I wish I owned Pokémon and/or Naruto. World Domination would be mine!

XXX

"Raaaaaah, where is he?" A twelve year old Naruto sat slumped in his chair, loudly moaning his complaint. His head rested on the classroom desk in front of him. In the same room were Sasuke and Sakura, both thinking along similar lines. It had been over an hour since the other jounin sensei had picked up their teams, but theirs still had yet to show. Even Iruka-sensei had left due to there being a curriculum meeting that afternoon. Supposedly, it was set for a time after all the gennin should have left. Naruto's patience finally reached its breaking point, so he got up and headed for the door.

"What are you doing, Naruto? We're supposed to wait here until our sensei comes for us." Naruto stopped and turned towards Sakura.

"Oh, come on." He pleaded, "This is stupid. We've been waiting for forever, and I want to do something fun."

"You can't just leave, especially not for one of your stupid pranks."

"I can, and I am. Now, you two can either come with me or stay here and keep being bored out of your mind." With that, Naruto opened the classroom door and walked out. Seconds passed in silence until Sasuke too left his chair and the room. Sakura stayed in her seat, unmoving for a moment, while a debate raged in her mind. Finally, she followed the two boys' example, not wanting to be left out.

XXX

"Get back here!" Naruto laughed as he sped away from the shinobi hot on his tail. Following just behind him were Sasuke and Sakura. They had almost finished booby trapping one of the western guard posts with itching powder when one of the packets detonated prematurely, alerting the chunin within to what the three were up too.

The chase continued until both parties reached the ring of forest surrounding the village, just inside the protective walls. Naruto saw his chance when they entered a particularly dense knot of trees, causing their pursuers to lose sight of them temporarily. He toke advantage of this by quickly creating three Kage Bushin and transforming two to look like Sasuke and Sakura. His teammates saw what his plan was and took cover within a group of nearby bushes. The clones took off, leading the unsuspecting chunin back towards the village.

Once the forest had grown quiet, the originals came out of hiding, catching their breath.

"See Sakura, we make a great team already." Her response was a sharp blow to his head.

"You idiot, what's great about almost getting caught?" Naruto cradled his injured cranium, a large bump already forming.

"You triggered the powder too early on purpose." The two turned towards Sasuke. That had been the first sentence he had spoken all afternoon. The orange clad ninja nodded, even though it was more of a statement than a question.

"Yeah, 'course I did. The chase is the best part of a prank. What's the point of doing one if no one even knows it was you?" Naruto and Sasuke looked at each other, and an unsaid conversation seemed to pass between the two. That fleeting moment ended almost instantly, and Naruto smirked. "Was the little run to much for you?" The Uchiha glared at him but didn't say anything, instead grunting and deciding to recline against one of the many trees nearby. Sakura felt out of place, not understanding what had just happened, and unsure of what to say or do. She made up her mind and turned to head back into town. Hopefully their sensei was finally at the Academy by now.

"I wouldn't do that if I were you." Naruto said when she started to leave. "Those guys will still be looking for us for awhile. They don't know when to call it quits." An idea popped into his head and he sauntered up to her. "So, Sakura, since we have some time to kill, you wanna-Gaaahh!" He had reached out an arm, wanting to place it on the trunk she was standing near, in an attempt to try to look cool. He did not count on his arm passing straight through, the rest of his body tumbling in after it. Sasuke's and Sakura's heads whipped around to where Naruto had suddenly vanished.

Their bodies tensed, not understanding quite what had happened, each trying to keep their senses alert in case they were under attack. Moments went by, and there were no signs of immediate danger. Slowly, Sasuke headed for the tree as Sakura started to examine it.

"I've never read about anything like this. It looks to be a sort of localized genjutsu that only affects this one tree." She said, puzzling over the strange phenomenon. "But why would there be a genjutsu on a tree trunk,"

"And where is the person casting it?" Sasuke finished for her. They continued their observations when Naruto's disembodied head suddenly appeared right in front of Sakura's face.

"Boo." She screamed and fell back onto her butt. Naruto's head began to laugh uproariously. "Ha ha ha ha ha ha ha ha, you should see the look on your face Sakura." The rest of the blond's body appeared as he stumbled out of the tree, holding his sides because he was guffawing so hard. He eventually composed himself and motioned for the two to follow him. "Come on, don't you guys want to see what's in here?" Naruto once more disappeared into the trunk. After a few moments of silence, Sakura was the first to follow after getting up off the ground with Sasuke right behind her.

