Disclaimer: I don't own naruto or Pokemon if I did I would be richer than Donald Trump.

Chapter 1: The World We Live In.

This world is filled with beautiful and mysterious things. Two of those items are Pokemon and shinobi. Shinobi and Pokemon have co-existed and worked together for centuries in order to achieve peace. Shinobi have alway lived dangerous and cutthroat lives and each shinobi village had their own rules and policies. But there was one rule that every village upheld.

No Killing Pokemon.

No matter what this was one of if not the worse crime you could commit.

Our story takes us to Hi No Kuni, the land of fire. In the land of fire resided one of the big 5 shinobi villages, konoha. This village was considered the strongest of the big 5 for all the great shinobi it produced. In this village there was an academy that all future shinobi must attend and meet the minimum requirements to graduate. At the academy you learned the basic skills that any shinobi has and how to catch, raise and train Pokemon. They started at the age of 6 with the first two years focused more on pokemon training and raising them including type differentiation, weaknesses and advantages, berry growth and tastes for different types, battle style and strategy and so on. Civilians can also take classes to become pokemon doctors and breeders.

In the classroom of the soon to be graduating class sat a twelve year old boy named Naruto Uzumaki. Naruto had blonde hair that matched a summer's sun and azure blue eyes that a certain Hyuga heiress got lost in. he was wearing a black and orange jacket that stopped at his mid waist and on the back was a red uzumaki swirl. Under that he wore black tank top, he also wore black cargo with an orange line going down the sides and black shinobi sandals.(A/N. I can't draw to save my life so sorry that I don't have an image for you to see for a better view on it.) Naruto was taking notes on the current lecture which was pokemon natures and the adverse effects on battling styles. This was a shock and normal at the same time. Everyone at the academy knows naruto hates to studying with a passion but since the subject was pokemon he was paying full attention. He has played with his Jijis pokemon for hours since he was a little kid. He loved pokemon, It is one of his main reasons he wants to become the hokage, the strongest shinobi and trainer in the hole village. So he would study properly to take care of his future family/friends.

"Alright, class it's time for history of the shinobi nations. Let's start with Kaminari No Kuni." the chunin instructor said eliciting a groan from everyone. As of late all they did was study politics, history and pokemon theory.

Naruto deciding that he would prefer to take a nap over listen to history.

(later)

When Naruto woke up he saw it was almost sunset and everyone was gone.(A/N I can already hear you guys saying why didn't Hinata wake him up. Answer. She was to shy to approach him)

"Damn jerks, didn't even wake me up to go home" Naruto muttered.

Naruto gathered his stuff and left the academy. Deciding to go to one of the battle parks around Konoha. He wants to see if there were any people out battling before heading home.

When he arrived he saw that there was a battle going on between two chunin. One using a Yanmega while the other was using a Pignite.

"Pignite use flame charge" the pignites trainer commanded. Pignite did as he was ordered and began to stomp his feet kicking up a cloud of dust.

"Yanmega use double team." 20 copies of Yanmega was produced and started circling in a counterclockwise motion around pignite confusing him as to which he was supposed to attack, he took a gamble and charged one who popped up on his left. This ultimately backfired on him as it as a doppelganger.

"Now use supersonic" Yanmegas trainer ordered. Doing as he was told yanmega began to flap it wings releasing a high pitched sound at Pignite. Pignite became confused and began to move drunkenly around.

"Hit it with sonic boom" Yanmega released a pressurized blast of sound from it wings blasting pignite back. Pignite stood itself up and continued to move drunkenly.

"Pignite use fire pledge" pignite moved drunkenly but performed the move anyway. Because he was confused pignites attack was off and only grazed Yanmega.

"Yanmega end this with air slash" the blast of air hit pignite dead center knocking him out cold.

"Pignite is unable to battle yanmega wins"the referee says. After the pignites trainer recalls him he walks over to the winning chunin and gives the sign of reconciliation and they walk off talking strategy.

After walking home he saw it was approaching 10:00 PM so he decides to grab a quick shower before going to bed.

(next morning)

Naruto awoke next morning at the brink of sunrise and got ready to do his latest prank. He changed into his old orange jumpsuit and put his goggles on before grabbing himself a quick breakfast of cup ramen and left the apartment with several cans of paints and a paint brush.

(three hours later)

"Get back here punk" One chunin shouted as he chased after naruto. The reason for this as because Naruto had taken and painted graffiti all over the hokage monument. Naruto turned around while jumping roof to roof and took a thinking pose.

"Hmmm tempting but no. seeya slowbros" naruto said as he jumped down from the building and passed by a fence before disappearing in a burst of speed to the next roof.

