● Chapter Interlude:

Naruto's past

###

Naruto grinned as he ran through the village, ignoring the customary hateful glares of the villagers. Nothing could spoil this special day. The day he took his first step to becoming a Pokemon Master. The day the Shinobi Academy students recieved their first Pokemon. The Day he got a-

"MAGIKARP!" Naruto wailed as he now stood in the fenced in garden of the Pokemon breeder. All his classmates were here too, bribing the various Pokemon to come to them with berries. "Seriously, GO AWAY!" Naruto yelled as he walked away from the flailing fish.

Naruto tried to give his berries to the other Pokemon, but they all ran away at his approach. No matter how slowly he went to them, or how unthreatening he tried to make himself, they ran away each time. Naruto didn't yet know they were scared of the Legendary who shared his soul.

Magikarp was just too stupid to be afraid... or was it something else.

The determined little Magikarp (as it appeared to be a runt on top of just being a Magikarp) jumped about on his side as he ran in front of Naruto, after yet another failed attempt to give a different Pokemon a berry. Naruto shoved the Magikarp away with his foot. Not really kicking him, just trying to force some distance.

The breeder glared angrily at Naruto, "Keep treating my Pokemon like that and I don't care what the Hokage says! I'll have you thrown out of here on your little hell spawn ass!"

Iruko, their class teacher, walked over and tried to ease the annoyed 10 year old, "Naruto, remember what we covered in class. The Pokemon chooses the trainer and this little Magikarp has clearly chosen you."

Naruto scowled at the thought. Everyone knew Magikarp was the weakest of all Pokemon. It didn't even know any attacks!

"Seems like a perfect fit to me." Naruto glared as he turned around to see Sasuke smirking at him as he somehow managed to get a shiny Ditto to sit in his lap and eat berries from his hand. "A pathetic Pokemon for a pathetic trainer."

All the kids immediately started laughing. Thankfully Iruka was quickly able to silence them, with a far more impressive glare then Naruto. Although, a few snickers still escaped from a brave few.

Naruto huffed at his class, before looking back at Magikarp. The little guy had a look in his eye... a look of... understanding. This pitiful Pokemon refused to leave him alone, despite the other Pokemon avoiding him at all cost... This little guy knew what it was like to be laughed at... to be treated like nothing.

In Magikarp's eyes, Naruto saw that Sasuke was right. They were the perfect match. The world underestimated them both... but maybe together they would prove they were the best.

Naruto crouched down and finally offered the little guy some berries. The fish attempted to splash on land in his excitement at finally being accepted.

Naruto smiled at Magikarp, "Come on Fishstick, We have some training to do."

###

● Later That Year

"NARUTO!" Iruka threw a book at the boy's head as he and his Magikarp loudly snored in class.

Both boy and Pokemon jumped up with a start and quickly grabbed their book, shoving their faces into it. They pretended as if they had been reading the whole time.

"HONESTLY!" Iruka screamed at them, "This is perhaps the most important lesson for your Pokemon and you are SLEEPING in my class!"

"Karp Karp," Fishstick denied it.

Iruka groaned, rubbing his temple, just in time to hear the bell ring. All the kids gathered their gear and left... all but Naruto.

The boy looked around as everyone left, as if amazed school could already be over.

"I hope your nap was worth it." Iruka glared.

The boy looked down in shame, "I just don't understand this stuff." He muttered.

Iruka sighed. He knew Naruto wasn't really one for book learning. The boy learned better by doing. "Follow me to the back and we'll go over what we learned today,"

Naruto smiled and grabbed his stuff as Fishstick jumped on his head and started splashing excitedly in the boy's yellow hair, crushing the well gelled spikes.

Iruka directed him to the training grounds behind the school. Once their the man explained, "Today we were going over how to train your Pokemon to use moves it normally couldn't. You see Shinobi have secret training methods that allow us to give them extra bonuses. Like never forgetting moves they previously learned, no matter how many they know, as well as teach them secret moves known only to our village or the clans. There is even a list our village has discovered that a Magikarp can learn."

Naruto's eyes widened, "REALLY!" the boy gaped, "I tried buying some TM scrolls to teach Fishstick some stuff, but none of them worked and the guy refused to give me a refund!"

Iruka clenched his teeth. "Can I see the TMs you bought?"

Naruto slouched but got out the Scrolls. There were over a dozen of them... and none of them were for a water type. Whoever sold these to Naruto must have been deliberately scamming him well trying to hinder his Pokemon.