The two found themselves in the somewhat cramped interior upon entering the tree. Looking around, they saw nothing that out of the ordinary.

"What are we supposed to be looking at, loser?" Sasuke questioned. While the genjutsu had been peculiar, nothing so far had seemed to be worth such an investment. That was when a short blink of red light caught his attention. Sakura saw it as well, and both of them squeezed closer to get a better look. The flash had come from a medium-sized button at about chest height on an adult.

"What do you think this does?" Sakura wondered out loud. The boys shrugged, not knowing themselves. "Naruto, press it." Said genin reeled back.

"What, why should I be the one to press it?" She smirked at him.

"Because you're the one that found this place, so you should get the honors."

"No way, you press it yourself!" He demanded.

"Are you kidding me? I'm not going to press a random button we found hidden in a tree. Come on Naruto, be a man." Sakura tried to goad him.

"Ladies first." He countered. Their back and forth bickering continued, neither willing to let the other have the last word. Finally, being fed up with his teammates attitudes, Sasuke pushed past them and slammed his palm against the button.

The moment he did, the wooden floor they were standing on began to drop, carrying them down below ground at a frightening speed. After a few seconds, all three were knocked from their feet by the platform's sudden deceleration. They groggily rose; the unexpected fall had taken its toll on them.

Naruto, Sasuke, and Sakura looked around the space. After the decent, they were still in the same small area, except now their only source of light was the flash from the button every few seconds.

"Well, this sucks." Naruto said. "We just found a hidden whole in the ground with nothing in it." He lazily kicked at one of the sides to prove a point, expecting to hit wood or dirt. Instead, a metallic clang rang out. His curiosity was peaked once again, and he squatted down were his foot had connected. The next instance of red light brought a surprise.

"Hey, guys, I think there's a door here." He placed his hands on the metal and moved them around, trying to find a way to open it. "Damn it, where is the handle?" The other two quickly joined his search. Again, the only light source brought an answer.

"They're sliding doors." Sasuke stated, seeing the the straight line dividing the curved wall into two parts. Setting his feet, he wiggled his fingers in to the crease and pulled with all his might. His side of the door gave way slightly. Gritting his teeth, Sasuke grunted out, "Grab the other side." Naruto paused for a moment. Sasuke had actually just asked him for help. He decided that gloating could wait until later and grabbed the other door.

A rusty screech and the grinding of gears was heard. Together, the two boys slowly pried the doors apart. Dust showered down, dislodged from its resting place high above by the movement. They finally came to a groaning halt, unable to open any further, and the sounds were swiftly engulfed by the darkness surrounding the genin. Seconds passed while Naruto and Sasuke regained their breath.

Their forced entry must have triggered something, for lights began to slowly flicker to life, one by one, bathing the area in a soft glow. It was not much, barely enough to see what was in front of them, but anything was better than the blackness to them. Before the children was a large, spacious cavern. Metal panels covered the walls and rounded ceiling. The floor was made of dirt, and had strange, white lines outlining a section of it. A muted whirling reached their ears, like the sound of machines turning on.

Naruto entered the room first, followed closely by Sasuke and Sakura. They gazed around in wonder. None of them had ever heard of such a place existing below the village. As they commenced their exploration, Naruto felt the hair on the back of his neck prickle. Something in the back of his mind told him to get out of there, but he shook his head and forcefully pushed the feeling away.

The three soon found three other doors like the one they had just come from. The one on the left side led to what seemed to be a living area. Inside were a good number of beds, two bathrooms and a kitchen. The right side room only had an odd looking machine with a glass dome inside. Other than that, it was empty, so they left and approached the final doorway, directly across from the lift.

"Leave this place."

A menacing voice resonated within Naruto mind right as the three were about to pass through the opening, and they froze. He turned towards the other, his hands twitching nervously.

"Please tell me you guys heard that too." Sasuke and Sakura nodded, the blonde letting out a shaky sigh of relief. From their faces, Naruto could tell they were just as nervous as he was.

"M-maybe we should go back." Sakura stuttered. Naruto saw a chance to play the hero and put on his brave face.

"No way. We're going to be doing stuff like this all the time now that we're ninja. I don't care what that stupid voice in our heads tells us; I'm going through." He grinned at the pinkette, and she felt her fears abate slightly. They formed an even tighter group and began walking forward again. The three approached the last door, and Naruto felt the feeling from before return, commanding him to turn back. His resolve was only steeled by this. It was obvious there was something hidden in here, and Naruto was determined to find out what it was. Besides, Sasuke and Sakura were not, so neither would he.

