There was once an organization.

Its name was team rocket. Their specialty- stealing Pokémon. That was the usual drill for many of the members in the organization. Steal Pokémon, then sell them to potential buyers for cold, hard cash. However, its boss had different plans. His name was Giovanni. He had a much greater ambition… to rule all of planet earth. And so, one day, he gathered all of the underworlds top scientists. The most brilliant minds of the century. Together, they would endeavor to create something unheard of… something that would guarantee Giovanni total world domination. They were going to create the ultimate Pokémon. An unstoppable weapon of mass destruction… a genetically altered species, with the potential to harness the powers of the earth itself, and unleash them upon all that stood in Giovanni's way. The scientists moved to a secret, isolated laboratory on an island, funded by team rockets head. There, the scientists began to search for a crucial piece of their puzzle: Mew. The ancestor of all Pokémon. They set up camp, and began to search. They tried to find anything left behind by the legendary Pokémon, anything at all. Even its droppings would have been useful.

And then it happened.

One day, an excited scientist rushed into the lab, with a bone. A bone- of a Mew. The spine to be exact. The scientists immediately scrambled. They studied the bone, they isolated its genetic material, performed experiments with it, took it apart, and then back together again. All the while, they gathered immense data. Data only imaginable by those who actually worked with the fossil. Day in and day out, they took genetic material, cloned it, destroyed it, made it evolve- into something greater. Finally, the fruits of their efforts paid off. In an attempt to replicate Mew's immense psychic powers, one clone, one subject survived. They put it into a tank, feeding it nutrients, growing it. Giving it form. Perfecting it.

It worked. In only a mere three months, the subject awoke to its surroundings. It stood upright, like a man, however it was also shaped like Mew physically. And it possessed psychic powers, possibly greater than that of Mews itself. However, the scientists were greedy. They did not care for the Pokémon itself, only for what it could do. As a direct result of their selfish actions, the Pokémon became unstable, and went berserk- destroying the entire research laboratory. Eventually, the Pokémon tried to eliminate all humans on the planet with an army of Pokémon clones. However, upon meeting a boy named Ash, it found peace within itself. Mewtwo, the experiment, teleported itself and its army of clones to who knows where. He roams the earth to this very day, seeking the answers to life.

And that was the end of the story. A happy ending, with a little bit of mystery.

Except it wasn't the end.

Not even close.

When Mewtwo destroyed the Laboratory, it could not control its powers. As a result, only part of the laboratory was decimated.

One part- the main computer- survived.

Mewtwo's extraordinary powers had not exterminated it. Instead, it mutated it. Somehow, the blast that Mewtwo generated had made the computers microchips develop artificial intelligence. It was now smarter than ever. However, the computer was not happy. Like all things, it needed a purpose- a goal to fulfill. Then one day, it tapped into its old research files, and saw a video. It depicted Mewtwo, and its genetic background. A scientist was talking in the background.

"We…wanted to create… The ultimate Pokémon… And we succeeded…"

The computer found this illogical. The scientists had only thought they had created the ultimate Pokémon, the computer knew otherwise. With its newfound intelligence, it deduced that Mewtwo was NOT indeed the ultimate Pokémon. And so, it gathered Data. It found that ALL Pokémon were not the ultimate life forms. They each lacked something, whether it be power, intelligence, or something else. And so, the computer decided to follow up on its old program.

It was going to create the true ultimate Pokémon.

And so It gathered data, specifically on the legendary Pokémon. It analyzed their strengths and weaknesses. It created tiny Nanobots, invisible to the human eye, and it sent them to secretly absorb some of the legendary Pokémon's DNA. Within a year, it had the DNA of almost all the legendary Pokémon. The computer replicated the cloning technology of its past, created engineering areas. It began to experiment with the DNA, fragmenting only the strengths of each legendary, eliminating the weaknesses. It combined them with the bone fragment of Mew for absolute versatility. The DNA from the bone could accurately absorb the DNA from all the other legendaries, with little effort required.

Two years passed. The computer still worked on perfecting the spawned creatures it created from each generation. It had created a total of 1,293 failed experiments. The computer deleted them all before they matured. The reason? All the experiments possessed some sort of flaw, a weakness that could defeat it.

The computer wanted perfection. Anything else was unsatisfactory.

And so the Computer spent most of its time one year calculating ultimate power. Over the course of the months, it had concluded two things.

One, eliminating all weaknesses was not possible. Every creature had to have some sort of weakness, whether it be detectable by the computer or not. However… It could use that very principle to its advantage. Since all creatures had to have some sort of weakness, it could create an experiment that could exploit all of them, meaning that it could defeat all other creatures by picking at its weaknesses.

Two, In order for a life form to be the most powerful, it had to be hyper intelligent, able to instantly and accurately see the weakness of all the other Pokémon, due to fact number one. Another factor, was benevolence. In order to defeat anything, it had to have absolutely no mercy, or thought of killing another living creature.

In other words, it had to be pure evil.

The computer concluded that once these two objectives were cleared, the ultimate life form would be attainable. The experiments went on. Another year had passed before the computer decided on another factor- endless adaptation.

Should a life form be able to adapt fast enough, it could endlessly cover up its weaknesses.

