An ordinary looking man in a white lab coat was walking down the halls of a secure facility. He was on his way to meet with his boss to discuss the current project he was working on. As he walked he thought about what to say to the man.

Entering into a pitch black room with only one light which was shining down on a man in a chair. The man in the lab coat bowed before the man before speaking. The man then spoke about all of the specifications that were completed in his current project.

"So how long until I can begin my operation?" The man in the chair spoke.

"Sir Project M2 is nearly complete. Just a few more days and we shall be able to initiate your plans."

"Good, Good. Now what else can you tell me about Project M2?"

"Well the subject is looking more and more ready by the second. But we are still developing the control and enhancing devices that you wish to equip it with."

"What about its powers?"

"Its powers are off the charts sir. We measured it up against the strongest Pokemon that we have and Project M2's powers totally eclipse those of our Pokemon." The man in the chair chuckled as he heard this. His plans were finally coming to fruition.

"Finally with the help of Project M2 I shall have the power I so desire. With its help I shall succeed in bringing those of myth and legend under my control."

The man seeing that his boss was in his own world decided to leave him to his thoughts. So the man left his boss to continue his work for the organization.

"Soon I shall have their power."

XXXXXXXX

Finally he had made it Cinnabar Island. It was around mid day when Naruto arrived after leaving the island which Bobby inhabited. Stretching his legs and returning his Dragonair that he had used as a mount for the journey over the sea to Cinnabar.

He looked around and saw how small the town was with only five buildings. He spotted the Pokemon Center and decided to head there first to heal his Pokemon and to see if anyone knew where Gaara was. Entering the building as always he was greeted by Nurse Joy before she took his Pokemon to be healed.

His stomach growled so he decided to put off looking for Gaara until he quenched his hunger. Heading into the mess hall he saw only one person eating lunch. He smiled and thought. "Looks like I don't have to search around at all."

So Naruto went through the line as he picked up the food items that were prepared for any trainers that happened to be in the center. After he loaded his tray with enough food for two men he went to sit next to his friend. Parking his rear end in the chair across from his friend he smiled.

"I take it that you succeeded then?" Gaara said.

"Of course had a little trouble on the last two days but we managed." Naruto replied.

"So how many badges that put you at now?"

"With the Limit, Soul, and Boulder Badge that makes 3 with my fourth coming up tomorrow."

"Tomorrow? Why not today?"

"My Pokemon need rest they deserve it after pushing themselves so hard all week. Besides I have been wanting to do my own training to test out my ideas."

"Training?"

"Yeah I've been thinking about trying to replicate a Pokemon's moves and use them myself."

"Do you think you can do it without knowing the hand seals?"

"You give me too little credit Gaara after all I have been able to replicate other techniques."

"Yes but do you think you can do that with unknown elements like the dragon or bug types?"

"Yeah those will probably take a little longer to get the hang of since I have to use my sage mode to feel out the energy that my Pokemon use when performing those types of attacks. But still I'm pretty sure that I'll be able to get it down."

"We'll see you may be able to replicate the look of the attack, but you may not be able to replicate the effect. The Pokemon use a different energy then we do it's similar to our chakra yet it's unrefined."

Naruto didn't answer back as he continued to think about how he would make it happen. The two continued to eat with the conversation over with. Gaara finished first and opened the book that he brought with him from his room as he waited on Naruto.

XXXXXXXX

Naruto and Gaara were now looking for a place to train. So as they searched around the island for an open area big enough for their teams to come out and train. They finally settled on a spot near the water so they summoned their Pokemon.

Gyarados, Dragonair and Charmeleon all looked refreshed as they appeared before their trainer. As Gaara's Pokemon appeared Naruto noticed a new addition to his team. The six Pokemon stared at each other before they all paired up.

Gyarados and Dragonair were partners as always. Charmeleon and Sandslash partnered together, leaving Rhyhorn and Aerodactyl as partners. Naruto seeing that he didn't know anything about Gaara's two new Pokemon scanned them with his Pokedex.

