Chapter II: Glitch City
"Where?" Deoxys asked, confused.
"This is the home of Missingno." Dialga explained. "That's why there are static beings and question marks everywhere."
One made an odd sound to them as if greeting them.
"Er, hello?" Dialga replied.
"Krrpstatpafon" The being said.
"Huh?"
Suddenly, there was an explosion. The Missingno. started rushing everywhere in a panic, and then it was dark. It was silent as a red beam burst through the darkness and an unfamiliar being appeared at the bottom. Ho-Oh flew up to the clouds and incinerated the darkness, only to have it come back. While Ho-Oh was still in the sky, the red beam blasted him in a flash. Ho-Oh dived head-first into the planet. Deoxys quickly turned to its Speed Form and dashed towards where Ho-oh would soon land, while he could see where he was going, and used a non-offensive form of Psycho Boost. It cushioned the fall, and Deoxys set Ho-oh down gently; he then shot to where the red beam originated. He turned to his Attack form and charged up a Hyper Beam, which, just inches away from the thing, almost fully charged, faded.
Dialga shot a Flash Cannon at the sky to light it up enough, while Deoxys stood there, limp, for a while, as if being choked. Dialga then noticed that he wasn't being choked, but his energy was being drained. Dialga lurched towards the shadow and prepared another Flash Cannon. The shadow looked at him menacingly, and then faded away. Dialga's Flash cannon went through nothing and exploded. Suddenly Dialga felt weaker and weaker, until he fainted. He wondered where Groudon had gone before completely blacking out.
Groudon awoke in a daze. He heard very loud crying, but the room was dark. He shook his head hard and shot a Fire Blast strait up, destroying the ceiling. Groudon then used Drought, destroying the darkness. He saw the babies: Mew, Jirachi, Manaphy, and Phione. But, where was Mewtwo? He had to be around here somewhere. He pulled the babies up onto his back after comforting them and quieting them down, and then looked around for Mewtwo.
The light disappeared as he went farther in wherever he was, until he heard faint echoes. Groudon jerked his head in the direction of it, and Manaphy whimpered. Suddenly, a purple ball whizzed past his head as he barely dodged it. He looked in the direction that the ball came from, and saw glowing blue eyes. Familiar eyes. Groudon set the babies down and told them to go to a safe distance. He saw another ball glowing in the hand of Mewtwo as Groudon prepared himself. It was too dark for a SolarBeam, which would be perfect for destroying a Shadow Ball, so Groudon had to think fast, because Mewtwo's Shadow Ball was coming straight for him.
The ball was too quick as it nailed him in the chest. Groudon flew backwards. He had never realized how strong Mewtwo was. Mewtwo was floating above Groudon, their faces inches from each other's. Mewtwo was gone. Groudon could tell; the life in his eyes was gone, replaced by a horrible icy-cold blue. Groudon couldn't bear to look anymore. He heard Mewtwo say in an in-human voice:
"Goodbye."
Groudon sat there, waiting for death, but it didn't come. He opened his eyes, and Mew was before him, projecting an Aura Sphere to match Mewtwo's. But Mewtwo's was too strong, and it blew them both back. Groudon lay sprawled on the floor again, as he watched the brothers fight. It was unbearable to watch them fight like that, and Groudon wouldn't stand for it. He got up, he couldn't hit Mewtwo, for fear of hitting Mew. He looked around for the other babies. He found them in a corner and scooped them onto his back. He looked back at Mew and Mewtwo. Mewtwo had the upper hand. He could tell how much it hurt Mew to fight its brother like that, and Mew finally gave in.
Mew lay face down on the ground as Mewtwo prepared to finish him with a Shadow Ball. Groudon acted quickly. He blasted a powerful Eruption straight up, and when Mewtwo was briefly distracted, he dashed forward and Slashed Mewtwo across the face. It shocked him enough for Groudon to snatch Mew and get away. He had no idea where he was, he just knew that if he kept running, he would escape.
Deoxys and Palkia ran franticly away from Kyogre as he rampaged after them. The shadow had gotten to Kyogre, and something awful had happened to it. Deoxys grabbed hold of Palkia to Teleport out of the way of an Ice Beam. Deoxys had Teleported them behind Kyogre, and in the moment that Kyogre wondered where they went, Deoxys blasted it with a Psycho Boost as Palkia aided with an Earth Power. Kyogre writhed in pain at the powerful attacks and fell to the ground. Palkia suddenly realized that Kyogre hadn't intended to hurt them.
"What should we do?" Palkia asked Deoxys.
"I don't know," Deoxys said anxiously, "we should probably look for Lugia, but who knows what else could happen to Kyogre?"
"I'll stay here with Kyogre. You go find Lugia," Palkia said finally. Deoxys nodded, and disappeared.
Deoxys reappeared back at the place where they had last seen Lugia: Above the darkness where It was light enough to see. The sky was even darker now, and it took several Hyper Beams to clear it, and even then, it was only light enough to see a hand in frond of a face; and Deoxys was exhausted. He looked around. The darkness was creeping back, and Deoxys couldn't manage another Hyper Beam, so he looked around quickly for a sign of Lugia—or anyone. He saw nothing. Nothing, except the shadow. Deoxys was ready. He wouldn't be taken like his best friend was. He gathered what energy he had and stored it.
The shadow gathered in front of him and created a physical form. It was torture to look at him, like his eye contact could kill. Deoxys closed his eyes and remained calm.
"Who are you?" Deoxys asked fearfully.
"I am the one who defied. . .the Banished One." The shadow replied.
"Banished One? What does that mean?"
"The one who defied your so-called 'God',"
"Does that mean that you're. . .?" Deoxys was unable to finish before being completely immobilized, as he slowly began losing his life.
"Your life is delicious," the shadow rasped. Deoxys knew it: he would die as his best friend had. It took all his strength to open his eyes, and even then, it was torture. He closed them again, for the last time, as the world around him slowly faded away.
Dialga awoke in a cold sweat after what seemed to be a nightmare became a horrifying revelation: Deoxys had been killed. Killed by the horrible shadow. Dialga sat up. He knew where he was: he was in the same place he had been before blacking out. Consumed in darkness, the land before him was invisible. He shot a Flash Cannon once more at the sky, partially destroying it. Dialga didn't know what else to do. He called out to Arceus, called for help. Arceus appeared before him, dispelling the light and replacing it with a warm, happy feeling.
"What was that thing?" Dialga asked.
"Malunus," Arceus replied.
End of Chapter II