Disclaimer: I don't own the rights to the Naruto and Pokémon anime, manga or games… Sigh, maybe one day.

"Pokéball Go!" Speech.
'Pokéball Go!' Thoughts.

Summary: On a trip with Jiraiya to Mio City in Shin'ō-chihō in order to find out about a new organisation in the region that may have connections with Akatsuki from Dr. Nanakamado, a seven year old Naruto is attacked by a second group and is lost adrift. Washing up on the shore of Masara Town in Kantō-chihō, Naruto is found by Dr. Yukinari Okido and nursed back to health. Now, three years later, with his starter Pokémon at his side, Naruto returns to Shin'ō-chihō joining Satoshi in his journey around the region. A Naruto Pokémon crossover.

Intro: This world… is inhabited far and wide by creatures known as Pokémon. For some, Pokémon are pets. Others use them to battle. Some even study them for a profession. Of course this is knowledge known by the general population. However unknown to most of the population exists the hidden ninja villages scattered throughout the regions of Kantō, Jōto, Hōen, Shin'ō and Ōre. These villages practice the secret art of Ninjutsu, abilities that can rival any Pokémon. For generations these ninja have kept themselves isolated from the rest of the world. But now… watch as the world of Pokémon and the secret world of ninja begin to twist and converge with each other, with the birth of a legend.

The Secret Ninja World of Pokémon
Ch01 Birth of a Legend

The sun had just set a few minutes ago leaving a small orange glow near the ground. The new moon now hung in the sky over the village of Konoha as a few of the many stars in the sky became visible. The village of Konoha itself was in a state of being repaired after sustaining damage, mainly around the outskirts of the village, from the Kyuubi attack the previous week. Within the village was a mountain which had the faces of the Shodai, Nidaime, Sandaime and Yondaime Hokages carved into it. A large tower was built on top of the mountain that currently had a light shinning out through a large window.

Sarutobi Hiruzen the current, reinstated, Sandaime Hokage was sat behind his desk within the Hokage tower. He was at the age of fifty-seven and had greying dark brown hair with a small beard and equally brown eyes. He wore white robes and had on a large red and white hat on with the kanji for 'fire' written on it. He took a puff from the brown pipe in his mouth before he let out a sigh as he looked over the papers for the newly deceased ninja. Looking over at the side of his desk revealed a small week old blond haired baby boy sleeping in a small cot. The baby had spiky golden blond hair and sky blue eyes. He had three whisker like birth marks on each cheek and a spiral tattoo on his stomach. Upon further inspection however the 'tattoo' turned out in fact to be the 'Shiki-fujin' seal.

Looking down at the baby in the cot a small smile appeared on Hiruzen's face before he looked back down at the pile of papers on his desk and he let out another sigh. It had only been a few hours since the funeral for Namikaze Minato, the Yondaime Hokage, who had died 'defeating' the Kyuubi No Yoko. It had also been a few hours since the announcement that the Kyuubi No Yoko had been sealed into the body of Uzumaki Naruto, the baby currently sleeping to his right. 'What a mistake that was.' Hiruzen thought to himself. The moment the villagers had found out they started calling for Naruto's immediate death. As a result Hiruzen was forced to create a new law that prohibited anyone from talking about the fate of the Kyuubi and its connection to Naruto, especially to Naruto himself. Hiruzen was then brought out of his thoughts as a knock came from his door. Looking up at it Hiruzen let out a slight sigh before responding "Enter!"

The door to Hiruzen's office then opened to reveal Hiruzen's former teammates and the other two members of the Konoha council Mitokado Homura and Utatane Koharu. Behind them were the members of the different clan heads, Uchiha Fugaku, Hyuga Hiashi, Inuzuka Tsume, Aburame Shibi, Nara Shikaku, Yamanaka Inoichi and Akimichi Choza. Hiruzen let out a sigh at seeing the gathered group of people in his office "To what do I owe to this unexpected visit?"

Hearing this Utatane stepped forwards "Sarutobi we have come to talk to you about the 'child'."

Hiruzen just narrowed his eyes at this "What about him?"

Fugaku was the one to step forwards this time "Hokage-sama, this 'child'" he stretched the world venomously, causing Hiruzen's eyes to narrow further "could become a threat to the village, a potentially dangerous threat that must be taken care of."

Hiruzen hardened his gaze into a glare hearing this "And you all feel this way?"

Hiashi shook his head at this, showing his disapproval "Not all of us."

"Unfortunately, Hokage-sama, those of us who do not agree with this have been outvoted." Tsume finished off from where Hiashi started.