"Sandslash: The Mouse Pokemon, It is adept at attacking with the spines on its back and its sharp claws while quickly scurrying about."

"Aerodactyl: The Fossil Pokemon, A ferocious, prehistoric POKEMON that goes for the enemy's throat with its serrated, saw like fangs."

Gaara too saw that Naruto had a new Pokemon so he too brought out his Pokedex. Pointing at the red lizard that had a white flame on its tail he waited for it to scan it. When the Pokedex acquired its target it began to speak its information.

"Charmeleon: The Flame Pokemon, When it swings its burning tail, it elevates the air temperature to unbearably high levels."

"So your Charmander evolved." Gaara stated.

"Yeah it evolved on the last day of the test. It looks like your Sandslash also evolved." Naruto said.

"Yes it evolved when Aerodactyl attacked the research facility after it was revived."

"Nice. Now enough with the talking its time for some training."

Naruto then told his Pokemon what he wanted them to train before he himself started training. With his Pokemon set he started to meditate. As he entered sage mode he could feel the Pokemon's different energies.

Dragonair's energy felt like it was ancient. Gyarados had a mixed feeling of water and wind. Charmeleon's energy felt just like fire. Gaara's Pokemon were a mix of earth and wind.

As Naruto meditated he thought that he had already had a grasp of the earthly elements. The only one he did not already have a grasp on was Dragonair's energy. So he decided to make feeling Dragonair's energy his first priority.

Naruto and Gaara spent several hours training before calling it a night and returning to the Pokemon center. They gave their Pokemon to Nurse Joy before heading to their room.

XXXXXXX

"So are you challenging the Gym today?" Gaara asked his friend as they got ready for the day.

"I thought about it but I think I need to train al little more before challenging it. After all I haven't really seen what the evolution has done for Charmeleon. I need to know what I'm working with, with this new Pokemon." Naruto replied.

"So while you train I will fly back to Pewter City to get my pay while you train."

"Alright then maybe we can meet somewhere in between."

"Yes maybe we should head to the center of the region Saffron City right?"

"Yeah that's cool they have a Gym there as well so it's a perfect spot for us to meet up."

"Saffron City it is I'll see you there." Gaara said as he left the center and summoned his Aerodactyl.

Naruto watched him fly off in the direction of Pewter City. Then he himself picked up his gear and left back to the same area they trained in yesterday. Setting his things down he reached for the balls on his belt and threw them.

"Alright guys today since I haven't seen what Charmeleon can do I will be training him today. So Gyarados and Dragonair you two should spar as well seeing that we will be challenging the Gym on this island."

As Charmeleon stood before his trainer he saw him unfasten the device that kept the egg strapped to his belly. Before standing before him and getting in a fighting stance. Catching on to what his trainer wanted he to got into a ready stance.

Then Naruto charged the lizard and threw a straight at the him. Charmeleon not expecting his trainer to be so fast took the full force of the punch and tumble head over heels backwards.

Naruto waited for the Pokemon to get back to his feet. Charmeleon looked at his trainer as he finally stood. Opening his mouth he prepared to launch a Flamethrower at him.

Anticipating the move Naruto prepared hand seals for a Water Dragon. When Charmeleon fired the blast Naruto used the water near them to fire a powerful Water Dragon at the stream of fire. When the two attacks hit a thick cloud of steam covered the area.

Naruto used to fighting in such conditions charged to attack. When he came in view of his Pokemon he could see as he threw a kick at Charmeleon. Charmeleon once again caught completely unprepared was blasted out of the steam and into a tree.

The impact of his attack even garnered the attention of the two serpents who were in mid battle. Charmeleon struggled to get to his feet as he saw his trainer exit the cloud of steam slowly. He stood before his trainer on one knee and breathing heavily.

While this was Charmeleon's first battle against anyone human or Pokemon Naruto expected better. Though he restraining himself to what a genin could do he was disappointed. He was about to say something when the air around him began to show signs of heating.

