“Kekeke!” A black form laughed manically. “Keke! Everything’s falling into place. The fool boy took the bait. Now the war will really start getting fun!”
“Don’t be stupid, Weavile.” A creature that looked like a blue anthropomorphic fox chided. “I can’t believe I put up with you. Just one aura sphere, that’s all it’d take…”
“Peace.” A third figure said. “I won’t have you two fighting on this beautiful moonlit night.” This one looked like a deformed human skeleton, with three fingers.
Both Pokemon bowed. “Yes Lord Mewtwo. Of course.”
Mewtwo stared again at the moon, and touched the green silk scarf around his neck, a memory of a partner long since dead. “We shall wait here for Ryhyperior and Hitmontop to return with their report. Then we shall return to camp. But until then, look at the stars and marvel at my sister’s creation. Before we crush it.”

Chap 1: The Fourth Pokeball

The young man strolled casually into the city accompanied by his Absol. They both were tired and weary. The Absol bore many cuts and scratches, several recent, and most bleeding. Without a sound, the Absol stared at the young man.
“Yeah, I’m beat too, Shade.” The youth said. “If we don’t find somewhere to crash, it’s all over for both of us.”
The youth touched the three other pokéballs at his waist. Selecting two, he set out his Typhlosion and his Eevee. The Eevee perched on his shoulder and affectionately nibbled the man’s ear.
“Thanks Chibi.” The man laughed softly. He was glad the Eevee was okay. He had caught it as it was being attacked by a flock of Skarmory, and nursed it back to health. He hoped it would evolve into an Umbreon soon. “Hey, Blaze,” the young man addressed his Typhlosion. “Can you carry Shade for a bit? I think her leg is bothering her again.”
The Typhlosion hefted the Absol in his hands like a newborn child, and the man once again grimaced at the scars on his starter’s back. That Zangoose really got Blaze good…
“Hey!” A man waved from across the street.. “Hey stranger, what’s your name? You better get those Pokemon of yours to a Pokemon Center, and fast.”
“I’m Nick,” the youth replied. “And thanks for your concern. Will you show me the way? I’m new to these parts.”
The man smiled. “’Course I can. It’s right this way. But… if you don’t mind my asking, what’s that fourth Pokemon you got there?”
Nick put a protective hand over the pokéball, as if it might be snatched away. His voice took on a cold, steely quality. “I don’t really think that’s any of your business, now it? What I choose to capture is for me to know, and my foes to fear, got it?”
The vendor held up his hands. “Easy, easy. I was just curious is all. But anyway, my name is Luke. My Ludicolo and I run a bar a couple streets over. If you’re going to stay here a while, you should check it out. We get all kinds of people, you may find out something you’re interested in.”
Nick nodded curtly, and traveled the rest of the way to the Pokemon center in silence.

Nick sat on a bunk in the Pokemon Center, petting Chibi absentmindedly. Blaze and Shade were in the treatment room, and Nick hoped for their survival. If only it wasn’t for you, none of us would be in this goddamn mess! Nick thought angrily at the pokéball on the bedside table. It’s because of you we all nearly died.
Chibi must have felt Nick’s anger, and gave a plaintitive “Vee?”
Nick sighed and scratched the Eevee behind it’s right ear, making it purr. “I’m sorry Chibi. It’s just… why did I bother? What could I possibly stand to gain in all this? If only it wasn’t for those ****ing dreams. Now I have to be on guard everywhere I turn. I don’t want to be in this war, but damn it, here we are.”
Chibi didn’t respond. The small creature had fallen asleep. Nick hugged it close. Blaze and Shade were powerful, but Chibi had so much potential If any of his partners should come to harm, Nick would try to help them, but for Chibi, he would go to the ends of the earth.

Nick awoke from a sleep he didn’t know he entered. A Chansey stood next to his bunk, and beckoned with it’s hand, as if to say, follow me. Nick roused Chibi, and made sure the fourth Pokemon was at his belt. Then he set off down the long, white corridor after the Chansey.
They arrived in an operating room, where a nurse was tending to Blaze. Shade rested in the corner. Both were bandaged, and it tore at Nick’s heart. Chibi jumped out of Nick’s arm and ran to Shade, licking the Absol’s face.
Blaze eyed the pokéball at Nick’s waist and turned away. He puffed a bit of smoke out his mouth, and his back started to glow. Nick put a hand on his partner’s side to calm him down, and murmured. “I didn’t want to, Blaze. But it was fate. I can’t escape it.”
The Typhlosion refused to look at him. Tears welled in Nick’s eyes. “If you would just follow me for a moment,” the nurse was saying. Nick came back to reality as the nurse described the procedure for the medications Shade and Blaze would have to take for the next few weeks.
Screw it, Nick thought. I’ll just have ‘it’ use Recover on them.
That was when all hell broke loose.
The room exploded, or rather, the walls did. Flames danced along Blaze’s back, and Shade stepped protectively in front of Chibi, crescent glowing. From the two holes in the wall, six Pokemon fought each other, three on each side. A Dusknoir and a Charizard grappled. A Gardevior traded psychic pulses with a Mismagius. A strange, tiger-like Pokemon tussled with Ryhorn. Nick whipped out his Pokedex, a tool he hadn’t ever needed, and scanned the tiger-like Pokemon.
“Raiko, the legendary beast of thunder. Resides in the Johto region. No further data.”
No way! Nick thought. That’s impossible.
“Hurry!” The Gardevior said. “To surprised to realize a Pokemon had just spoken to him, Nick called his Pokemon to his side.
“Lady Creselia wants to see you immediately!” The Gardevior said. “Raiko will take you there. Please return your Typhlosion and your Absol to their soul-catchers. The Eevee can probably remain with you.” Nick assumed ‘soul-catcher’ meant pokéball. As he did this, Chibi leapt onto his shoulder.
Raiko disengaged from the Ryhorn, and made his way to Nick. You aren’t much. I don’t see why Azelf chose you. But I rarely know what he’s up to. A voice rumbled in Nick’s skull. Well, let’s go then!
“Are you… talking to me?” Nick asked.
Raiko made a sound that might have been a laugh. ‘Course I am, who’d you think it was? Now, let’s go. We have not got all day!

Raiko raced across the countryside, stopping only once, so that Nick could relive himself. As they ran, Nick asked, “Can all Pokemon talk like you can?”
If you listen close enough.
“I see. So… could Chibi talk to me, right now?”
No. Not at this very moment. But soon, she will be along with those you call Blaze and Shade.
Nick would get no more out of Raiko for the rest of the journey.

That's chapter 1. This is my first attempt at a fanfic, so I'm open to all suggestions