As stupid as it might seem, this is a Naruto/Pokemon x-over. And let me tell you, there is a surprising amount of these out there. Other than no flames, on to the summary.
Summary: After the Garchomp incident, the once ignorant Elemental Nations become aware of the Pokemon World. But the Pokemon World does not know of the Elemental Nations. War is on the horizon for the Pokemon world and the only question is, who will the EN, or at least, what faction within the EN, will throw their weight behind? PostWar!Naruto Ken, fuin, wind jutsu Naruto. Fully powered Kakashi. Renne-sharingan!Sasuke and whatnot. Naruto will be slightly emotionless. Not completely though. I'll start from Ash's perspective. Takes place in XY/XY&Z and starts before the Garchomp Incident.
Naruot Main Characters: Naruto Uzumaki (Fox), Sasuke Uchiha (Wolf), Sakumo Hatake(OC Dog), Hinata Hyuuga (Turtle), and Sakura Haruno (Slug). (Team 7 + 1 as ANBU)
Pokemon Main Characters: Ash Ketchum. Serena Yvonne. Clemont and Bonnie (pick a last name)
Notes: PostWar. Ay as Raikage, Kurotsuchi as Tsuchikage, MeiTerumi as Mizukage, Gaara as Kazekage, Kaksahi as Hokage, Major OOC! The Garchomp Incident lasts 72hrs because of civilian clean up. Orre Island will replace the Sevii region that will be east of Kalos instead of west of Kanto.
Clement and Bonnie had just walked out of the lab section and were observing the various Pokemon that were enjoying themselves in their environment when Ash came to join them.
"So Ash, how's Froakie?"
"He's doing just fine. Froakie's real strong."
Soon after, Bonnie ran off to play with them.
"Wow! So many Pokemon. There are too many to count."
Ash smiled at the sight. It was then that Ash asked Prof. Sycamore about what he researched.
"If I told you, Pokemon had an additional evolutionary stage, what would you tell me?"
"Are you serious?"
"So you're saying Garchomp can still evolve?'
The professor shrugged.
"Possibly. That's my research topic. There have been several reports of Pokemon evolving in a way that we researchers refer to as mega-evolution."
"Woah. Mega-evolution. A lot of the mechanics are still a mystery but we believe that a strong bond as well as a special stone play a key role in evolving."
"Strong bond, huh"
Ash whispered.
"Pika?"
"Once more, a Pokemon is able to return to its original form after it evolves."
Ash gasped.
"It can turn back?"
Meanwhile with Jessie, James, and Meowth
"Mega evolution. Strong stuff."
Said the only talking pokemon in the world.
"Further evolution. After evolving!"
Said the man with purple hair and a male version of a Team Rocket outfit known as James.
"Then the way is clear. The time for catching pokemon is here"
They all smiled evilly and donned their "disguises."
"Oh fellow researchers?"
Said the disguised Jessie.
"We've come to research mega-evolution!"
Said the disguised James.
Soffie walked in the front room with a sceptical look on her face.
"I wasn't told anything about this."
Her lab tech/assistant came in.
I'll check with the Professor."
Team Rocket whispered to each other.
With Froakie
Froakie opened one of his eyes to see a disguised team rocket trying to do something evil in the lab knowing it wouldn't be good, he waited for his capsule to open and rushed out to expose the three evil doers.
When Froakie enters the room and I'm only writing that because I just his a major roadblock i can't get around
"Froakie fro!"
Froakie said while pointing at the trio.
"That's the one that blasted us off. So it should feel our research wrath first."
"Now let's get ready to research!"
James said.
"Now please step aside. This is not for the faint of heart."
Soffie was pushed away by Jessie
James tossed a control device at Froakie. And it would have hit. Had Garchomp not gotten on the way.
Jessie ran back to her team.
"Not our intended target but this will do. They did say Garchomp can mega evolve."
Froakie tried to get the machine off Garchomp but ended up getting blasted back in the process. James pulled up the control panel and pressed several buttons.
"Garchomp. We insist that you come along for the ride."
Garchomp let out an agonizing scream that alerted the entire lab. Ash was the first to respond.
