This next story takes place after Ash and Misty get back from Hoenn and their near death experience.  The last one (sorry I forgot to tell you) comes between Shockwaves and MM.
The Awakening
By Saliaven Chronotis
Part 1

Chapter 1:
Professor Oak’s Illuminating discovery

    As Ash and Misty swam together off the coast of Palette during one of their breaks, a pidgeotto flew up to them with a message. Ash took it and found that Professor Oak needed them immediately. “I wonder what this is about.” said Ash as they came out of the water.
“Probably another hair brained idea of his” Misty answered, taking off her mask and shaking out her hair.
    They trekked on and eventually came to Professor Oak’s laboratory. They went around back, that being where Oak usually is and yes, there he was. Next to him were Gary and Nurse Joy. “Hello Professor, we came as soon as we could” Misty entered.
“I can see that” said the Professor. Ash and Misty looked at each other and laughed along with everyone else. As they were laughing, a very masculine laugh came out of Nurse Joy and the two realized that it was Brock! “Why are you dressed like that, we have an excuse, you know” said Misty.
“You caught me, it was actually because the girls wanted to see me like this” Brock said.
“I think we should get back to the matter at hand” Professor Oak interjected. “We are here to witness the possible birth of a new pokemon. I have been studying how pokeballs and the environment interact and I think I can use the technology to fuse pokemon. I am going to try for a massive pokemon presence. As you can see, I have over two hundred pokeballs laid out here. They contain every pokemon that isn’t legendary or unique.” The assembled trainers looked stunned and were so speechless that Professor Oak decided to go on. He smiled and said “POKEBALLS GO!” The pokeballs opened and released their energy. They power began to center in one place and when the release was over, the energy didn’t reform into anything.
    Professor Oak took out some instruments and a large monitor. “The information from my scans will show here.” Oak said.
After about half an hour, the screen flickered and started showing categories and actual readings. It wasn’t good. The entire screen was covered in omegas. Ash said “But what’s that supposed to mean?”
“It means that every category registers as off scale.” Oak said, awed like all the others now.
“If it has the combined power and intelligence of all pokemon, why does it just sit there?” Gary inquired.
“Wait! If it does have that power then…transform to um…um…” Ash spluttered.
“Gengar!” Misty yelled. The glowing orb settled to the ground and turned into a Gengar. The instruments settled at a much lower number.
“The component parts must only be partially fused” Oak said.
“Go back to your natural shape” Oak commanded. It complied but turned purple.
“It’s the right shape, but why purple?” Ash said.
Oak thought and then said “Turn into rattata and then back.” This time, the orb was the correct white. “As I thought, it changes color when it changes type.”
“What is to be done with this?” Ash asked.
“I figured that after I had done enough studying on it that I would have a tournament to claim it.”
Ash and Gary smiled “Hey, Ashy boy. Ready to lose?” Gary taunted.
“Strong words from someone who has never caught a legend.”
“You cheated.”
“All is fair when catching pokemon. Other than stealing of course.” And so the pre-tournament preparations began.

Note: I don't.