Suddenly the white flame on Charmeleon's tail began to grow in size. It finally stopped growing when it was at least 3 times it's normal size. Charmeleon himself had forced himself to a standing position and roared as he shot a stream of fire into the sky.

"So you finally realize how serious I am about this training." Naruto said with a smile.

"Char!" Charmeleon replied with vigor.

"Good." Naruto said before hi rushed the Pokemon.

This time Charmeleon was anticipating the attack and ducked as his trainer threw a left hook at his head. But he had made a mistake by ducking and was caught with a rising knee by his trainer. His body was lifted from the ground and then he received another kick to his stomach which sent him flying back once again.

Gyarados and Dragonair felt pity for the little flame lizard. They had each only once faced their trainer directly once and it ended in defeat for both of them. Gyarados by a ball of spinning energy and Dragonair by being baked into a prison. But their experiences were nothing compared to how he was completely outclassing Charmeleon.

Charmeleon just like before struggled to get to his feet, but he managed it. It was hurt, that much Naruto could tell by the way he was hunched over. Charmeleon, desperate to do something launched one last Flamethrower with his remaining energy.

Naruto countered this stream of fire with his own stream of fire. When the two streams met in the middle they battled for dominance. Charmeleon did his best to hold up the attack and overpower Naruto but failed to do so. Now he was forced to watch as his attack was overwhelmed and Naruto's attack continue onto him.

Naruto stopped the attack once Charmeleon was on his back. He knew that Pokemon were more resistant to elemental attacks but he didn't want to push it and accidentally hurt his Pokemon badly. Walking over to the unconscious lizard Naruto pulled out his Poke ball and returned him.

"Looks like we need to work on your battling skills." Naruto said to himself then thought in his head. "Pokemon are less effective when they don't receive orders from their trainer during battle. If my Pokemon can learn to think for themselves in battle like they do in the wild they'll be more effective. The only way to train this up is through battling."

"Alright Gyarados, Dragonair!" Naruto called his Pokemon to him. "Things are going to be a bit different now. For now on I will be commanding one of you while the other tries to defeat the one I am commanding." His Pokemon looked confused at this.

"This will help you experience battle, get us used to teamwork between myself and the one I am commanding. Now I know that it sounds more beneficial to the Pokemon on my side but it is just as beneficial for the other. Why? Because this will help you learn to think for yourselves." Again his Pokemon looked lost.

"There will be times when I cannot relay my orders to you. For example in my battle with Charmeleon when we were both in the steam cloud I only knew where he was because I could feel his flames heat. Now if I wasn't in the cloud like you two I wouldn't know where to have you attack. So when a time like this comes I want you guys to be able to continue the fight without orders from me." His Pokemon finally got what he was trying to convey and nodded.

Naruto and his Pokemon continued to train until exhaustion. When he called it a night he once again packed up and recalled his Pokemon with words of praise for their hard work that day. Heading back to the Pokemon Center he left his Pokemon with Nurse Joy for the night and turned in.

XXXXXXXXXX

The Next Day

Naruto and his Pokemon were back at their training spot. Explosions and shockwaves rang out through the area. When the smoke from the explosion disappeared it revealed a slightly winded Naruto facing off against all three of his Pokemon who were riddled with bruises and shallow cuts.

His Pokemon had realized he was serious about fighting against all three of them when he whipped out a kunai and slashed Dragonair's face leaving a shallow cut under its left eye. Then brutally heel dropped Gyarados creating a crater where Gyarados impacted the ground. Finally he appeared behind Charmeleon and grabbed his tail before throwing him into the air.

When his Pokemon recovered from the attack they all charged him. First came Gyarados since he was very volatile in nature. Gyarados charged at him mouth agape and snapped his jaws shut when he came close to Naruto.

He missed of course and was rewarded with a rising uppercut from Naruto before being drop kicked in his under belly. Naruto was then forced to roll to his side when a white hot stream of fire courtesy of his smallest Pokemon. Dragonair took advantage of this and used Aqua Tail and slammed it down where Naruto was currently at, or so it seemed.