With Ash and co.
"That was Garchomp!"
Everyone came running towards the front room.
Back to everyone else
Garchomp let loose a random hyper beam that destroyed a good section of the indoor balcony and started to thrash around causing more destruction. But suddenly, the device went from blue to red, causing the pokemon to go on a rampage.
"Well this isn't going according to plan."
"Come on Garchomp, get with the program."
Right after Meowth said that, Ash and co. walked in.
"Garchomp!? What's going on?"
Soffie filled them in.
"Professor! Those three!"
He gasped.
"Alright! Who are you?!"
I am not going to bother with the Team Rocket motto because I find it boring as hell.
"You are such annoying bad people!"
Came Bonnie's lound comment. The Professor was curious.
"Who are these people?"
"Team Rocket. Bad people who try to steal other people's pokemon and cause problems."
Jessie mocked him.
"Tryyyy? We succeed."
"And now Garchomp will fill that need."
"There's nothin' like doin' an evil deed'."
"Unbelievable. A talking meowth."
"The wisdom gushes out of my mouth."
Garchomp, having enough, even in its enraged stage, fired a hyper beam at the terrified Team Rocket and it sent them flying through the roof.
"We're blasting off again!"
"Come on Garchomp. What's going on?"
Ash worriedly asked as Garchomp thrashed about. In response, Garchomp let loose a hyper beam that almost took everyone's heads off.
"Hey! What was that for?!"
Clemont may have had the answer.
"Hey, look at its neck."
"It's some kind of color."(Spelling)
Said Prof. Sycamore.
Soffie filled everyone in.
"Professor. It's from those people!"
"What?!"
"Garchomp jumped in to save Froakie."
And just a few short seconds later, Garchomp started to glow an eerie red and then released some sort of energy. An energy every living thing felt and it didn't go away.
"What was that?!"
And then Garchomp proceeded to crash through the front wall and wreak havoc in the streets.
"Garchomp!" Garchomp must be in a lot of pain."
"Pika!"
Bonnie's eyes began to water.
"What's gonna happen to Garchomp?"
Ash ignored her unintentionally.
"Let's go after it."
"Pika."
Ash was about to rush out the front door when Froakie stopped him.
"Fro!"
"Do you wanna come too?"
"Fro!"
"Great! Come on!"
Prof. Sycamore gave his warning.
"Please be very careful. Soffie. Check to see if everyone else is alright."
She nodded.
Then Bonnie turned to Clemont.
"Clemont. I wish we could help poor Garchomp out."
"Then let's go too."
Prof. S sighed. As one of the main powers in Kalos, he should stop them for safety reasons. Simply because if Ash dies or gets hurt, it'll be a political nightmare. But he knew that there was no stopping people like Ash. So he let it be.
"I'm 22 years old and I feel like I'm 60. That's just not right."
Line break
Garchomp was rampaging and Officer Jenny was warning people.
"Attention citizens. There's a rampaging Garchomp. Please evacuate the area immediately."
It didn't help that Garchomp was letting out random hyper beams and when they weren't random, they were targeting something.
Like the news helicopter.
"Garchomp just made it to the top of Prism Tower. And just fired a hyper beam right at our helicopter."
Soon after, Ash made his way to the base of the tower.
"Garchomp!"
"Pika!"
"There you are Ash."
Said Bonnie. Ash looked at Garchomp.
"I have to try and get close to it."
Clemont was very surprised.
"What?! That's dangerous!"
"No. Garchomp's the one who's in danger. I've gotta find a way to get that thing off."
Clemont thought for a moment.
"I know, if getting close to Garchomp is what you need to do, I think I just found a way."
"You did?"
Line break
"There's an emergency stairwell that leads to the top from here. Good thing I brought my backpack."
I'm going to skip the "Science is so amazing", part
Ash was first to enter the building but Garchomp fired a hyper beam at them and if Clemont didn't grab Bonnie and jump, it would have been very, very, bad.
"Are you guys okay?"
"We're fine Ash! You go on ahead!"
"I'm on it!"
Ash took off into the building.