"It's not Naruto himself that we are worried about." Inoichi stated "Rather it's the villagers and their treatment of him."

"Speak for yourself." Fugaku muttered under his breath causing Inoichi to shoot a glare to him.

"It's too troublesome…" Shikaku stated with a sigh "but if you look throughout history, Jinchuuriki have been met with scorn and hatred, turning them into society's outcasts. In most cases the Jinchuuriki turned into psychopaths, slowly killing the members of their village. We only need to look back through Suna's history of their own Shikaku Jinchuurikis to see this."

Hiruzen let out a tiered sigh as he rubbed his temples before Homura stepped forwards "It is because of this that we believe the Jinchuuriki, Uzumaki Naruto, before it turns on us must be put to death."

Hearing this many of the clan head's eyes widened. "Nani?!" Choza called out before narrowing his eyes at Homura "We agreed that something would need to be done in order to secure the safety of the village but we never once mentioned anything about this!"

"Regardless!" Utatane started "Homura is correct, the Kyuubi Jinchuuriki… Uzumaki Naruto" She quickly changed seeing Hiruzen's narrowed eyes "must be dealt with permanently."

Hearing this Hiruzen grit his teeth together before he growled out "Under no circumstances, shall we EVER resort to killing an, innocent child. Especially one that is only a WEEK OLD!"

Hiashi shook his head at this while narrowing his eyes at the two council members "Not to mention how that would affect the seal imprisoning the Kyuubi."

"Indeed" Shibi spoke for the first time "Minato-sama intended for the boy to live a full life. It would make sense that the seal would slowly drain the Kyuubi of its power, and connect it with the boy. If any harm were to come to the child so soon after the sealing, before the seal has had a chance to take affect, it is most likely that the Kitsune would be unleashed upon us once more."

Utatane just narrowed her eyes at them hearing this "Then what do you propose that we do about it?"

Before they could get into a debate on this however they heard another voice coming from the doorway "Perhaps I may pitch forth a proposal."

The group of assembled heads turned their attention towards the doorway to find a man walking into the room with short black hair, with an x shaped scar on his chin and bandages covering most of his face along with his right eye. "Danzo!" Hiruzen called out as he narrowed his eyes at the man "What is this about?"

"I am merely here to address the future of the Jinchuuriki." Danzo stated looking down at the baby in the cot "It would be a waist to let such a potentially powerful tool slip through our fingers due to fear and miss site."

Hiruzen narrowed his eyes further hearings this "He is not a tool, Danzo."

"All shinobi are tools for their village, Sarutobi-sama." Danzo practically spat the 'sama' out.

It was at this point that Utatane turned her attention towards Danzo "What is it that you propose, Danzo?"

"Killing the Jinchuuriki would be a waist of its power." Danzo stated as a small smirk tugged at the corner of his mouth "Why waist such a powerful tool when we can train him to be the perfect weapon, one that will obey every command. That will willingly throw its life away to protect the village."

Homura rubbed his chin in thought hearing this "Interesting."

Hiruzen let a slight growl pass through his mouth hearing this "Enough!" He then looked straight at Danzo with narrowed eyes "I will not allow you to turn him into an emotionless drone!"

A smirk appeared on Utatane's face at this point "A most intriguing idea. It would most certainly settle the issue of what should be done with the child." She then turned to face Hiruzen again "I take it you would much rather prefer this to the alternative?" She said stretching out the word 'alternative' as her smirk seemed to widen slightly.

Hearing this Hiruzen let out what sounded like a cross between a frustrated sigh and a growl as a small amount of killing intent seemed to be leaking out of him. However before anything could be said they heard a sigh and turned their attention towards the source, only to find it coming from Hiashi as he spoke up "Although I am loathed to admit it." He started before shooting a glare at Danzo and the two council members "It does appear to be better then doing nothing at all and certainly better then the 'alternative'."

"Very well." Hiruzen said letting out a sigh "I shall allow his training." Danzo's smirk widened hearing this until Hiruzen continued "I will allow you to train him until I am able to find a 'suitable' trainer for the boy."

Danzo's smirk quickly disappeared, being replaced by a sneer "Are you saying that I'm not suitably adequate to train that boy!"

Hiruzen just hardened his glare at this "That's exactly what I'm saying, Danzo. I will not allow you to turn Naruto into one of your little drones!" Danzo looked like he was about to say something before Hiruzen cut him off "That is my final word on this matter!"

Danzo turned on his heal and stormed out of the room hearing this but not before looking back over his shoulder "Very well, Hokage-sama!" He spat out before leaving the room with a final remark "For now."