Naruto had used a replacement technique and switched with the now shattered log under Dragonair's tail. Dragonair was confused when she lifted her tail and was greeted to the sight of a log and not her trainer. But then she suddenly sensed an attack coming from behind her.

She was indeed right when a Dragon made of water was seen coming towards her. She knew she could not dodge so she used Ice Beam to freeze the water to stop it. Dragonair succeeded but was caught off guard when she saw her trainer running at her on the frozen water. His hands forming seals as he ran when he was near the end he was cut off by Charmeleon whose Flamethrower smashed into the frozen construct.

Dragonair nodded to her teammate thanking him for the rescue. A load roar resounded in the air and drew the attention of the three combatants. Apparently Gyarados had gotten up from being winded by Naruto's attacks and was now quite angry about it. He slammed his tail into the ground causing the earth to shake from the power of his Earthquake attack. Gyarados then began to shoot off consecutive Hyper Beams.

Naruto and could see that his Pokemon was in the state that the Pokedex called a rage. He knew that Gyarados would attack and attack until he grew too fatigued so he made the decision to take him out quickly since he was a danger to his other Pokemon.

Naruto placed his hands together and focused his chakra. A growing ball of rapidly spinning chakra formed in his hands until it was at least the size of Naruto himself. Naruto then charged the rampaging serpent with the upgraded Rasengan. He dodged a few of the monsters attacks when finally he was right beneath him.

Naruto thrust his attack upward into the belly of the beast. Gyarados was reminded of his first encounter with his trainer. He roared in pain from the spiraling ball of energy as it lifted him off the ground and into the air until it ran out of energy. When it did run out of energy gravity pulled Gyarados back to earth where he created a crater upon impact.

Naruto was satisfied when he saw that Gyarados did not get up and turned his attention back to his other two Pokemon. Dragonair and Charmeleon looked on in horror as they saw the biggest of their group get dropped with one attack. Their horror faded when they remembered they were still in battle.

Afraid that if they got close they would end up like Gyarados they launched ranged attacks. Naruto dodged until finally he was caught up in a Twister fired by Dragonair. Charmeleon saw this and fired his Flamethrower at the funnel of wind. This in turn caused the attack to turn into an even more powerful attack.

"They work well together…though I don't know if this combination attack was planned. I guess it's time to show them how outclassed they are." thought Naruto as he was trapped in the Fire Storm.

Naruto crossed his arms in front of his chest and gathered wind chakra. When he felt he had gathered enough he screamed and thrust his arms to his sides. This caused the Fire Storm to dissipate which freed Naruto from the attack.

"That was a nice combination attack guys." Naruto praised them.

"Now let's finish this." Naruto said before he disappeared from view.

Dragonair and Charmeleon turned left and right to find their target. They didn't have to wait long before several Naruto clones came forth separating the two. Naruto went after Dragonair while he had his clones keep Charmeleon busy until he defeated Dragonair.

Channeling chakra into his legs he used the extra strength given to him to jump up into the air at the same level of as Dragonair. She saw him coming and tried to fly upwards but failed to escape when Naruto had grabbed a hold of her tail. With her tail in hand Naruto flung her down to earth to take away her advantage.

Dragonair had stopped herself from hitting the ground by using her powers. Turning to the sky she saw Naruto falling down while preparing a heel drop. She dodged and fired an Ice Beam at the ground where Naruto was going to land.

Naruto seeing the ground below him changed his position and channeled chakra into his legs so he would be prepared for the slick floor. He landed on the cold ground and sighed as he felt his feet stick to the ice. Dragonair seeing that her strategy hadn't worked charged fired a Thunderbolt from the horn atop her forehead.

The yellow 100,000 volt electric current raced towards Naruto. Naruto looked up as soon as he heard the attack being charged. He stood firm and waited for the attack to hit. When it was close enough Naruto struck his right hand forward absorbing the attack. Then he pointed his left hand back at Dragonair and fired his own attack back at her.