.

.

.

.

After a moment passed naruto appeared out from behind a camouflage tarp

"Idiots. How they're chunin is beyond me" naruto said with a sigh and began to away before he was hit in the head by an extremely pissed off Iruka. Umino Iruka was twenty- something year old man who was a teacher at the academy. He was a tall man at 5'9, a good foot taller than naruto wearing the standard chunin uniform of a chunin vest over a long sleeved blue anbu shirt, blue anbu pants and standard ninja sandals. His hair was in a spiky ponytail and on his head was a leaf headband. The most distinguishing about him as the scar on his nose the ran to his cheek. By his side was his partner Wattz the Jolteon.

"Oh. hey Iruka-sensei how are you?" naruto says as if he was not just caught desecrating a national monument. This pissed of Iruka more than anything.

"The real question is why is it that you are not where you are supposed to be" iruka as only half listening because he was busy scratching watts behind the ear

"Because it's boring that's why, I know all of it already I just don't see the value in it" naruto replied. Pissed Iruka did his favorite trick when dealing with naruto.

"Watts use Thunder wave" watts did and released a small static shock of lightning at naruto paralyzing him. Iruka for good measure ties up Naruto up and begins to drag him through the village back to the academy.

(At the academy)

Naruto sat in the middle of the room being reprimanded by iruka in front of the whole class. After Iruka finished chewing him out he just huffed irritating Iruka even more.

"Okay class since it seems that naruto has not learned his lesson the whole class is going to practice the transformation jutsu all day" this elicits a groan of displeasure from almost everyone. They spent the next four hours doing nothing but the henge no jutsu.

After school naruto had to spend his afternoon cleaning the hokage monument of his prank with iruka watching over him and after word Iruka treated Naruto to some ramen. He heads to his apartment and gets ready for tomorrow. He practices the three academy jutsu. Henge and Kawarimi he had down pat but Bushin …..

"Bushin no Jutsu" naruto said as a puff of smoke appears around him and as it fades we can see a rough copy of naruto that looks extremely sick. After staring at he dispelled it.

"AAAHHHGG. I hate this jutsu so much. If only my control didn't suck not mention my chakra capacity is so damn big" naruto complains. He looks at the time and sees it is 9:00 PM and hops into a bath and then cooks him some ramen. Before going to bed naruto prayed up to the heavens above that he would pass the graduation exam. He prayed it would be the Henge jutsu for graduation and not Bushin.

( tomorrow afternoon)

Naruto sat on the swing outside of the academy watching all the students who passed received praise from their parents. He heard chatter about what pokemon people were going to pick for their starter or parents promising to buy a pokemon egg for their child. It sickened him sometimes at how kids took for granted what they had and didn't appreciate it as much as they should.

Naruto was broken from his thought by the presence at his side. He looks and sees Mizuki-sensei and his vullaby staring at him with mizuki pity Vullaby looked at him with disdain which was its normal expression.

"Naruto how are you feeling?" mizuki asked him.

"Fine. A little disappointed in myself but fine nonetheless. I know that if the exam was the henge or kawarimi I would of had no problem passing" naruto said. Mizuki stroked his chin before and idea "came" to him.

"Well we don't usually do this but there is a secret test that we allow students to take to prove that they deserve to become a shinobi. But this test is harder than the graduation exam you up for it." mizuki asked him.

"I Am up for anything dattebayo." naruto said with all the confidence in the world.

"Okay here is what you have to do.-"

(midnight) konoha woods

Naruto was at the rendezvous point with the scroll of sealing, it was the item that held the most important jutsu,weapons, items and TMs that were made by the kages and other S-class shinobi of the village. Mizuki told him he had to learn a jutsu inside here before he came or someone else. And he was determined.

"Okay. Let's see what the first jutsu is Kage Bushin no jutsu. Seriously my worst jutsu is the first one. Alright let's get started." naruto spent an hour trying to learn the kage bushin. After he was positive he had it down pact he looked for another jutsu to learn when he noticed he was in the TM section he decided to look and see if there was any that jumped out at him. He looked through each and every one was organised by hokage he went to the section of the shodaime and looked through it until stopping at one that peaked his interests. He performed a one handed ram seal and brought the item out the TM was red signifying it was a fire-type move "lets see fire"

"NARUTO"

Naruto jumped out of his skin at the voice calling him he quickly stuck the TM into his back pocket and roller up the scroll of sealing. Just as he finished Iruka appeared right infront of him watts into with Irukas other pokemon,venomoth, who was named mothball(reason his venonat was nicknamed mothball and it didn't respond to its new nickname) and scraggy who didn't have a nickname riding on his shoulder.