Homura and Utatane shared a quick look before they both nodded towards each other. The two of them then headed towards the door but not before Utatane turned back towards Hiruzen "We shall speak further on the 'child's' training later."

Once they left Hiruzen turned his attention towards the clan head members "Is there anything else?"

Hiashi just shook his head at this "No, Hokage-sama, there is nothing else. We shall be leaving now." With that said they too left Hiruzen's office.

Once the door closed behind them Hiruzen let out a sigh before lifting his head back up "Well, what do you think?"

"Danzo's up to something." Came a voice before the window, behind Hiruzen, opened and a tall silvery white haired man climbed through into the office. His hair was spiked wildly resembling a main that was pulled back into a long spiked ponytail. He had dark grey eyes and two red stripes running underneath his eyes, almost looking like two trails of blood tears. He wore a fishnet shirt with greyish green robes and a sleeveless red overcoat. He had on a pair of wooden sandals and a metal headband with the kanji for 'oil' on it.

Hiruzen let out another sigh "No doubt he's rebuilding his ROOT division, to regain the power he's lost. He probably plans on turning Naruto into his own personal weapon in order to secure his position within the village."

The silver haired man, Jiraiya, let out a sigh as he moved over to the cot and looked down at the baby Naruto "So, what do you plan on doing?"

Hiruzen took another puff of his pipe before letting it out in a sigh "I need to find a trainer that I can trust to teach Naruto and keep him safe."

"That will be harder then it could seem." Jiraiya said as he held out his right index finger towards Naruto with a large grin on his face before turning serious again and turning to face Hiruzen "Danzo will be doing everything in his power to get to Naruto's trainer in-order to place his views and will towards him during his development."

Hiruzen nodded his head at this "Yes, I have a feeling that may very well be the case. I know Kakashi would be will to teach his sensei's son, however, I feel the boy is still to young to be able to properly train a student, especially one so young."

Jiraiya let out a sigh "Not to mention that since Minato's death he seems to have closed in on himself even more. I gave him a copy of my new book to help him cope." He finished with a grin on his face as he pulled out an orange book titles 'Ichi Ichi'.

"Must you corrupt his fragile mind?" Hiruzen asked with a twitch of his eyebrow.

"Corrupt?!" Jiraiya shot out indignantly "It's best to learn these things early in life then to fall short when it is needed."

"You'll never change." Hiruzen spoke while shaking his head "Anyway, back to the matter at hand." A small smirk then appeared on his face "I think I know just the person."

Before Hiruzen could continue however, Jiraiya narrowed his eyes at him "Don't even think about it!" Hiruzen looked up at Jiraiya hearing this before he continued "Minato was my last student, sensei. I can't go through loosing another one."

"I understand how you feel Jiraiya, believe me I do." Hiruzen said as he let out a tiered sigh "It's never easy to loose a student, weather they die or, sigh, well you know." Jiraiya just nodded his head at this with a grim expression on his face before Hiruzen looked back up at them "Besides Jiraiya, you're his godfather, the closest thing he has left to a family."

"That may be so." Jiraiya said letting out a sigh "But there's my spy network to attend to as well. What kind of sensei would I be to him if I had to leave the village for weeks, possibly months between lessons?"

"Take him with you." Jiraiya gave Hiruzen a slightly shocked look hearing this before he continued "It would do him good in the long run to get out of the village and see more of the world and how it works. Also… sigh, I doubt that even with the restrictions on speaking of the true nature of the Kyuubi's defeat that the village will truly treat young Naruto as a part of it. It will no doubt do his sanity some good to get out of the village every now and again."

Looking down at Naruto, Jiraiya let out a sigh "I don't know."

Hiruzen let out a slight chuckle, causing Jiraiya to give him a confused look "If nothing else Jiraiya, then do it for your own safety."

Jiraiya just raised an eyebrow at that "Now what are you implying?"

"None of us live forever Jiraiya. Even the strongest of us will eventually meet our end." Hiruzen said before letting out another chuckle "And I'm sure that Kushina will be there, waiting for you."

Sweat started poring down the back of Jiraiya's head hearing this "Damn, you had to bring her up. And with my luck she probably will be waiting for me. Not to mention she'll probably beat the crap out of me for the rest of eternity or at least until her son here joins us." A small smirk appeared on Hiruzen's face hearing this while Jiraiya let out a sigh "Alright, I'll train him."

"Excellent…" Hiruzen started only to be cut off by Jiraiya "However I will need time to sort out my connections before I begin his training. I shall return to Konoha in five years to begin his training."

