Note: This is manga-universe, it is not recommended to read this if you have not read the manga, thought it's possible.
Summary: Two weeks before Red's Birthday to 17, he disappears training in Mt. Silver, worried for his friend Blue searches for him, only to disappear himself. The fact that the two most powerful trainers disappeared stressed the third strongest trainer, the third original Pokedex owner, Green, who is now forced to lead a search for her two friends, who she knows for a fact were attacked.
Confrontation at Mt. Silver
Red was training in some of the highest planes in Mt. Silver. It was summer, not even in the highest peak on Mt. Silver, the coldness Mt. Silver in the side of Johto didn't affect the much hotter areas of Kanto. The sun was hot, drops of sweat dripped from his forehead hitting the ground. In the rough plain there were ten, massive, aligned borders.
"Saur, use your Solar Beam right at the center of the boulder."
A beam of light shot out of the Venasaur's body, shooting right at the aligned boulders, and after another each boulder practically exploded. When the last boulder was blown to smithereens Red couldn't help but smile.
"You did well Saur!"
"Saur!" the Pokemon responded happily.
He returned his Saur back to his pokeball. He feel his Pikachu's constant moving from shoulder to head to shoulder.
"You wanna give it go Pika?" he asked as he noticed it seemed excited.
Pika jumped off his shoulder to the ground, landing as if it had gotten off a chair and it was surrounded by electricity due to it being excited. No, Red
realized Pika looked wary, suspicious as its ears perked, looking around.
He felt it too. Someone was here. He didn't want any trouble. It had been only two months since the Battle Frontier Incident. He smiled, remembering the tournament after the incident but his thoughts were interrupt by Pika jumping back on his shoulder, slightly unprepared he slightly took a step back but was initially fine.
What happened next happened quickly. The ground broke, a massive Onyx-like Pokemon came out. A Steelix Red quickly recognized. Immediately, Red's Snorlax came out. The large Pokemon thought not larger than Steelix easily held the massive steel type in it's track.
"Snor, use Headbutt!" the powerful Snorlax immediately tackled the Steelix with it's head. Although Red clearly saw his Snorlax getting hurt by Steelix powerful defense, Steelix was forced to slither back. The Steelix remained still for a moment, so did Red's next order.
Then the Steelix tackled the Snorlax again.
"Now, Mega Punch!" the Snorlax threw it's punch at the Steelix as it literally flew for a second before falling to the ground, fainted.
"Impressive." a voice said behind him. He turned around. He could feel the darkness in the area. His Pika seemed to shiver on his shoulder. Red could hear the heavy footsteps of his Snor walk slightly towards him.
The one who spoke was a girl. Probably 16, around his age, she wore overly expensive cloths to be in Mount Silver, a dangerous area, her eyes were a intimidating dark-brown. Her hair was long and blond.
"Of course if you had lost to that Steelix it would be embarrassing, Champion Red."
Before Red could react she took out an empty Pokeball and withdrew the Steelix behind her.
"That was yours?" he asked curiously, yet with a stingy voice considering the Steelix had attacked him.
"Yes. I must say I was impressed how you handled-"
"Your Steelix attacked me." Red replied, cutting her off. His tone visibly annoyed.
The girl frowned. "Yes, I know, I ordered it to-"
"My, I see you don't want to talk." she said in a mocking tone, "Fine. Be that way."
She threw a Pokeball.
"Nidoking use Focus Blast!" an odd aura formed around the Nidoking.
"Snor use Double-Edged quickly!"
For such a big Pokemon, Snorlax ran quickly, and it showed no mercy to Nidoking as it hit with strength, Red visibly felt the shake when Nidoking fell to the ground, fainted. The girl took returned the Nidoking to her Pokeball, with a frown.
"Who are you?" Red demanded.
"Even such powerful Pokemon like Nidoking and Steelix beaten by a single punch....." the girl muttered. Red was slightly worried who this girl was now. It was clear she wasn't friendly. He was about to demand her name again but she reacted quicker.
"Magmar!" the red bipedal, tailed Pokemon appeared, it's flames blazing. Red wasn't risking Snorlax fighting three times in a row.
"Poli!" Red's Poliwrath appeared. Red's first Pokemon.
"Thunder Punch, Magmar!"
The Magmar charged, quickly, with speed.
"Poliwrath, Hydro Pump!" Poliwrath shot the powerful moved it had learned just weeks ago, the powerful burst of water straight at Magmar.
"Protect!" the girl cried out instantly. The Magmar stopped and put both it's hand forward in an x formation. The Hydro Pump initially hit the Magmar, which seemed to not even be bothered by it. But it became clear Magmar was no where near Poliwrath's level as it was pushed back, and then falling on the ground beaten.
The girl returned her Pokemon, grumbling something.
"I ask again; who are you?" Red asked slowly.
"None of your business!" she snapped. Red felt it then, the growing darkness around. No, the growing darkness everywhere, coming from her.
"I'll have to use this Pokemon after all." she mentioned. He didn't see her carrying any more Pokeballs. Or was she hiding it?
Then he saw it. The shadow of her. It was changing. Her shadow literally stood up. Like as if it were a 3d person which was laying and simply stood up. Then it changed form as it stood behind the girl. The girl didn't seem happy about it but she later smiled, it was a devious smile at that. The thing behind her grew more, and it looked like it was her shadow. Which it was.
The shadow gained shape.
It looked like it was her shadow rising, but it wasn't her shadow, yet it seemed like it was her shadow. A large, gray, centipede-like body. It has a tail and a thick black stripe running vertically along the front of its body. There is a series of red horizontal stripes running across the large black one. Three gold half-rings circle the back half of its neck at the same points that three of the red stripes are at on its front, resembling a ribcage. On its back are two large, black wings that are decorated with red, conical objects that also could be claws.
Red is strong, especially in Manga. He could take on a one of the Three Birds, or the Three Dogs, probably Ho-Oh and Lugia too. But he didn't beat Deoxys, only with Mewtwo's help...any questions just ask and I'll answer.