"High Iruka-sensei, you got here really fast I only had the chance to learn one jutsu but it should be enough to let me pass right?" naruto asked. Iruka looked confused as did watts and mothball, scraggy you can never really tell with him he always has a blank look on his face.

"What are you talking about? Pass what?" iruka asked and now it was naruto's turn to look confused.

"The secret test that you allow kids who fail the graduation exam to take so that they can prove they have what it takes to become a shinobi. At least that was what Mizuki-sensei told me" the moment Iruka heard Mizuki Iruka knew that something was up. Iruka worked his mind trying to figure out what Mizuki's game plan was but before he could come to any concrete conclusions he heard the whistling sound of several items being hurled through the air recognizing it iruka quickly moved to grab and pull naruto out of the and Kunai flew over to of them with a kunai and shuriken hitting iruka on the left side.

"Well, well iruka you have faster reflexes than I thought. I figured with all the time you spent as an instructor you would have been slowed down but it seems I might have been off about it." a voice call from the treeline iruka and naruto looked towards the vicinity of where the projectiles originated and saw Mizuki stand atop a tree holding a dai shuriken and his three pokemon floating around him. Vullaby, Beedrill and Gastly. Two of the three pokemon were glaring down at naruto and iruka but Gastly. Gastly just looked like he was looking for something entertain it.

"Mizuki what is the meaning of this. Why did you have Naruto steal the scroll of sealing. Why?"Iruka demanded form mizuki. Mizuki smiled darkly.

"Why else so I can kill the demon brat of course. And to add on to it I am going to steal the scroll of sealing and give it to my master so I will be given a top position." he says before he looked at naruto.

"Have you ever wondered why people look at you with such disgust and disdain. Do you know what happened the day of your birth?" mizuki says ignoring the yelling of irka telling him to stop.

"The Yondaime killed the kyuubi no kitsune. That's what you and Iruka-sensei taught us" naruto said uncertain if it was true now.

"That was the lie that the fool of a hokage made us tell the younger generation. That day te yondaime hokage sealed the Kyuubi into a new born child. That right you were that child. you are the kyuubi now die." Mizuki tosses the dai shuriken at naruto who was to shell shocked to move.

"NARUTO"

Naruto was broken out of his stupor when he was tossed onto the ground. He looks up and sees iruka above him guarding him from the dai shuriken that was now lodged in his back. Irukas pokemon rushed over to check and see if was alright

"I. Iruka-sensei" naruto said barley above a whisper. His mind was slowly shutting down on himself from all the information he was hearing.

"You are the monster that killed hundreds of people including Iruka beloved parents" mizuki tells him.

When naruto hears this he looks up at Iruka and into his eyes for some sign of it being a lie. But when he looked all he saw was pain and regret. Naruto pulled himself out from under iruka and and took off running with the scroll in hand.

"NARUTO WAIT" iruka exclaimed worried about all the wild pokemon in the forest.

"Crap he got away with the scroll. Gastly chase after him" Mizuki ordered and Gastly took off after naruto. UNbeknownst to the three people and six pokemon there were 12 sets of eye watching them, 8 of those sets were up above them watching while the other two were watching in an office.

(up above)

Up above the forest a Hydreigon was flying carrying a man in his late teens to early twenties on his back. The man wore a black pair of training clothes and black ninja sandals. His face while young looked aged with his tear troughs and his stoic expression the most outstanding feature about the man were his glowing red eyes with three rotating tomoe.

(should I intervene? This has gotten out of hand but at the same time I am curious as to how naruto will fully handle the truth and what his decision is. No I will wait a little longer and intervene when it looks as though someone is about to die.) the figure thought.

"Hydreigon follow after naruto" the man commanded and with a low growl of acknowledgement the dark dragon sped after the young boy.

(in the office of the hokage)

The third hokage Hiruzen Sarutobi sat in his office looking at the scene happening in the forest through a crystal ball with his trusty Infernape by his side slightly whimpering in sadness at seeing the young boy he used to play with in such distraught.

"I know old friend I am hurt to see this as well but it is time he learned the truth" Hiruzen said to his infernape. Infernape nodded in agreement.

(with naruto)

Naruto was running through the woods trying to get away from everything. His mind was going through everything he was told and the looks of hatred and disgust that the villagers had given him. He continued to run until he tripped over a fallen branch he fell putting a tear into his jump suit pant leg.

"Dang it that won't be stitchable and this was my last pair to go with the jacket." Naruto says as he slams his fist into the ground in frustration both at the tear and all the information that was basically shoved down his throat. .

