Prologue: Opposites Clash
(11 years after Team Rocket were defeated in Kanto, 10 years after Groudon and Kyogre were stopped from destroying Hoenn, 8 years after the Rocket's resurgence in Johto was put down)

"Your next battle will be against Phil and his Murkrow!" announced the referee.

"Fine," replied the boy standing at one end of the battlefield. He was eighteen years old, average height for his age and slightly thin, with dark hair and deep blue eyes. He was wearing a red jacket and long, baggy yellow and black trousers.

The first Gym of the Champions' League, here in Adelta Town, was going to be more of a challenge than he had originally believed. Although the first two junior trainers he had battled were easy to defeat, his Pokémon were getting tired, and he still had one more trainer to deal with before he reached the Gym Leader.

"Please send out a Pokémon," the referee said. The boy nodded, and took a small red and white sphere, a Pokéball, from his belt.

"Go, Ampharos!" he yelled, throwing it into the centre of the arena. It cracked open in a flash of light and a tall yellow Pokémon with a bright light on its tail and black stripes along its neck and tail materialized. It looked at the room around it.

The Yellow Room, designated for former Champions taking the Champion's League Challenge, was painted, appropriately enough, yellow. But, after a few years of battles, the walls were covered in stains ranging from impact craters, to scorch marks, to blood spatters. A standard battle arena, a rectangle bisected by a line halfway along its length, was painted in white on the wooden floor. There were no windows; so several lamps on the ceiling lit the room. Overall, the room was barely wide enough to hold the arena, but the ceiling was too high for humans. Of course this was to allow for the largest Pokémon.

"The battle of Hiro Sirit against…" started the referee.

"Gold, if you please," the trainer interrupted.

"Very well, sir," the referee sniffed with annoyance. He raised his flags into the air. "Gold against Philip Auris, begin!"

"But he's not here," Gold noted.

"But I am," came a voice from the shadows in the corner of the room. Somebody stepped out of them. He was similar to Gold in stature, but he was clothed in a pale T-shirt and jeans and his hair was as black as the Pokémon on his shoulder. It was a Murkrow, a small black bird-like Pokémon commonly associated with misfortune. Phil had a wry smirk on his face. "Shall we begin?"

"Krow!" shrieked his Pokémon. It took off and flew into the arena, while Phil moved to position directly opposite Gold.

"Thunderbolt!" Gold ordered, to get the battle going. Ampharos glowed as electricity built in its body, and then it discharged. Lightning forked through the air towards Murkrow.

"Faint Attack!" Phil commanded his response. Murkrow faded from view, and the Thunderbolt swept through empty air, eventually impacting a wall in a cloud of dust and paint particles.

"Amph?" wondered the confused Ampharos, as it glanced around the room, looking for Murkrow. Then the air behind it shimmered. Murkrow rematerialized in mid-air directly behind Ampharos and immediately began attacking with its wings.

"Murk-k-k-k," Murkrow chuckled. Ampharos took the punishment as it was still recovering from the surprise of the attack.

"Iron Tail!" Gold yelled. He had to get that bird off of his Pokémon's back. Ampharos was his best Pokémon, and he couldn't let it fall before he reached the Gym Leader.

Still under a flurry of blows from Murkrow, Ampharos was able to muster enough strength to do something. Its tail began to glow, and it suddenly leapt forward, out of Murkrow's reach. The bird attempted to catch up and renew its attack, but Ampharos quickly swung around 360°, smacking Murkrow with its tail and sending it tumbling through the air.

Hiro looked up at Phil, expecting him to be panicking, or at the very least concerned. But instead, the other trainer was apparently unfazed.

"Murkrow, get yourself together," he groaned with a roll of his eyes. The Pokémon flapped its wings to steady itself, and it quickly turned to face Ampharos once more. "Good," Phil continued, "now Drill peck it!"

"Thunderbolt!" Gold exclaimed. Now he was the one panicking. Calm was important in battling, but it was hard when your trusted friends were on the line. Hiro took a deep breath and watched.

Murkrow was spinning faster and faster as it approached Ampharos, and in return Ampharos was charging up another attack. It released the bolt moments before Murkrow impacted. The bird was lit up with light, but it kept going and smashed into Ampharos. The force of the attack sent the larger Pokémon sprawling into a wall. As it struggled to get back up, it was obvious it was exhausted. Murkrow wasn't much better. It skidded across the floor, twitching slightly as the last few bolts of electricity left its body.

"Ampharos!" Gold cried out. He couldn't let Ampharos be knocked out. Perhaps some rest in a Pokéball while another Pokémon dealt with Murkrow was better. He took two Pokéballs out, one of them Ampharos' the other belonging to his next Pokémon, Sudowoodo. "Return!" he said, with his arm outstretched, pointing the Pokéball at Ampharos. A beam of light shot out, aimed directly at it.

"Not so fast!" Phil interrupted, "use Pursuit, Murkrow!" Murkrow, who had been barely able to stand, even with support from its wings, suddenly burst forward with an energy that had seemed to come from nowhere. It entered the beam even as it hit Ampharos. Both of them transformed into light and were sucked into the Pokéball. A few seconds later it began shaking violently.

"No! Ampharos, hang in there!" Gold pleaded to the ball. The vibrations quickly got so bad that he had to drop it to the floor. Gold could do naught but watch. It was the first time he'd seen Pursuit effectively deployed. After a few moments the shaking stopped, and he went to reach for the ball. Just then it exploded open, throwing him back, and Ampharos and Murkrow onto the arena.

"Muurrrk!" Murkrow groaned, giving a sarcastic salute to Phil before keeling over, completely drained. Ampharos said nothing, and fell in a heap upon the floor.

"All of Philip's Pokémon are out, Gold wins!" announced the referee, with his flag raised towards the challenger, who was rubbing his head after getting up off the floor. The two combatants recalled their Pokémon in silence.

"I achieved my goals," Phil suddenly said, "I weakened your team, so that you will be easier for my Gym Leader to defeat"

"You ordered your Pokémon to continue, even when it was clearly close to collapse. Why?" Gold asked. He was walking across the arena to the door that led to the Gym Leader.

"Whatever your relationship to a Pokémon outside of this arena, once you are in battle they are merely a means to an end," Phil replied, fiddling with Murkrow's Pokéball. Gold stopped just in front of him.

"You can't think that!" said Gold, shocked at this coldness. He looked into Phil's eyes, and he realized that that was exactly what Phil felt. Then he noticed something deeper, something that he had never seen before yet was very familiar, a strange darkness penetrating into the depths of Phil's heart. Gold looked away, and it was gone.

"The light…" muttered Phil. Gold looked up again and saw the other trainer was staring straight at him. "Never mind," Phil said as broke his gaze. Then, in a voice infused with sarcasm, he continued, "have fun against our Leader…" After saying those words, he put Murkrow's Pokéball on his belt and then marched towards the exit. Gold watched him leave. There was something about that trainer… He shook his head; he was probably just imagining things. Turning back to the door, he steeled himself for the next challenge, and then opened it and stepped through.