The Pokemon were all created by the scientists, one scientist had a son, who wished Pokemon were real and the day the boy died; the scientist discovered a way to make his wish come true. They found out about the alpha Pokemon Arceus. They created a machine that look like it's symbol on it's back. The scientist accidently turned the machine on and Arceus came out of it. The scientist told it to make Pokemon, and it did. 

The Pokemon were not kind like in the tv show and in the games, so the scientist was killed, he hoped that someone would be able to discover a way to tame them, but for now they were all sucked back into the machine including Arceus. The story sounded like a lab accident like what happens to superheroes or supervillians in comics and in movies, but instead of getting power, he made power. He was hoping someone would make pokemon and people come together in the future. He wanted his dead son's wish to come true.