"The shop keeper told me... I must be a pretty lousy trainer for not being able to teach my Pokemon these moves." Naruto muttered.

"None of these are for a water type, Naruto." Iruka gently explained, "It has nothing to do with your ability as a trainer. I suggest you alert the Hokage. You were scammed out of your money and he would probably want to know."

"I... I WAS!?" Naruto gaped. "THAT BASTARD! We'll show him, won't we Fishstick? He's going to get the pranking of a lifetime!"

Iruka sighed, "Just tell the Hokage."

Naruto waved off, "That never does any good. Fishstick and I got to handle this ourselves!"

"KARP!"

"Anyway," Iruka gave up, "I have a few Scrolls Magikarp can learn from. Keep your other Scrolls. You might get Pokemon who can learn them in the future. Magikarp, due to his Evolution chain and Mega Evolution, can learn a few types of moves. Next time only buy Water or Dragon type TMs. While Magikarp isn't a dragon type, our region's Gyarados is. That means, through Shinobi training methods, your Magikarp can learn Dragon Moves- NARUTO!"

The boy jumped, as his eyes had been glazing over, "I was paying attention!" He swore.

Iruka sighed, "Let's just get to the part you came here for." The man smiled as he pulled out a scroll from the inside of his vest pocket. Handing it to the boy, he informed, "This is called 'Bouncy Bubble'. It will be crucial for your Magikarp. You see, Fishstick naturally has very low health and this move not only does massive amounts of damage, but a good chunk of the Pokemon's health will be transferred to Fishstick, healing him. As long as no one one shots your Magikarp, which is unfortunately very likely, this move will help Fishstick recover from nearly anything. I also have some candies to increase his health permanently, making him harder to take down."

Naruto grinned widely.

"However," Recognizing that tone, the boy flinched, and waited, "If you EVER fall asleep in my class again, I will bare your hide and blister it in front of the entire class!"

"But... you still help me afterwards... right?"

Iruka sighed, "Naruto, I don't help you because you fall asleep. I help you because you are having trouble. If you don't understand what we went over in class, just come up to me afterwards and I will tutor you. You'll find it will actually work out better as I won't be mad at you."

The boy blushed.

"NOW, let's get started on what you missed in class."

###

● 2 Years Later.

Naruto felt like crying, something he swore he would never do again. After all the work he did these past few years, after all the hours Iruka put into training him after school... he failed... Naruto failed his final test to graduate and become a Shinobi... he only needed to pass 2 of his exams but he failed all 3... he really was the worst trainer ever... they were going to take away Fishstick, as he was trained as a Shinobi partner. Civilians couldn't have such powerful Pokemon, even if it was a Magikarp.

Fishstick cuddled the boy's stomach as he sat in the child's lap. They looked out at the village as they sat on the School roof. Looking at Fishstick, naruto noticed a speck of water fall on the karp... a tear... the boy was already crying.

"I won't let them take you." Naruto promised.

A voice spoke from behind the pair, "Maybe I can help with that?"

###

Iruka was pacing in the old Hokage's office, back when the office still belonged to Sarutobi Hiruzen. A year before the old man retired and named Tsunade his Successor.

Sarutobi leaned back in his chair, smoking his pipe, while wearing a grave expression.

"I regret Naruto didn't pass his test-" The old man sighed out but wasn't allowed to finish.

"IT WAS RIGGED!" Iruka insisted, "I have been personally working with Naruto for YEARS to pass this test! These past few months he has excelled at all his practice exams! There is no logical reason Naruto should have failed unless the instructor administrating the exam deliberately sabotaged the boy!"

"I am aware," The Hokage sighed, "But there is no way to prove that is what happened... While I hope it is just a result of blind prejudice that fuels this-"

"How is that the best option!"

"Because it will mean minimal push back when I give the boy his headband anyway." The Hokage informed.

Iruka... blinked...

"You didn't think I would actually allow this to stand, did you?" The Hokage eyed, "That boy is my honorary grandson. I will not allow ignorance to hold him back..."

Iruka looked sheepish.

"However... if this is some greater plot, we need to act quickly."

"Greater plot?"

"ROOT has been trying to gain control of Naruto since the day he was born... this, conveniently, gives them an opportunity."

###

"Soooooooo... you guys are like super spies?"

Danzo grinned at the boy's ignorance. The Hokage had kept the boy so sheltered. It made this easy.