The final room was the weirdest of them all. The front and back walls were lined with bizarre devices, covered in pulsing lights, and emitting random beeps and chirps. On each side were multiple shelves, lined with hundreds of red and white balls that were about the size of a person's palm. The strangest part, though, was the creature near the back of the room.

Contained inside of a tall, glass tube, it sat suspended in a reddish-orange liquid. Wires fed from the top and bottom of the vessel were attached all along its body. Its color was difficult to discern because of the low light and fluid, but the creature's stomach and tail were definitely of a darker hue than the rest of its body. Three fingered hands ended long, lanky arms crossed over its chest. Powerful, bulging legs were tucked up close to the body. The thing's head had a vaguely feline shape to it. Its eyelids were down, and the face had a peaceful look on it, as if it were in a deep sleep.

Sakura let out a gasp at the sight of it, and all three stood staring in amazement. None of them had ever heard of such a monster. They realized at the same moment that what had started as a simple exploration of a mysterious tree was now far over their heads. They had to get out now and tell someone about this.

Before any of them could even twitch, the creature's eyes snapped open, a brilliant blue flame burning within. A piercing feeling seemed to lance directly into their brains, and the group fell to their knees, clutching their skulls in pain. Naruto could not remember anything hurting this badly. It was like something was trying to tear his head open from the inside. He could not move; his body refused to respond to any of his desperate orders. Every second became an eternity, until all three of them reached their breaking points.

"STOP IT!" They cried out, a deep power resonating in each voice. The fire in the creature's eyes died, the torment ending along with it. It blinked in confusion as it stared at the genin from within its clear prison.

The pain had gone, only to be replaced by a horrible exhaustion. Naruto's body felt weak, his limbs like lead. He fell forward onto his hands and threw up onto the floor. Naruto hazily heard the retching sounds of Sasuke and Sakura following suit. He could feel what little energy he had left rapidly dwindling away.

"Quickly, chose one of these and press the middle button." It was the same voice before, ringing in the blond's mind. Three of the orbs from the right side wall floated down and settled in triangle in front of him. "Do it now!" The voice ordered. Acting on instinct, Naruto slowly reached out, his arm drawn to the one farthest from him. His hand cupped it, and he did as he was told. With a distinct pop, the sphere split apart. The final thing Naruto saw as he fell into unconsciousness was a white shape springing forth.

XXX

Warm. That was the first thought of Sasuke Uchiha as he started to come to. On his right side he could feel a cozy warmth radiating onto his torso. His whole body felt relaxed for the first time years; he had not rested this comfortably since the night before the massacre five years ago. Reluctantly, Sasuke forced his eyes to open. The first thing he saw was the monster from earlier floating cross-legged in the air, a blue aura enveloping its body.

In panic, the Uchiha leaped out of the bed he had been lying in and threw a handful of shuriken at the creature. He noticed that as soon as he did this, the warmth he had been feeling was gone, but he put that aside for now. Sasuke was shocked when instead of hitting the creature, the shuriken simply stopped in mid air, inches from its face, then fell to the ground.

"Calm yourself. I mean the three of you no harm." Realization jolted Sasuke's mind in response to the voice in his head. This thing was what had been communicating with them before. At the mention of three, he glanced to his left and glimpsed the rough outlines of Sakura and Naruto lying on beds of their own. Sasuke quickly refocused back towards the monster. He had no reason to trust that it would keep its word.

Minutes passed. Neither one moved a muscle, letting silence reign in the room. Movement in the corner of Sasuke's eye caught his attention; it was not one of his teammates. On his bed was an odd, orange colored lizard with a fire burning on its tail. If that last fact bothered it at all, the reptile did not show it. It only stretched out and then curled up into a tighter ball. This would normally have caused Sasuke to be even more on guard, but his gut was telling him it was no threat. Besides, he had bigger problems at the moment. Namely a giant humanoid cat which could hover and stop Sasuke's weapons without opening its eyes.

A feminine shriek alerted the raven-haired boy to Sakura's awakening, and it seemed she too had an unwelcome guest in her bed. She was instantly at Sasuke's side, clamping herself to his arm. He roughly shook her off without any hesitation. This was no time for coddling a frightened girl.

The pinkette's scream woke Naruto up. He repeated Sasuke's earlier actions, except with a kunai and a shout of "What the Hell?". The result was the same though. After the failed attack, the creature dropped to the ground and stood up straight, displaying its staggering two meter height to the children.

"Now that you are all awake, how did you three find this place?" Naruto's jaw dropped.

