The story is actually untitled, so I gave it the title "Ketsuban", another name for Missingno.
“Rhydon, use fissure!”
All at once, an enormous crack opened in the earth. A gaping maw stretched across the gym floor, speeding rapidly towards the move’s target. Closer, closer…and the fissure opened up beneath the opposing Blastoise, sending it tumbling down untold feet into the darkness below. Then, as quickly as it had appeared, the tear was gone. The gym floor shone flawlessly under the cold, synthetic light, and Blastoise was nowhere to be seen.
The opposing trainer’s tears fell swiftly now, splashing silently onto the pristine tiling into which his Pokémon had vanished.
“Where…where’s Blastoise? Where… did he go?” The trainer was staring listlessly at the ground, refusing to move an inch. He was obviously in shock over the sheer magnitude of his defeat; Giovanni would have to remedy this.
“Pay up, kid”, ordered Giovanni in a low voice. The trainer acquiesced resignedly, forfeiting half of his life savings into Giovanni’s waiting palm. But he still refused to leave. “Go home”, commanded the leader, now slightly irritated. “You’re holding up the line.”
The trainer looked about himself in a dazed state, and noticed the challenger standing behind him, a small, black-haired boy of perhaps ten years of age. “Oh…sorry, I…I didn’t notice”, mumbled the defeated trainer with a small nod, and he at last began to pace resolutely back towards the Gym’s front door.
Giovanni turned his attention to the black-haired boy, who had stepped forward. He was wearing a red jacket over a black t-shirt and had a red-and-white cap pulled low over his eyes. Giovanni was intrigued by this challenger; something about him was unsettling, something about his slow, measured pace and expressionless visage seemed somehow…alien. But that was of no consequence; nobody had ever defeated Giovanni’s main team, and he was not about to let this child become the first.
“Welcome,” spoke Giovanni in a cool, intimidating tone. “I am the Viridian City Gym Leader. Do you dare to challenge me?” Giovanni rose to his full height. “I am the greatest trainer the world has ever known! I have defeated countless thousands in this very spot! Thousands upon thousands of championship dreams, terminated right where you’re standing! And yet you still dare to forever risk your only aspiration by blithely challenging my undefeated team?” The speech had been delivered flawlessly, and Giovanni felt quite proud of himself; surely, the child had by now realized his insignificance, surely he was at this moment quaking in his boots.
And yet, the challenger showed few outward signs of his distress. Giovanni’s oratory had reduced countless grown men to sniveling, crying imbeciles by means of that very speech, and yet here was a child, a whelp no more than ten years old, standing his ground. Rather than break down, the challenger nodded and stepped noiselessly forward. The effect was disconcerting, and Giovanni’s voice displayed an imperceptible faltering. “Very well…then let us begin.” Giovanni threw his first Poké Ball.
A stream of crimson light issued forth from the Poké Ball, quickly coalescing into Giovanni’s Rhyhorn. Rhyhorn was Giovanni’s usual lead, and had served him admirably in the past by gauging the strengths and identifying possible weaknesses of his opponents. The terrifying spectacle of the three-foot tall Rhyhorn’s single-minded charge attack had caused many to resign their challenge in terror by itself. But the child stared unflinchingly at Giovanni’s Pokémon, and threw down a Poké Ball of his own.
But there was a problem; the device was malfunctioning. This was unheard of; Poké Balls were made on assembly line now, and, as Kanto’s only major export, each Poké Ball had to be flawless. Those with faulty machinery were without exception weeded out somewhere in the manufacturing process; as a former head of Silph Corporation, Giovanni knew that. So what was wrong with the child’s Poké Ball?
Instead of releasing the customary beam of light, the Poké Ball was shaking eccentrically, without any discernable rhythm, and emitting periodic bursts of red light from its central seam. As bloody sparks jumped across its surface, the Poké Ball seemed ready to explode from the pressure of whatever was inside of it. Suddenly, the Poké Ball released its laser, but, instead of the customary red, it was a pale and sickly orange.
When the light faded, Giovanni caught his first glimpse of the thing that the Poké Ball had vomited. It was a pile of trash, just sitting there on the floor of the gym. Without warning, and before Giovanni could get a closer look, the pile of trash expelled a stream of pale brown-colored liquid, hissing and spurting as it did so.
“Water Gun,” commanded the challenger.
The fluid squirted through the air and impacted Rhyhorn squarely in the face. Giovanni’s face betrayed his worry; Rhyhorn did not usually survive any decently-powered Water- or Grass-type moves. Yet Rhyhorn did not falter; the pile of trash’s Special must have been completely pathetic for Rhyhorn to take such a small amount of damage.
But something was wrong. Something was… off about Rhyhorn after the brown liquid contacted him. Giovanni could sense it, though he couldn’t quite discern what it was; something seemed different about the shape of Rhyhorn’s back or the pattern of his armor plates. Giovanni only became truly alarmed when Rhyhorn did not turn his head, as usual, to receive orders; he stood unmoving, frozen to the spot from which he had received the attack. Giovanni walked around Rhyhorn to examine his face, and found it scrambled, with no discernable features. Various pieces of eyes, mouth, and nose were scattered haphazardly around its ruined face, which resembled a disassembled jigsaw puzzle on a featureless grey background. Giovanni was aghast. “Rhyhorn? Rhyhorn… use… Fury Attack! Rhyhorn?” Rhyhorn was not fainted, and showed no signs of collapse or fatigue. But he was clearly dead.