The boy was clearly studying Danzo, not at all knowing how to do so without being caught. They would fix that soon enough. Danzo knew he was a terrifying sight to children, covered in bandages and scars, but they always learned other reasons to fear him.

"We work to keep this village safe." The old man explained. "We are unregistered Shinobi, as we work for a secret department of the ANBU. Most of our members have never even been to the Academy. They train here, to unlock their full potential. You and your Magikarp will be a fine addition to our organization. Once it evolves you will be a fearsome team. However, until then, we have a new partner to introduce you to."

Naruto groaned. "Most Pokemon don't like me. The only reason Fishstick sided with me is... well..." he wasn't really sure. Because they were kindred spirits?

"If our hunch is right, this one will obey you." Or kill the boy. A win-win really. Danzo grinned, leading the boy into a bright room in the dark base, "Wait in here."

The boy blinked but did as he was told. The door sealing behind him, without Danzo following in.

There a was a large mirror on the other side of the door. After a moment Danzo's voice came over the intercom.

"Not all Pokemon will accept any trainer to give it berries. Not all Pokemon will run from trainers they don't like. Some will only allow you the OPPORTUNITY to catch them, if you prove to them you are a worthy trainer. Some Pokemon demand you battle them and will accept nothing more then a trainer capable of defeating them. Let's see if you are that trainer."

A wall opened up and something was Lurking in the shadows behind it... something ferocious, something that radiated power.

"Vee!" A cute little fluff ball jumped into the room. The most adorable pout on it's face...

Naruto... blinked, looking at the window, assuming it was 2 way, "Seriously."

Well maybe it wasn't that little. It was about the size of a small Arcanine. However it was still a cute bundle of fluff, regardless of it's size.

The Eevee suddenly jumped at the window. Mid jump it transform into some kind of scorpion fox thing with bug like wings. It stuck to the glass before slamming it's dagger like tail through it. Punching a hole into the foot thick glass.

"Karp!" Fishstick exclaimed in total fear.

"Insecteon!" The bug roared, jumping off the mirror and buzzing it's wings to keep it in the air... the thing was as big as Naruto, bigger if you were including the tail.

The thing had a savage look in it's face... until it suddenly blinked. The moment it blinked it tilted it's head, in a cute manner. It hesitantly sniffed.

Naruto hesitantly called on his training, becoming as non-threatening as possible and pulling out some berries. Yeah, That scarred up guy probably wanted him to battle it, but the Eevee... thing, had calmed a lot just by the look of him. Naruto plopped down on the floor and threw a berry in front of the creature.

Suddenly the bug burst into light. It shrunk down and... turned back into an Eevee. Naruto had never heard of a Pokemon de-evolving.

The Eevee gleefully accepted the berry... but scowled when Naruto pulled out a Pokeball. Naruto sighed and put the Pokeball down in front of the Eevee. Then through him another berry, but the fox didn't munch it this time.

"There scared of you." Naruto calmly informed and the Eevee seemed to calm by the first syllable he uttered. "And your scared of them."

"Vee!" The critter protested.

"You don't have to look tough for me. I know that look. I have worn it often."

Eevee paused.

"The world sees you. Feels something inside of you. You know it is there, how dark it is, but nobody dares talk about it. They just hate you for it. They condemn you for it. Even the guy in charge of here looks at you and has just decided your evil... he looks at us both the same way... I don't think your evil, Fluff Butt, I think your scared. But I make this promise to you. I will always protect you, always love you, for as long as we are together, I will never look at you with any trace of fear. Cuz you're not scary, oh fluffy one. I think you just need someone to give you a chance."

The Eevee hesitated, then nodded, making a decision. He gently touched the Pokeball with his nose. It opened up and turned the little fox into light, before sucking the light inside. The ball didn't even shake once before the red ring around the button turned green, then made a clicking sound. Naruto smiled, picking up the ball, "Welcome to the Team"

"Not exactly as I had planned." Naruto stiffened at the voice over the intercom, "But very revealing all the same. Though you are mistaken, Naruto-chan, I don't fear you. I see your potential. I believe you will go far. With my help, you will become the greatest Pokemon Master in the world. Armies will flee at your very name... While Konoha sings your praises at being their one true protector. I can make them love you, Naruto-chan. All you have to do is trust me."

"Tough talk for a guy behind a foot of glass!" Naruto growled, standing tall.

