Prologue:
It's been 7 years since Ash won the Hoenn League, and assassinated Giovanni. His surprise move rocketed him to famedom and soon he became a Pokemon Master in the eyes of the adoring public. Gary, however, went missing, and in a couple years Professor Oak and Gary's sister, Daisy were killed in a brutal murder. The Oak Laboratories came into the hands of Gary, who seemingly appeared out of nowhere to claim his prize. Unbeknownst to all, he was planning the murders of his relatives as he built up the remnants of Team Rocket, forming the Rocket Shadow Corporation. He soon added the power of Teams Aqua and Magma through the handling of Archie and Maxie. This conglomerate became the Shadow Co, an organization dedicated to the ideals of Giovanni. Now, they have created a plan so daring, so evil, that even time cannot replay history and stop the events yet to come…
"Who are you?" The tall 17-year-old stared at the man cloaked in black. Around them were the marks of a battle arena in the dilapidated concrete building. The cracks showed where previous battles had left their mark. The boy's red cap was turned backwards and he had a certain yellow mouse on his shoulder.
"Ash Ketchum! I CHALLENGE YOU TO A 1-ON-1 POKEMON BATTLE!" The man yelled. "My Scizor versus your Pikachu!"
'I'm ready for anything!" Ash yelled.
'Go! Scizor!" The man threw a strange Pokeball into the arena. It was marked with a gray band across the middle with a black dot inscribed in the band. The main sphere was purple with black bumps and a gray teardrop shape in the center of the top. The teardrop housed only an S, made with jagged slashes, like those used to create the black X that cut through the orb.
"Team Shadow?" Ash asked, his eyes leering. "Who's your leader?"
"How'd you guess?" The man smirked, ignoring the last comment, and his red Bug type appeared through a laser issued from the black dot. "Scizor! False Swipe!"
"Pikachu! Thunder!"
"Scizor, Counter!" Scizor charged with a glowing bladed fist, while Pikachu countered with a massive bolt of electricity. They crashed in the middle, and Pikachu was sent flying into the wall. Scizor, however, remained intact due to a red aura surrounding it. Pikachu got back up, and ate an orange berry around its neck. An Iapapa Berry. Ash grimaced as the Pikachu began swirling around, dazed, but still a threat.
"Oh no you don't! Scizor, METAL CLAW!" Scizor screamed to Pikachu, its claws glowing gray and white. The Pokemon was sent spiraling, and Ash was knocked out as an after effect. The man smirked again, and called, "Scizor! Now finish Ash off with another Metal Claw!" The claw glowed once more, and this time streaked across the trainer's chest. Ash's body went limp. Amidst the blood seeping out of the former trainer's body, the man drew another Pokeball, quite similar to the one used for Scizor, but instead had a yellow lightning bolt instead of an S.
"Go! Volt Ball!" He chucked the ball, and a laser absorbed the yellow mouse. "Mission complete." He chuckled a little, reminiscing about how easy it was. He drew a multi-colored locket from his pocket, which contained a couple PokeBlocks. He gave them to his Pokemon, and withdrew back into the Shadow Ball. He turned on his headset. The smell of heat mingling with the drying blood was too much to handle. He sighed, annoyed, and pulled his trenchcoat up higher as a filter. He breathed in relief.
"Mr. Oak, its Slice." He spoke into the intercom that was at the collar of his trenchcoat.
"Ahh, Slice. What's your status?"
"I'm still in the Oak Lab. I've taken care of Ketchum. And the Pikachu is in the Volt Ball."
"Good, good. There is a chopper heading your way now. It'll take you to our Mahogany Base. You know the new passcodes."
"Yessir. I'll be there. What about the body?"
"Let it lie there as a reminder that we, Team Shadow, are superior above all."
"Yes sir."
"Good." With that, the link was closed, and the sounds of the chopper grew nearer and nearer. Slice stepped out of the charred building, and watched as the black helicopter landed on the helipad, in the middle of the harbor. Men covered with black and gray and the same jagged S inscribed on their vests jumped out of the vehicle, to secure the location. Slice grimaced, and tossed the Volt Ball to one of them. He winked, and they flew off again, back to Island 7. He tossed a Shadow ball with a purple eye instead of an S into the air, and called forth a Gardevoir. He touched its shoulder, and they teleported away.
xXxXxXx
"Mr. Oak? There are two people here, in white with blue and red hair. Girl and a boy." The intercom crackled to life in the dark conference room. On one end sat the speaker and Gary. He couldn't help but chuckle slightly.
"Send them in Martha." He closed the videolink, and two minions walked in. They sat with their talking Meowth at the other end.
"You call, Boss?" The guy said, his blue hair waving wildly.
"Yes, James. I have a mission for you three."
"A mission?" Now the girl spoke up. She had long red hair, and it was hanging over the end of her chair.
"What mission?" The cat spoke up. It was going to evolve soon, but nobody knew.
"Simple. You'll use the time machine to travel into the past, and talk to Giovanni. Or rather deliver a message."
"Reward?" The cat stopped abruptly as it began to glow white and change shape. It stopped glowing, and looked at itself. "Yes! I'm a Persian!" He purred contently and turned back to Gary.
"That was it." The brunette spoke simply, and the he walked up to them. He fastened a necklace with a timer on it to the cat's neck. It flinched a little, and the other two reached out to grab it. Within seconds, they had all but disappeared.
"Mr Oak, sir?" The intercom crackled to life yet again. "Archie and Maxie are here top see you!"
"Send them in, Marsha."