"I guess it paid off being on the receiving end of Sasuke's stupid lightning attacks. After all I might not have learned how to redirect them if he wasn't constantly firing them off."

Dragonair stunned by Naruto's act of taking the attack head on, was unprepared for her own attack to be fired at her. It struck home and paralyzed her. Naruto knew about her ability to heal herself of status effects like paralysis formed hand seals for a technique.

"Earth Release: Swamp of the Underworld!" Naruto shouted as he slammed his hands down.

The technique trapped Dragonair who was still paralyzed from the electric attack. Naruto knew she was done for after all when he was learning that technique he had gotten himself stuck in there for awhile. Turning his attention to his last remaining Pokemon he could see that Charmeleon was holding his own against his clones.

Dispelling his clones he Naruto stepped forward in front of the winded lizard. He gave Charmeleon a little time to catch his breath before attacking. When Charmeleon stood erect Naruto knew he was ready…well as ready as he could be after fighting several clones of himself.

Naruto charged at the lizard and threw a right hook at his head. Charmeleon ducked and spun swinging his tail in an attempt to sweep the blondes feet. Naruto performed a back flip to get away from Charmeleon's sweep but was slightly burnt due the flame on his tail.

Charmeleon charged at Naruto and slashed his claws with fury. He succeeded in slashing his in several times before he himself was forced on the defensive. Naruto came forth with tenacity that slightly scared Charmeleon.

Suddenly Charmeleon could no longer keep up the close quarters bout as Naruto's blows became faster and more powerful as the fight dragged on. Naruto who was still holding back a great amount of power could see the damage he was inflicting as he rained down blow after blow on the lizard. Soon enough Charmeleon crumpled under his power.

Backing off once again to see if Charmeleon was willing to keep fighting. He was surprised to see the flame on his tail become larger like the day before. Charmeleon charged at Naruto and fired off a close range Flamethrower barely missing its target.

Naruto had to step up his speed to stay clear of the fire attacks that were thrown at him. Naruto used his Body Flicker to get in close and threw a punch. But he pulled back immediately when his hand received a burn and his sleeve caught fire. He then began go through hand seals for a technique he felt would stop the flaming lizard.

"Earth Release: Earth Flow River!" Naruto shouted as the ground near him became muddy.

"Earth Release: Earth Dragon Projectile!" Out of the muddy ground came a dragon head which proceeded to shoot mud balls at Charmeleon.

Charmeleon dodged to the best of his abilities but was hit several times. This in turn caused his evasiveness to fall. Naruto kept up the attack until Charmeleon was fully covered in mud before cancelling the techniques.

Naruto thought it was over but then suddenly the mud around Charmeleon was blasted off. The white flame on the tip of his tail began to expand until it covered his whole body. This surge of power reminded Naruto of the times he had used the Kyuubi's chakra cloak.

Charmeleon charged at Naruto with incredible speed. He managed to make contact with him which caused huge explosion. The result of the attack blasted the two combatants away from each other.

Naruto recovered from the blast quickly due to covering himself with chakra before Charmeleon impacted. Looking around for the lizard he was surprised to see that the Pokemon had fainted and was laying face first in the ground.

Standing up he surveyed the damage to the area. Trees had been toppled and craters had been created. Looks like they were done training in this area.

Unfastening the three Pokemon's Poke balls from his belt he returned each of them. He then went on to make sure his things were safe and secure. Upon reaching the area he left his gear with he panicked when he saw that the egg he had been carrying had a small crack stretching horizontally across the shell.

"Damn that's probably not good for whatever is in that thing." Naruto said to himself as picked up the egg.

"Well it doesn't look to damaged so I guess it is okay for now." As he inspected the egg in his hands for other marks.

"Now that I'm done with their training I can finally get back to learning how to use some of their attacks." Naruto said as he sat down and meditated.