"Very well…" Hiruzen said with a sigh "I will be awaiting your return, and in the meantime I shall prepare Naruto for your arrival."

"Good." Jiraiya said as a grin appeared on his face "Now that that's taken care of…" His grin then turned lecherous as the fingers began to twitch "I need to conduct my research."

Hiruzen just let out a sigh hearing this before a loud pop was heard coming from Jiraiya. A large white light then appeared in front of Jiraiya, just to his side, before fading away to reveal a dark bluish purple toad like creature, that came up to just about Jiraiya's waist. It had three fingers and a thumb on each hand; however the middle finger on each hand was a large red spike. Finally under its chin was a large red sack, which inflate and deflate as it breathed. It then turned its head slightly and looked at Jiraiya out of the corner of its eye before letting out a croaky "Doku…"

Seeing this Jiraiya blinked a few times before looking down at it "Dokurog? What are you…Agh!" Jiraiya started before the spike on Dokurog's right hand started glowing and he spun around on the spot, stabbing his spike into Jiraiya's gut, causing him to cry out in pain as his face turned slight green colour before he fell back onto his back. Dokurog then moved around Jiraiya before he started to drag him away by his foot.

"Some things will never change." Hiruzen said to himself before looking up towards Dokurog "Make sure to keep him out of trouble, Dokurog, and bring him back in five years."

Dokurog stopped in his trek to the doorway hearing this before turning his head towards Hiruzen. "Rog." Dokurog called back with a nod of his head before he continued to drag Jiraiya out of the room.

Watching them leave, Hiruzen let out a slight chuckle "Well if nothing else I can at least count on Dokurog to keep you safe, right Naruto." He finished looking over towards the now sleeping form of Naruto.

From outside his room, Hiruzen could then hear Jiraiya groan out "Ugh, research…"

"Doku!"

"AGH!"

"Then again, maybe this wasn't such a good idea." Hiruzen said to himself as he watched Naruto wake up and giggle before he let out another sigh "I'm getting to old for this."

There we go; the first chapter of The Secret Ninja World of Pokémon is up and ready to go.

AN//. Okay first of all Kyuubi will NOT be a Pokémon; it is still a demon and before anyone asks. No, Naruto will not be getting a Rokon (Vulpix).

Secondly if your wondering what Naruto's Pokémon are going to be, well three are sort of sorted out. I say sort of because they are his starter, which will be either Fushigidane (Bulbasaur), Hitokage (Charmander) or Zenigame (Squirtle). The second one is an egg he will be getting along with his starter that will either hatch into Eievui (Eevee) or Rioru (Riolu). Seriously, I can't decide on which one to use for either of these choices so you know what I'm just gonna put up a poll on my profile, I'll let you lot decide which one I should use. Oh and if you're wondering what the third one is, well that one's guaranteed, the first Pokémon he will catch will be Poppo (Pidgey). Why? Well partially for the fact that Naruto's a wind type but mainly just because I like Pigeot (Pidgeot). I'm not sure about the other three yet so I'm open to suggestions.

The third thing is that Sasuke will NOT be Naruto's rival in this story. His rival will be Gin (Silver). Gin's first Pokémon will be Nyula (Sneasel), you'll find out why during his and Naruto's first battle. Although Gin's first Pokémon is Nyula, he will be getting one of the Shin'ō starters. The starter will be determined by what Naruto's is, like in the game. So if Naruto's starter is Fushigidane then Gin will get Hikozaru (Chimchar), if its Hitokage then he'll get Pochama (Piplup) and if he starts with Zenigame then Gin will get a Naetle (Turtwig).

Finally this will be about the age of the characters from when Naruto gets his first Pokémon. Masato (Max) will be 8. Naruto, Hikari (Dawn) and Gin will be 10. Haruka (May), Shinji (Paul) and Jun (Barry) will be 11. Satoshi (Ash) and Kasumi (Misty) will be 14. Kenji (Tracey) will be 18. Takeshi (Brock) will be 19. And finally Musashi (Jessie) and Kojirō (James) will both be 29. I'm guessing that the Kantō, Jōto and Hōen leagues would of lasted about a year each while the Orange league and Battle Frontier would of lasted about 6 months each, meaning that it would have been about 4 years since Satoshi first started out with Pikachu.

One last thing, sorry this chapter was so short but it was only meant to be a prologue so it will be the shortest chapter of the story. Don't worry the others will be longer.

Next time "Ch02 Farwell Konoha" till then see ya, and don't forget to review.