Chapter 1: Prepare For Trouble
*New Island During Mewtwo's Storm*
"Pikachu!" Ash yelled, bursting free from the water. He didn't let his eyes leave the ball that contained his friend, as he followed Mewtwo's device to the hole across the room where the rest of the balls had gone into. "I'm coming buddy!"
The mechanism above the hole began to lower as soon as the ball with Pikachu disappeared from sight. Ash slid down into the gap, narrowly making it and sliding down into the tunnel. He gritted his teeth and held his hat to his head as he disappeared into the darkness, his mind set fully on rescuing Pikachu.
The tunnel ended abruptly, catching the boy unawares and causing him to flip face first into the conveyor belt. Light shone again and he looked up, scrambling onto the moving surface.
"It's the twerp!" a familiar voice cried. Ash looked up, although he spared only a glance to the three felons standing next to the belt as he regained his balance.
"I don't have time for your dumb motto today!" he deflected, not wanting to hear another word from the useless trio. He lunged at the ball that was disappearing through the arch of the machine in front of him, hands clamping onto the device. Mechanical claws reached down and picked him and the ball that confined Pikachu up off of the conveyor belt, one plugging into the eye-like port on the front.
"Who's that Pokemon?" he heard the trio outside call. "It's Pikachu!" Ash grunted in frustration, biting down on the pieces and yanking, pulling, trying as hard as he could to free himself and Pikachu from the machine.
One of the machine's claws grabbed at his hat, but Ash ignored it and focused on the real problem at hand; saving his friend from Mewtwo's clutches. He felt a claw grab at his hair, and he yanked his head away, feeling a chunk of his hair torn from his scalp. He gritted his teeth in pain, but he continued to struggle nonetheless.
Meanwhile, the arm that held his hair disappeared into the inner workings of the machine with its new sample.
Soon the determined trainer began to make it out, the metal arms snapping as he pulled. Then finally, with a great lunge, he was free. He flew forward a few feet and dropped the ball, which cracked open and disintegrated, leaving his electric mouse friend in front of him.
"Pikachu!" Ash sighed in relief, hugging his friend tight against his body. The machine popped like a cap gun and the Pokeballs Mewtwo had created rained down from the air, being spewed out of where they were being held.
The screens went blank as the connections were cut, but the machine still continued working, slowing down more and more as small explosions wrecked the mechanisms.
"Guys, you're ok!" Ash said, hugging all his Pokemon tight, before looking around at the assembled Pokemon from all the trainers. "Mewtwo won't get away with this. We have to go and stop him and the other clone Pokemon. Are you with me?"
The Pokemon looked at him and nodded, wearing determined expressions. They all filed from the room as one, following the boy. Even Team Rocket followed after a moment, leaving the smoking machine behind them.
They didn't notice the distinctly human looking form that appeared on the main screen.
Whirs and clicks filled the room, soft and steadily building until the main tube bubbled. A curled form was released and fell into the base of the nearest tunnel. The black membrane opened as a pale hand reached out, followed by another and then a head, which opened its mouth and gasped a breath of air. The human crawled from the machine without clothes and felt around in confusion, his vision blurry and unfocused. It hurt to breathe or move; his muscles felt like they had never been used.
"P-Pikachu? Are you there?" he said confusedly, curling into a fetal position on the floor as the coldness of the room overwhelmed him.