Prof. S pushed through the crowd and when one of spectators saw Ash and pointed it out, he had to resist the urge to facepalm.
'This is an international incident waiting to happen.'
He whispered to Officer Jenny.
"Officer. It's me. Prof. Sycamore. As head scientist of the Kalos Region, I need to make sure he doesn't fall. If he dies, we'll look like morons for letting a kid climb a building and Kanto will look irresponsible for allowing him to leave the region. I'm so sorry I have to use my position like this."
"It's fine I promise. I'll make sure he doesn't die."
With Ash
Ash looked back down at everyone and approached Garchomp slowly. It didn't stop Garchomp from yeeting a hyper beam that forced ash and his pokemon to dodge into the building. Ash tried one more time but it just flew to the roof.
"Garchomp! Come back!"
Ash looked around and found a ladder and began to climb it.
"I'm here to help Garchomp."
News chopper
"Unbelievable! That boy has climbed to the top of Prism Tower."
With Ash and Pokemon
Garchomp fired another hyper beam at the trio and they dove towards the wall. Pikachu prepared a thunderbolt.
"No Pikachu!"
"Pika?!"
"Wait. We don't want to attack Garchomp. It'll only make things worse."
Ash jumped back as another hyper beam was fired.
"Ah! Garchomp! I know it hurts. But you have to calm down."
Garchomp seemed to at least slow down and back up a little. Until he reached the edge.
"Garchomp! Look out!"
Thanks to Froakie's quick thinking and frubbles, he anchored Garchomp to the ground.
"Good thinking Froakie. Garchomp! Let me get this thing off of you!"
Ash said as he jumped on Garchomp's neck.
"It won't come off. Iron tail of the color!"
"Pika! Pikachu!"
And with that, the Arcius forsaken machine fell off and Garchomp collapsed onto his knees.
"Glad that's over. Don't worry, help's on the way."
Pikachu tried to run over to Ash but the edge of the tower gave out and he started falling at a fast pace.
"Huh? Pikachu!"
Ash jumped off the building and hugged his pokemon tightly in hopes that Pikachu would survive the fall. But none of them would have survived. If not for mega Blaziken.
"Woah it's you. Thanks a lot."
Blaziken set them down and jumped off into the distance. And Prof. S came running towards Ash and Pikachu.
"Ash Ketchum! Don't ever do that again! You have no idea what would happen if you got hurt, or worse, died! I won't explain to you but please don't do that again. We were so worried. Are you okay."
Ash sighed.
"Yeah. We're all doing great. And Garchomp's back to normal."
"Good. Good. Go back to my lab and get some rest. Pokemon knows you need it."
Ash nodded.
Meanwhile in the Elemental Nations (EN): Lightning country
A squad of Cloud ANBU were talking about the strange energy flare they all felt coming from off the northern coast.
"Did you feel that?"
"I sure did captain. And I wouldn't be surprised if even Hidden Sand felt that."
"Turtle and Mouse. Go to Raikage and tell him about the energy flare. He'll undoubtedly conduct an investigation."
"Yes sir!"
Turtle and Mouse said together.
Outside the Raikage's office
Turtle was the first to speak.
"How do you think he'll take this?"
"Like a bull, no doubt. However, he won't go charging in blindly. If anything, he'll send a SHOCK squad to investigate. I would call that overkill but I think the whole planet felt that I know for a fact that wasn't chakra. And he'll call for another summit depending on what we find. This could either be some sort of accident or a world-changing event. We shall see."
Mouse sighed and continued speaking.
"Well, the man won't wait forever. Let's get this over with."
Turtle nodded.
They two ANBU entered Ay's office and bowed respectfully.
"Turtle and Mouse. I assume you're here about that unknown energy flare that came from beyond the northern coast?"
"Yes sir."
"In that case, Turtle, you and Mouse are in charge of a full squad of ANBU SHOCK. Your mission is to investigate this strange energy that can still be felt. I will write a letter to the other nations asking if they felt this as well. Pack enough food and water for a year long mission. You leave in 2 days. You're dismissed"
"Yes sir!"
They said together. And with that, they body flickered out of the room.