XXXXXXXXXXX

One Week Later

Naruto and his Pokemon had finally felt it was time to move on. His Pokemon felt as if they were ready enough to take on the best of the best. Naruto wanted to move on for fear of angering Gaara by making him wait so long.

So they made their way into to the volcano where Nurse Joy said he could find the Gym Leader named Blaine. Naruto had all of his Pokemon out of their balls so they could each watch the battles. Near the base of the volcano they encountered a man who stood in front of the path that lead up the volcano.

"Ah young one what can I do for you and your Pokemon?" the old man asked.

"Well can you point us in the direction of the Gym?" Naruto asked.

"Oh yes well you must take this path up to the peak to reach the Gym. But on the way there you will encounter several forks in the trail. When you come upon these forks there will be a sign in the middle with a question. The questions will be yes or no questions. If you answer yes you must go left if you answer no you must go right."

"So just answer the question correctly in order to move up?" the old man nodded.

"Alright thanks. C'mon guys let's get moving." Naruto said as he his Pokemon up the trail.

The group trekked up the path until they came upon the first fork in the road. Naruto looked to see the sign.

"Caterpie evolves into Butterfree? Yes or No?" Naruto read before picking yes and following the left fork up.

Apparently he answered correctly since they came up to the next sign.

"There are 9 certified Pokemon League Badges? Yes or No?" he choose no this time and ended up taking the right fork.

Again he answered correctly as they came upon the next sign.

"Poliwag evolves 3 times? Yes or No?" No was the answer and so the group moved up the right fork.

The next sign they came upon read.

"Are thunder moves effective against ground-type Pokemon? Yes or No?" again the group went right as they answered No.

Naruto could see that they were coming closer to the peak of the volcano as they approached their fifth question.

"Pokemon of the same kind and level are not identical? Yes or No?" Naruto went Yes and lead his Pokemon up the left fork.

They came upon the next sign which read.

"TM 28 contains Tombstoner? Yes or No?"

Naruto had no clue as to the answer for this one. So he went with his gut instinct which was almost always right and went up the right fork. The group traveled with nothing happening leading Naruto to believe that he answered correctly.

They soon came upon the peak of the volcano and saw that their was a platform hanging above the opening. On the other side stood the old man from before.

"So you've made it. It's been a long time since I've had a challenger." the old man said.

"So you're the Gym Leader Blaine?" Naruto stated.

"Of course after I'm not known as 'The Hotheaded Quiz Master' AHAHAHA!" Naruto sweat dropped at the antics of the old man who strangely reminded him of Jiraiya.

"Well why don't we get this battle started youngster?"

"Are there any rules?" Naruto asked.

"Three Pokemon each, First one to KO the others team first is the winner. You may substitute if you wish." Blaine said. As he grabbed his first Poke ball and prepared to throw it.

Out of the Poke ball came something Naruto had never expected to see in his life again. A Nine tailed fox stood before him. Its fur was different but its eyes were the same blood red as Kyuubi's.

"Kyuubi…" was all Naruto whispered but not low enough for the fox to hear as it made eye contact with Naruto.

The image of the Ninetales rippled before becoming a spiral masked man with a black cloak with red clouds. The world around Naruto didn't mean anything compared to the anger he felt for the man in front of him. The power that Naruto had been restraining upon entering this world just exploded from his body.

XXXXXXXXXXXXX

AN: Sorry for taking for so long I decided to put this note at the bottom so you guys could get a chance to read this before hearing me talk. I've just been having so much fun skating that I really haven't found time to write. But I'll be heading back home in a couple weeks since I need to get ready for school again.

Okay someone requested that I list the Badges and Pokemon of the characters I've shown so here it is.

Naruto:

Badges -Boulder, Soul, Limit(Original)

Pokemon-Gyarados, Dragonair, Charmeleon

Kiba:

Badges-Boulder, Cascade, Thunder

Pokemon-Growlithe, Fearow

Gaara:

Pokemon-Sandslash(Shiny), Rhyhorn, Aerodactyl