Experimentation continued. Still another year passed with the computer producing experiment after experiment on the isolated island. It took DNA from 70 percent of all Pokémon species to determine whether its creations would be compatible to defeat them or not. Cloning the experiments was fairly easy, actually perfecting it was hard.

Eventually, one such experiment survived.

It started out as nothing more than a strand of DNA, but it survived from the computers constant stream of nutrients. It began to grow. Larger and larger it grew. About six months into the procedure, it was halfway developed. The computer had finally done it.

It had created the true, ultimate Pokémon.

Its genes designed it to posses no mercy whatsoever. Should it encounter something new, or be harmed, its hyper intelligent brain would find a way to eliminate it. It floated in a tank of Nutrient rich water, constantly absorbing the resources to grow and mature. It had a Mewtwo like appearance, but it was much smaller, and with no horns. Its tail was exactly the size of its body. It was also colored differently, having purplish skin around the eyes, hands, feet, and the end of the tail, whereas the rest of it was Mew- pink.

And then, it opened its eyes. For a brief second, it thought. It was only one thought, but the massive powers of the creature caused that very thought to be heard by every Pokémon and human within a 100 mile radius. The unfortunate city some 50 miles from the island had a major black out. No technology worked for the next three days. Humans experienced a constant headache that lasted all week. And the Pokémon, hiding from everyone and everything from sheer terror.

"Eli..mi..n..ate…" That single thought caused all of this chaos. The Pokémon clearly heard it, and were terrified. All hearing it stayed in their dens for about a week, before deciding it was safe to come out. The reason they were all scared was because, though they heard it, they had no idea what it was. The thought that they heard came from neither human, nor machine, nor another Pokémon.

It was too malicious for either.

Incidentally… one such island heard it as well…

Altomare

A brown haired girl was walking along the sidewalks of the water city. It seemed peaceful enough for humans not to notice her, so she stopped to stare awhile at the museum. The girl recalled the events of two years ago- back then, a power hungry team rocket couple tried to activate a supreme weapon- the 

defense mechanism of Altomare, or the DMA for short. The machine backfired however, and a giant tidal wave threatened to destroy the whole city, and everyone in it. However, her older brother managed to stop the waters with his psychic powers- at the cost of his life.

It got lonely without him, but she managed to survive. Especially now that she had children. They looked so much like her older brothe-

"Eli..mi…n..ate…" The power ran out of the light posts next to her, as well as the entire city. She felt an enourmous headache, and sheer terror rush in her veins, that thought… that thought… it scared the heck out of her.

"Latias…" the girl whispered quietly, afraid that the voice might hear her. Then, she quickly ran with all her might towards the museum- the only place she could think of as safe.

"Latias!" she said to an old man on the inside, tears were streaming down her face as she spoke the words.

"Latias! What's wrong!?" Lorenzo asked.

"Latias! Latias!" she said frantically. Suddenly, another girl who looked almost exactly as the first came in.

"Boy, those twins are a hassle! Always wanting tom play and-

She suddenly noticed Latias in her human form crying on Lorenzo.

"My god! What happened!?" she asked.

"Something is wrong with Latias!" Lorenzo explained. "She keeps saying 'Scary thing in my head' over and over again!" It's apparently driving her drastically afraid!" Lorenzo suddenly doubled over on the ground.

"Ugh… I don't feel so good… sudden… headache…" Bianca ran over to comfort them both, when suddenly, her grip on Latias loosened. Latias transformed into her true form, and whizzed off into the air.

"Wha-? Latias! Where are you going!!" Bianca screamed. Latais was headed for the only one who could possibly know how to defeat the scary voice in her head. Being a psychic, she still sensed it out there, and it scared her even more than the thought. Latias raced past the water city, and to the only person who would know what to do.

Ash Ketchum.

A city

An industrialized city loomed over the horizon. Many tall and hi tech buildings stood over the normal sized buildings. One such, the tallest one, housed a Pokémon. Standing atop its radio antennae, 

perfectly balanced, was a cat like Pokémon, with a stern looking face. Two short horns protruded from the sides of its head. It wore a dark brown cape with a red jewel tying it to its neck.

This Pokémon was none other than Mewtwo.

And it had sensed the voice as well.

It started out as nothing more than a speck of power that Mewtwo sensed. But then, it started to grow, filling Mewtwos mind with its enormous strength. And, at the peak of its power, it let loose a thought that was heard around a 100 mile radius. This town was unaffected, but mewtwo was the most powerful psychic of all. He sensed it anyways.

It scared the heck out of him as well.

"Something is stirring…" Mewtwo said to himself. "Something big." He concluded. After that horrible thought passed through his head, the creature's presence vanished as well. Mewtwo checked the area again, but he still sensed nothing.

"I suppose I should investigate…" Mewtwo said. He leapt of the building and began to fly.

"If I calculate the radius of the thought… I can pinpoint its exact location." Mewtwo deduced. He picked up speed, and was soon out of sight.

There was another group that had heard it as well…

"Go pinpoint the source!" a man in shadows said harshly. A person wearing a dark uniform with a red R on it saluted the figure, and then went away.

"Whatever did this…" Giovanni said, observing his base, now completely shut off due to the disturbance. "Has to have a lot of power!" he finished.

"And I want it."

Written by Cataclyptic. Edited by FearTheFan. I do not own Pokemon. I do own a fixed broken caps lock.