Giovanni could not look at the horror that his Pokémon had become, so he returned it to its Poké Ball. He could not lose; his team was undefeated, and this…thing would surely not prove a challenge to his stronger Pokémon. He decided to immediately move up a tier in strength, and so summoned Nidoking from its Poké Ball. Nidoking emerged with a savage scream, but Giovanni’s attention was focused on the pile of trash. As he searched for a weakness, he came to a sudden realization; most of what he had previously assumed to be trash consisted of discernable pieces of various Pokémon. Here was a Bulbasaur tail, there a Fearow beak and a Blastoise arm, all haphazardly stitched together into some kind of abominable mass and mixed in with… other things, things that he could not recognize. There were letters and numbers, pieces of signs and buildings, and chilling geometric patterns that he could not even begin to identify.
And it was distinctly larger than it had been thirty seconds ago. With each passing second, the thing… grew, Giovanni thought he noticed. It was a slow process, but the pile of trash appeared to be steadily expanding without any external source. But maybe that was just a trick of the light…
Giovanni didn’t even know where to look for a weakness, or what such a weakness would even be; but he did know that this monstrosity had to somehow be stopped. So he ordered Nidoking to attack.
“Nidoking, use Thrash!”
Nidoking looked around for a moment, wondering where the attack was even directed. Nidoking was considerably smarter than Rhyhorn, smart enough to notice that there weren’t actually any other Pokémon in the arena. Nidoking turned to look at Giovanni, who, presented with what might very well have turned out to be the last time he ever saw Nidoking whole, felt a sudden surge of regret. He pointed ruefully at the pile of trash, which had taken on an unmistakably crimson hue. Giovanni had seen it before, he thought, but he could not remember when…
Nidoking never got his close look at his foe. He was not one to disobey orders, for Giovanni was a hard master… and so Nidoking charged. He rammed fist after massive, armor-plated fist into the thing, but it showed no signs of any external damage or fatigue. It just sat there, glowing. As the word popped into his head, Giovanni knew what was about to happen. He tried to shout, tried a second too late to warn Nidoking of his fate. But Nidoking was so absorbed in its Thrash attack that it failed to notice, and so the end came quickly.
“Sky Attack,” said the challenger. His lips, Giovanni saw, did not move when he talked, but remained frozen open. In fact, he had not moved at all since the battle had begun. Giovanni suddenly began to wonder if he even could. The boy’s clothes were becoming distorted, becoming numbers and letters and Pokémon fragments one piece at a time. There were endless, mesmerizing geometric patterns in his eyes…
Nidoking flew through the air and smashed against the ceiling of the Gym with a reverberating crash. The collimated light from Giovanni’s Poké Ball intercepted the hapless Pokémon before the floor could; Giovanni did not want to have any opportunities to get a good look at the remains of his Nidoking. If only he had chosen a different move, Nidoking might have been saved…
The trash was not just larger now, but…spreading. The walls were spattered with it, oozing with Pokémon, and Giovanni’s pristine floor was covered in refuse. As Giovanni reached uncertainly for another Poké Ball, he discovered that his hand no longer fit securely around it in the position to which he had long been accustomed. For even he had not escaped the trash’s corrupting influence; his hand, though retaining its general shape, was gruesomely disfigured; a Weezing’s face, a Wigglytuff’s ear, and an Arcanine’s eye, along with other body parts too damaged to identify, protruded from his skin in tortured, hideous combination.
Giovanni tried to scream, but no sound came out. He fumbled with his Poké Ball, and tossed it onto the floor haphazardly, a novice trainer once again. Rhydon emerged, but even he was not free of the trash’s scarring. His skin had a reddish tint, and his spikes were misaligned with the ridge of his back… Giovanni could not order an attack, but he did not need to; Rhydon was as incapable of movement as Giovanni himself. Across the arena, the opposing trainer no longer bore any resemblance to a black-haired human being; he was already consumed, a pile of trash in a hominid shape. Only the cap remained, pulled low over where the trainer’s eyes had used to be. Giovanni could just make out the black, embroidered capital letters printed on the front. “Future Pokémon Master,” the cap read.
The boy’s lips could not move, but the trash’s attack came anyways. It let out a hideous scream, torn from the larynxes of nearly every Pokémon in Kanto, savagely twisted and ground together to form a single, unending screech. As the monster grew still larger, its cacophony grew louder, and Giovanni’s consciousness was fading fast. The walls of his gym turned to sludge, and Giovanni felt his body beginning to crumble around him. Rhydon was melting beside him, and the trainer and his Pokémon slowly merged into a single puddle of liquid death. The trash filling his vision at last invaded Giovanni’s final thoughts as he saw the world disintegrate, and the abomination consumed all.
Credited to an anonymous writer on F Yeah Pokemon Creepypasta.