Naruto was about to continue beating on the ground while trying to hold back the impending tears in his eyes when he was broken out of that line of thought and action by a deep and loud roar. To most people they would have thought it was a normal bear but naruto having studied pokemon for several years recognized it as being an Ursaring and an extremely mad one at that. Naruto knew it was close and hoped that it wasn't meant as anger towards him being near or in its territory. After keeping still and listening he heard the piercing shriek of a pokemon in pain.

Naruto rushed into the direction hoping to stop any violence happening and escalating. It took naruto three minutes running at top speed to reach the origin of the sound. Naruto slowed and quietly approached a tree to crouch behind and peak out from. What he saw shocked him. There standing in front of a huge Ursaring was a small rufflet looking like it went through an A-class jutsu it was covered in small cuts and bruises the most worrisome injuries that naruto saw were a large gash on his chest and a smaller one over his right eye. Naruto was confused he knows quite well that rufflet will challenge bigger and stronger opponents to become stronger but they usually don't fight this hard to the point they look like they are going to keel over and die. As naruto scanned the surrounding area for a reason as to why the young(he's guessing) Rufflet is fighting this hard, the answer came in the form of three baby pokemon. A Dedenne, Lillipup and a skitty were huddled up against a tree behind rufflet. Naruto understood rufflet was just trying to try and protect the three baby pokemon. Naruto being naruto was not going to let the small yet brave pokemon fight by itself so he looks for a rock of some sorts to help get the hibernation pokemons attention off of the baby pokemon and on him. He finds a good sized rock and tosses it at the ursaring before stepping out from behind the tree.

"Hey yogi go bother some combee" Naruto antagonizes the ursaring who lets out a roar of anger at the boy in front of him monetarily forgetting about Rufflet and the three young pokemon. While the three baby pokemon escaped the rufflet stayed and watched the young man stand up to the clearly larger pokemon. He watched the young man take another small rock and throw it at the Ursaring who swatted it away and began to charge the young man who ran in the opposite direction. Out of curiosity the rufflet followed after the young man and the ursaring.

(Naruto and the Ursaring)

(Crap. Crap. Crap. CRAP! Naruto you couldn't have left well enough alone but NOO you had to be a hero and try and save those pokemon well guess what now you're going to get mauled by an ursaring!) Naruto thought to himself as he ran, he looked behind him and saw that the ursaring was still hot on his tail and when he looked in front of him he saw a Gastly floating next to him as he ran naruto was so shocked he jumped back and almost took a slash attack to his back if not for his honed instincts. After looking at the gastly he saw that it was Mizukis gastly.

" I know your master probably sent you to track me but will you help me knock out this guy" Naruto begged the pokemon. Gastly looked at naruto before making a decision and nodding.

"Okay then use uhh use Sucker Punch" Naruto tried not knowing exactly what level Gastly was. To naruto's relief Gastly had no issue using the move disappearing and then appearing to the side of Ursaring and tackling it taking the Ursaring By surprise.

"Great now use Hypnosis on ursaring while it is recovering" naruto commanded. Gastly appeared in front of ursaring and and his eye began to glow red ursaring looked into its eyes and began to become sleepy slowly wobbling on it feet before falling backwards sleeping like Snorlax, snoring like one to.

"Yatta I won my first pokemon battle even if it wasn't with my own pokemon" Naruto said. Gastly floated over towards with a happy face on it. Naruto strokes the top of gastly head to show his appreciation for battling with him.

" I really appreciate you battling with me I wish I had some snacks to give you" this shocked Gastly as his master had never given him or the other pokemon snacks.

"Rufflet"

That sound caught the attention of both shinobi and pokemons attention. Out of the bushes came the injured rufflet seeming to be haggard naruto rushed over to it and took it into his arms.

"You look exhausted but then again what do we expect you to look like after battling a ursaring." Naruto said as he looked over the injured rufflet. He was broken out of his observation by the sound of tree branches shifting under weight and a thump on the ground. Naruto turned to look out from behind a tree before quickly pulling back hoping to not be seen by Iruka, Mizuki or there pokemon. Iruka slumped against a tree in pain as his pokemon battled Mizukis pokemon.

"Why do you fight to protect naruto you hate the kyuubi so why." Mizuki asks Iruka. Naruto sat against the trunk not really wanting to hear what Iruka was going to say knew he had to.

'You're right I despise the kyuubi for what it did to my family' Iruka said/ Naruto hearing this lowered his head in shame and sadness, shame because he thought iruka was the only one to care for him and was wrong and sadness because he was truly alone in life.