"Did that freaky thing just talk?"

"W-we were in a forest clearing wh-when we found the entrance and d-decided to look around." Sakura was able to stammer out as she cut Naruto off before he could say anything that would make the thing mad. The creature frowned.

"We were not meant to be awakened yet. Your exploration has set things in motion which cannot be undone." By now, Naruto's courage had returned, and he pointed an accusing finger at the anthropomorphic cat.

"You're mad at us for waking you up? You're the one who made this place so easy to get into and then attacked us for no reason." The blond jinchuuriki shouted, but his previous confidence withered under its harsh glare.

"This vault was hidden deep below a dense forest, with the only entrance being through a two-inch thick steel door, as well as multiple psychic barriers in place throughout the facility to prevent the random passerby from stumbling into here. If they are still able to gain entry, my semi-conscious self would continually place powerful suggestions within said person' s mind to leave, while also manipulating their memory in order to assure them they were simply here in a dream. Should all else fail, a full scale mental attack would be unleashed upon the intruder to disable and forcibly remove them from the area. Not only were the three of you able to bypass every countermeasure, you did so using something that should no longer exist." Sakura hesitantly rose her hand up, like she was asking a question in class.

"What was it that we used?" She quietly asked. The creature looked up towards the ceiling. Memories of a time long gone flashed through its mind before it answered.

"The Power of Dominance. The ability to control Pokémon."

The statement was underwhelming for the genin, for they had no idea what that was. Seeing their confused expressions when it looked back at them, the monster continued to speak.

"Do you know what a Pokémon is?" Each shook his/her head no, so he elaborated. "Long ago, creatures known as Pokémon once roamed this world. I am Mewtwo, the Genetic Pokémon." Mewtwo's eyes flared and three forms were carried from the beds and set in front of the psychic. Among them was the orange reptile Sasuke had seen earlier. He indicated at that one first. "This is Charmander, the Flame Pokémon," The middle one was on all fours, with a stubby little tail at the back and a strange off-white color to it. Around its neck was ring of tiny, green bumps. Sprouting from the top of its head was a large leaf. "Chikorita, the Leaf Pokémon," The last one on the right also had four legs, but was blue and had a large fin for a tail along with one on its skull. It had odd, orange projections on its cheeks. "And Mudkip, the Mud Fish Pokémon."

"What does this have to do with the power you were talking about earlier?" A hint of annoyance found its way into Sasuke's voice.

"Had it not been for them, all of you would have died." Each child's eyes widened at that. "You three awakened the power inside of you to halt my mental assault. However, the Power of Dominance can only be used on Pokémon who have acknowledged you as their partner. After using its strength for the first time, my body rejected your hold on it. That left the power with nothing to anchor and stabilize itself too, so it began to drain from your bodies, searching for anything that it could bond with. There are only nine Pokémon species in existence able to instantly forge a connection between themselves and a human. By your actions this day, for the first time in a thousand year, humans and Pokémon are now bound together once again."

XXX

Deep within Naruto, a beast stirred. The Kyuubi cracked open a massive eye , roused from its slumber by Mewtwo's onslaught. Anger surged forth at the sight of a cage door in front of it. The tailed beast let loose a roar and slammed a mighty paw against the bars. Onward it raged, crashing against every side of its new prison, refusing to accept the futileness of its actions. Eventually the fox calmed as the burning fury turned back into a cold hatred.

Now level-headed, the nine-tailed behemoth started exploring its new jail, testing the limits of the seal. It soon discovered that the dregs of its chakra leaking out allowed the beast to access its host's memories and senses. The Kyuubi looked through the memories first in search of anything it could exploit. What it found in the most recent ones caused a massive grin to appear on the monster's face.

"So, this brat has discovered the last remains of my former kind. Hmm, perhaps he won't be as pathetic a meat bag as I thought."

XXX

And cut! Now comes the mandatory Author's Note.

First off, don't worry. I know how much you guys love explanations, so next chapter will have even more of them. Next, this story will only feature Pokémon from Generations I-III. I can't handle any more than that, I'm just one person! As for fighting, it will be fast paced and unique like the manga, but not quite as bizarre *cough*Jynx Ice Dolls*cough*.

I guess I should mention that while The Dark Void will be occasionally be helping me with this, it will mostly be my own story. That's all for now folks,

Sincerely,

Glock3bb

P.S. I'll give a shout out to the first person who guesses the reference in this chapter. Hint- its from a video game. No, its not Pokémon, smartasses.