The door slid open, and the bandaged man stepped into the room. He smiled a Grandfatherly grin, now knowing exactly how to play this in order to earn the child's undying loyalty. He gently ruffled the child's hair, continuing to smile as he declared, "I'm so proud of you."

Naruto stiffened, not used to the sensation... or any real physical displays of affection.

"You've done well... my little kit." Danzo praised. Knowing the boy would soak it up like a dry sponge. "Your new Pokemon is a lot like you. He holds terrifying power, but he doesn't know how to properly use it. I can teach you both how to harness your gifts. The village fears you will misuse it, but I know you will prove them wrong."

"What?" Naruto blinked, "Do I got some secret bloodline or something?" thoroughly distracted by a few kind words.

"In a way." Danzo informed, "It must never get back to the Hokage I told you this secret, Naruto-chan. It could very well mean my death, but I believe you have a right to know. I'm trusting you not to reveal me."

Naruto's eyes widened, no one ever trusted him with anything. Iruka didn't even trust him to study on his own... Naruto gave a slow nod, and a promise to never reveal him... and Naruto Uzumaki never breaks a promise... he has had far too many broken towards him.

"Do you know who Orochimaru is?" Danzo asked.

"Wasn't he some psycho researcher that experimented on Pokemon?" Naruto asked... not entirely sure, but he had the general idea.

"He was a Shinobi that forgot our purpose is to protect Pokemon. Instead he wished to use them to increase his own power... That's where your new Eevee comes from. He was bred in a tank and grafted with the genes of all it's evolutions. He can Switch back and forth between all of them... but you are even more special."

Naruto stiffened, as the hand went to his shoulder and gave it a comforting squeeze.

"Thousands of years ago, the 9 Legendaries of our region grew mistrustful of humans. They decided to wipe us out. Mew created the Shinobi to stop them... and we did. We trapped them in 9 Master Balls and entrusted each of them to the 9 great Shinobi villages... some of those villages have fallen and their Master Balls lost. However, Konoha still had our Master Ball and it's prisoner."

"W-what's that got to do with me?" Naruto dared ask.

"You, undoubtedly, heard of the Kyubi's attack against our village. That the 4th Hokage lost control of it? That he died raining it in and that is why Sarutobi had to retake his throne."

"Yeah..." Naruto looked puzzled, "We learned about it in school."

"What they don't teach is it wasn't exactly the Legendary itself that attacked... more like it's son... nothing more then a tantrum that got out of control."

Naruto tilted his head at that. "I thought there was only one of each legendary."

"Normally, yes." The Bandaged man sighed, sadly. "Orochimaru didn't stop at experimenting on Pokemon. He tank bred several human children and graphed them with Pokemon DNA... even created a child and infused him with The DNA of a legendary."

Naruto's eyes widened, seeing where this was going. "No..."

"Your body was engineered to Harness the Kyubi's power. When Orochimaru was discovered, He released you and had you destroy much of the village as a distraction. The Hokage gave his life to seal your power, and with his final breath begged the village to take pity on you."

Naruto was shaking his head, not wanting to accept what he was hearing... but believing every word, despite himself.

"The seal is why you struggle to control your Chakra, but I can teach you better control."

Tears were once again falling from the boys eyes.

"Not even the seal can hold back all your power. It is obvious from the way Pokemon react to you... and why Fox Pokemon seem to trust you."

Naruto looked down at Eevee's PokeBall in his hand.

"Because of your power, the village will never give you your headband. They fear what you could do with it. If you were to complete your training, you would have the power of a god at your fingertips... possibly even command the god of foxes itself... at the very least you have power over all under her Dominion... but regardless of the villagers fear, I was able to pull some strings."

Naruto looked up.

"The world believes you will misuse your power, but I KNOW you will use it to save us all."

###

It wasn't long after that Naruto recieved his headband... believing he owed it to Danzo. He began training with the man to control his Kyubi bloodline... but he didn't begin to Master it until the Chunin Exam, where the boy met his Godparents. Who trained him themselves.

Eventually Sarutobi stepped down as Hokage and named Tsunade his successor... but only after an attack from the sound village nearly cost him his life, and destroyed quite a few buildings. That is when he realized... he really was "too old for this". He couldn't protect the village as he used to.

Tsunade created new laws to protect Naruto... even had him move in with her... it was nice... being part of a family, having friends in the form of his Teammates: Hinata Hyuga and Rock Lee... though since Tsunade had taken him in, the boy hadn't seen his true Sensei, Danzo. He hoped the old scar face made contact soon.