With SHOCK squad: time skips to when they see something.
It was 11PM and everything was quiet. And then it wasn't. They saw an island up ahead that looked like it had people on it. Everyone on the ship was fully stocked and ready to go so a fight won't be a problem. Turtle began to give orders.
"SHOCK Rat. You're in charge of exploring that island. Judging by the lights, I'd say there's some form of civilization. Do not attack unless attacked first. You are about 4 miles from the shore. I'd recommend a good shunshin every so often. Also, as soon as you come back, we will report straight to Lord Ay. That's all dismissed."
"Yes taicho!"
They said together. Turtle and Mouse looked at each other.
"What do you think they'll find?"
"Hopefully, a peaceful civilization. But something tells me this isn't the only region on this side of the world. So I doubt we'll decide to wipe out their entire civilization because one island did something stupid. Right now, the only thing we can do is wait for them to return."
Mouse nodded and went to his quarters.
With SHOCK Squad when they hit land
Seeing that Rat was put in charge, he was the one to give orders.
"Alright team, we don't know if we've been spotted or sensed so stay alert. Our mission is to explore the first 25% of the island. It's called the Orre Region apparently. Let's move."
Cat, Dog, Wolf, and Fox nodded and dashed off at mid-ANBU speeds. And a few hrs later. Rat ordered them to stop. They found a "Police Station" and decided to investigate. And although they didn't get a name the higher-ups were clearly corrupt. Wolf was first to talk quietly.
"Sir? Do I kill them?"
"No. No matter how corrupt the authorities are, a lititimant investigation will be launched if someone either disappears without a trace or suddenly dies of unnatural causes. However, Once we explore the whole region, the Raikage will decide if we should get a foothold or launch a total invasion. Come one, let's keep moving."
And with that, they continued to explore the region. Or at least, the 1st 25%.
Time skip: SHOCK'S return to ship
Turtle, being the first one, told the captain to report.
"Report."
"Yes sir. As weird as it sounds, there are other humans and these strange creatures of many kinds they call Pokemon. We don't know if they have a chakra network."
"Interesting. Continue."
SHOCK Rat nodded.
"Soon after landing, we found a police station. However, their corrupt beyond belief so assassination was out of the question without lots of planning. Also, the region is very unstable. It looks like the aftermath of the Battle of The Ten-Tails. My guess, it was ravaged by some war. Although 90% of people owned pokemon, we were knee deep in the desert and didn't find a single Pokemon. There were times when Cat felt unusual presences underground but these humans still give off the same feeling as any other ninja or civilian. Meaning, she felt Pokemon that are mortally terrified of humans because of whatever war or tragedy fell upon that region."
Ay was very interest.
'If wasn't interested before, he certainly is now.'
"Mysterious creatures? Can you give me a deception?"
"I'm sorry My Lord. All we can say is they look like mutated forms of animals or miniature prehistoric animals."
"It's okay Rat. Does the region have a name?"
"Yes. The Oree Region."
"Interesting. You're dismissed. I will write a letter to the other nations. We are the only ones who know about that place but if we don't say anything, it won't stay that way and that could be bad. It's best if we let this out on our own terms."
The SHOCK squad shunshin-ed out of the room and Ay started to write the first letter.
CLASSIFIED! KAGE'S ONLY
Dear Lord Hokage,
As I'm sure you know, there was some sort of energy flare that was not chakra and was felt for days. I sent a full squad of ANBU and we found an entirely different civilization. We don't know if it's just that one island or if there's more to it. Even more, the inhabitants have these weird creatures called Pokemon. The full report is in the seal below my signature.
With regards,
Ay, 4th Raikage.
"Coyote, send this to the Hidden Leaf and these other copies to the designated kages."
He nodded and left with the letters. Ay sighed
"I'm too old for this shit."
And done. I intentionally left out Serena's part in all this because she isn't important yet. Also, you COULD look at this like a sequel to The Second Great War even though that's true simply because it follows a similar plotline. Although you would have to fill in the plot holes yourself. And no, I will not do an EN vs. Pokemon war. Only shinobi vs. pokemon politics. Because not all battles are won on the battlefield.