"But Naruto is not the kyuubi he is a victim of its mayhem as much as any villager is and I see him as my little brother so I will protect him. No matter what the village thinks of me no matter if it cost me my life because I believe in naruto he will achieve anything he wants to" Iruka said. Naruto hearing this was shocked by this he was filled with joy at hearing that his trust was not misplaced with his sensei. The two pokemon next to him were happy for the boy even if they didn't know fully what the adults were talking about.(A/N this is not me saying they are dumb it is me saying they don't know that naruto is the holder of the nine tails.)

"Then you are a fool and will die a fool." mizuki said as he took his second dai shuriken and threw it a Iruka. Iruka braced for death feeling that he was not able to move. He waited and waited but death never came not even a little pain. Iruka opened his eyes to see the reason he was not dead.(not that he was complaining)

Standing on a high tree branch was naruto with the dai shuriken in one hand and the scroll of sealing in the other. By his left leg was an injured rufflet trying to look intimidating but failed on the fact he was tired and floating beside Naruto's right shoulder was gastly.

"What the hell are you doing you stupid pokemon you were supposed to capture him not befriend. I should have abandoned you when I saw you weren't anything like my other pokemon to soft and weak." Mizuki yelled at his Gastly who only lowered it head in sadness.

"SHUT UP. Gastly is a great pokemon and is more deserving of a better trainer than you'll ever be." Naruto shout at the top of his lungs at Mizuki at the way he was treating gastly.

"Yeah well he's my possession so I don't care what you think. What I do with him is none of your business." mizuki says not caring about the law thinking he himself was above it.

"No you can't just like if you lay another hand on iruka sensei or if you lay a hand on Gaslty I'LL KILL YOU" Naruto shouted. This greatly amused Mizuki. Gastly was shocked that this boy was willing to protect him even if he wasn't his pokemon.

"Oh yeah I like to see you try. I'm an elite shinobi while you're just a kid who can't form a single clone." Mizuki bragged not seeing Naruto as a threat.

This tict Naruto off." Oh yeah then watch this" Naruto yelled as he formed crossed ram hand sign.

"SHADOW CLONE JUTSU"

A large plume of smoke surrounded the area they were in and the sound of something popping into existence was heard. When the smoke cleared the two chunin were in shock at what they saw.

Among the trees were hundreds of clones of Naruto on standing in every limb of every tree in the vicinity. Iruka was in awe at what his young student was capable of doing.

(These aren't illusions they are real clones of himself, but how?) Iruka thought.

"So what now mizuki-teme are you going to be able to kick all of our butts." one of the Narutos said before jumping out of the tree with the army following after him. The look of fear was etched on Mizukis face before everything went dark.

It took Naruto all but 3 minutes to beat the living crap out of mizuki who was not a puddle on the ground.

Naruto stood in front of Iruka looking a t tad guilty thinking he might have gone overboard on beating up mizuki. His pokemon were beaten and unconscious by Irukas pokemon all except for Gastly who was floating next to naruto.

"So what is going to happen to mizuki-temes pokemon."Naruto asked Iruka.

"Well more likely the pokemon will be taken into the custody of anbu and they will decide whether to give them to another trainer or they will be released to to the pokemon preserve." iruka told him naruto looked sadden that the pokemon might not get another trainer that was better than mizuki especially his new friend Gastly. Iruka seeing this look had an idea.

' you know naruto if you want you could take Gastly as your own pokemon, I doubt the hokage will mind all that much." iruka said. Naruto got all excited before he remembered something.

"But Iruka-sensei I'm not a shinobi so that means I'll have to go through all the testing to find out if I'm capable of raising a pokemon as a civilian." naruto said with his head lowered in sadness. Iruka just smiled and told Naruto to close his eyes. Naruto was confused as to why but did so anyway. Naruto felt Iruka remove his goggles of his head and put something in there place.

"Okay naruto open your eyes"

Naruto did as iruka instructed and opened his eye to see iruka's smiling face but noticed something different about him. It took him a moment to realize that iruka was not wearing his headband. Wondering where it is he looked for it before realizing it was atop his own head.

"Congratulations naruto you have graduated." iruka said to naruto.

Naruto was struck with so much joy he was about to jump and hug iruka if not for the squawk of pain behind them when they looked naruto once again saw the injured Rufflet on the ground panting.

" oh crap i forgot about the little guy we have to rush him to the pokemon center." naruto exclaimed as he rushed to grab the eaglet pokemon before rushing to the pokemon center with his new Gastly following behind leaving an injured Iruka and a knocked out Mizuki in the forest with the scroll of sealing.

The first official chapter of trainers of a shinobi variety is done i hope you enjoy it.

Signed Hallowmask123