mewtwo prepared to deal a finishing blow to the "pesky" Zapdos, a sound of "thwip thwip thwip" echoed. In an instant, Mewtwo was pinned to the sandy shore of the island by dozens of black arrows piercing its shadow.
A Decidueye hovered gracefully, flapping its wings lightly as it looked down at Mewtwo with a piercing gaze.
The energy radiating from this Decidueye rivaled that of the giant Milotic, indicating it was another Level 100 Pokémon.
This Decidueye belonged to Mr. Kuni'o and was related to Yuga's own Decidueye. Yuga's Decidueye was the offspring of Ryuuichi's Decidueye, which, in turn, was a descendant of Mr. Kuni'o's Decidueye. The exact generation was something even Mr. Kuni'o might have forgotten.
Mr. Kuni'o's Decidueye was as old as he was, over a hundred years.
Pinned to the sandy shore, Mewtwo tried to move but found itself immobilized. Its eyes locked onto the Decidueye, flashing with an unreadable expression.
Decidueye nocked another arrow, aiming to fire Spirit Shackles at Mewtwo again, but before it could, it realized it was now caught by Mewtwo's psychic grip.
Just as Mewtwo was about to hurl Decidueye away, a Shaymin in its Sky Form appeared in its line of sight. The Shaymin immediately unleashed several Air Slash attacks at Mewtwo.
The Air Slash hit Mewtwo, interrupting its psychic grip on Decidueye and freeing it from the spirit Shackle pinning its movements.
Mewtwo soared into the sky, forming two Shadow Balls in its palms and hurling them simultaneously at Decidueye and Shaymin.
While Mewtwo was engaged with Shaymin and Decidueye, Mr. Kuni'o rode Tropius to the side of Manaphy, Zapdos, and the giant Milotic.
Green light spheres emerged from his palms, landing on the three Pokémon, and their wounds began to heal rapidly.
If Yuga were here, he would be astounded by his master's healing ability. While Yuga needed to physically touch a Pokémon to heal it, his master had already mastered energy projection.
This extraordinary skill made Mr. Kuni'o comparable to a humanoid healing-type Pokémon—and a powerful one at that.
Before long, Manaphy and the others regained their vitality. Although their injuries weren't completely healed, they were no longer hindered in battle.
Mewtwo, still entangled in combat with Decidueye and Shaymin, noticed that Manaphy, Zapdos, and the giant Milotic were surrounding it again. For the first time, its perpetually stoic face showed a flicker of emotion.
Three Legendary Pokémon plus two Level 100 Pokémon... Even it might not be able to handle this.
Decidueye drew its bow and launched a dozen black arrows at Mewtwo. Mewtwo dodged with a flash, but immediately Milotic's Aqua Tail swept toward it.
This time, Mewtwo didn't dodge. It grabbed Milotic's massive tail, swung it around, and hurled it toward the nearby Zapdos. Zapdos barely dodged and retaliated with a Thunderbolt.
Mewtwo evaded Zapdos's Thunderbolt but was simultaneously struck by Shaymin's Air Slash and Manaphy's Signal Beam.
Mr. Kuni'o's Shaymin was entirely different from the one that appeared during the Grass-Type Pokémon Duel Tournament in Verdanturf Town. This was a fully mature Shaymin, capable of unleashing its full power as a Mythical Pokémon.
Mewtwo let out a low groan of pain, clearly injured.
Breaking free of their encirclement, Mewtwo sped out of range and launched multiple Shadow Balls and Aura Spheres in rapid succession. Decidueye, Shaymin, and Milotic were all hit.
However, with Mr. Kuni'o present on the battlefield, his healing abilities provided immense sustainability to the five Pokémon.
Mr. Kuni'o was known as the strongest Master-level Trainer for a reason.
Having already expended considerable energy in the earlier battles, Mewtwo began to show signs of exhaustion under the relentless onslaught of the five Pokémon. Before long, it was hit consecutively by Milotic's Aqua Tail and Shaymin's Air Slash.
Despite its fierce counterattacks, Manaphy and Milotic were gravely injured once more. This time, their wounds were so severe that not even Mr. Kuni'o's healing abilities could restore them.
However, Mewtwo also suffered a direct hit from Shaymin's Seed Flare.
Shaymin had put its full strength into this Seed Flare, aiming to defeat Mewtwo in one blow. Already heavily injured, Mewtwo staggered and appeared on the verge of collapse.
Realizing it could no longer hold out, Mewtwo cast a lingering gaze at each of the five Pokémon before turning and vanishing into thin air.
When a top-tier Psychic-type Legendary Pokémon decides to flee, almost no one can stop them.
Seeing Mewtwo retreat, both Mr. Kuni'o and Steven let out a sigh of relief.
If the battle had continued, this entire sea area would have been completely destroyed.
After Mewtwo's departure, the League immediately mobilized personnel to rescue the wild Pokémon injured in the sea.
Elsewhere...
After escaping the battlefield, the heavily injured Mewtwo flew on and on. Its consciousness began to blur, and even it didn't know where it had ended up. Eventually, it crashed into a river.
Mewtwo's body had a self-protective mechanism. The moment it fell into the river, a psychic shield automatically formed around it.
Drifting along with the current, Mewtwo finally fell into a deep sleep.