Chapter 1
Okay so, this is a story with several changes prior to the Shippuuden series. I am planning to write a Prologue later that explains some of the changes, but for now I'll use flash backs or just mention them as I write.
Naruto is different in this story, he was trained when he was young by Shisui and he possess a pair of Sharingan which are capable of becoming Eternal Mangekyo Sharingan. Shisui taunt him a lot of Jutsu that were supposed to be secret and taught him to properly wield his Sharingan. Because of his relationship with Shisui and the way he grew up his personality is different and that means that his choices and feelings are different as well.
…Hidden Leaf
It had been two and a half years since Naruto left to train with Jiraiya. The village was at peace, until Konohamaru Sarutobi burst through and alleyway knocking over several barrels that were outside of Ichiraku Ramen. "Hey! watch where your going Naru-I mean Watch it Konohamaru!"
Konohamaru smiled back, wave to the man and raced off, chasing a cat.
Meanwhile, Sakura was in Ino's shop buying flowers. "So, who are these for?"
"For my house, my room seems a little dull lately. I thought that these could help a little."
"Your right they're beautiful. I bet your board, never going on missions and always training."
"Not really. But Naruto should be getting back soon…" noticing the stunned look on Naruto's face she paused for a moment, "what's wrong Ino?" she asked with a concerned tone.
"Oh… uh… nothing" Sakura could immediately tell that she was lying but she decided to drop it.
"Anyway, I best go… I'll try and finish early so that I can meet Naruto and the front gate. You should come to…" she was cut short when Konohamaru burst through the door, following a small cat that leapt onto the counter.
"Hey! Stop!" Ino yelled trying to get the young ninja's attention, but he wasn't paying attention, he was too engrossed in the chase to notice anything else.
'Damnit!' Konohamaru thought as he narrowly missed the cat and hit the wall.
The door was about to close, the cat slipped through the small gap and Konohamaru gave a loud sigh. "Damnit!" he tapped a collar that was around his neck "I lost it… wait, hold on."
The door opened and Lady Tsunade entered, holding the cat. "Lost something" she smiled, Konohamaru raced to the cat and took it from her.
"Thanks granny!" he cheered then told the others over the radio he had the cat.
"Granny?!" Tsunade looked at him, both shocked and angry.
'Isn't that what he called her?' Ino thought as she watched Lady Tsunade scolded the young ninja.
…
Konohamaru was standing alongside his team in front of Lady Tsunade in her office, Iruka Sensei, Shizune and Sakura all present. "Well done on your mission team Ebisu" Lady Tsunade congratulated the team.
"It was only a cat, I wanna go on a higher ranked mission one worthy of the seventh Hokage's time" Konohamaru complained.
"Seventh?" everyone said in unison, looking at him slightly confused.
"What happened to sixth?" Lady Tsunade asked.
"Sixth is taken, Naruto's gonna get that" Konohamaru smiled as did everyone else.
…Meanwhile, on a road leading to the gate of the Hidden Leaf
Jiraiya was walking along the dirt road, a bag and scroll over his shoulder. He reached the gate and walked straight passed the booth where two ninja spotted him "isn't that…?"
"Yeah" they whispered.
Jiraiya went straight to the office where Tsunade was with team Ebisu and Sakura. He knocked on the door gently. "Come in" Tsunade called out, unaware of who was outside.
"Hey!" Jiraiya waved as he opened the door, everyone smiled when they saw him, Konohamaru immediately looked behind him hoping to see Naruto. "I'm back Tsunade, did you miss me?" he asked.
But he got no answer, they were each confused as to where Naruto was, even with the door wide open and Jiraiya now inside the room Naruto was still missing.
"Where is he?" Sakura asked.
"What… you mean Naruto? We split up about four months ago" he stated shocking everyone there especially Tsunade and Shizune whom knew of the threats to Naruto's life.
"Can you guys give us a minute" everyone but Tsunade, Shizune and Jiraiya left the room.
"I feel like I'm in trouble" Jiraiya mumbled.
"Yes! you are! The whole reason you left with Naruto was to protect him from the Akatsuki, but for four months he's been on his own!... UGH!" she walked to the window and looked out at the gate at the entrance to the village. "He could be captured or… killed" she hesitated to speak for a moment.
"Tsunade, it's alright Naruto can take care of himself. Over the two years I spent with him he made massive progress and he is supposed to arrive today, so we'll know if something's wrong."
Tsunade looked out of the window, her face twisted into a concerned expression, similar to the one that Shizune had for her. 'Please be alright Naruto… be alright' Tsunade repeated over and over in her head.
…Forest a day of travel from the leaf
Naruto swung round a tree branch propelling himself into a strange figure that he was fighting. "You're pretty good" Naruto commented wiping some blood off the corner of his mouth. "Although I do need to wrap this up, I'll be late otherwise." He smiled cruelly.
*BOOM* suddenly a massive explosion shattered the tree he was standing on as well as blowing a massive hole in the forest.
A white bird, several times the size of Naruto flew passed him as he regained his balance, a hand grabbed him by his ankle and he was carried into the air. 'Crap, now I'm screwed.'
Naruto struggled to break free, reaching into the pouch tied to his leg he took out a paper bomb which he attached to the bird then using a Rasengan he broke free of its grasp. "AHHHH!" he cried out as he plummeted toward the ground.
He flipped so that he was facing upward and peered at the blond-haired attacker, dressed in the iconic black cloak with red clouds on it that the Akatsuki wear, two mouths on either of his hands.
Naruto was wearing a different outfit as well. A black jacket that was left undone and a white shirt, he also had black saddles and trousers which reached three quarters of the way down his legs. He still had his headband fastened around his head, but the band was rather dirty.
"What was your name again. I mean your cloak gives it away that you belong to that boy band… the Akatsuki but who're you?" he taunted the ninja.
"The name's Deidara, now hold still so I can destroy you with my art!" he threw a strange shape of clay at Naruto, and in a puff of smoke that clay transformed into a spider which landed on the same branch Naruto was on.
But, before it could explode Naruto dropped off the branch and bouncing off another branch he propelled himself toward Deidara with a kunai in his hand.
Shocked Deidara didn't have much time to react and was left with barely any room to dodge, getting cut by the kunai on his cheek. Grabbing hold of the branch Naruto then span kicking Deidara into the strong trunk of the tree then stabbing him in the shoulder.
"GAH!" Deidara tore himself from the kunai, ripping both his cloak and his flesh. With a small explosion he then distracted Naruto while he escaped, his torn-up expression told of both his pain and the frustration of having to retreat.
'He got away… damnit… oh well, at least I got a souvenir out of it' he picked up the torn piece of cloak, a large piece of fabric with the red cloud on it. 'At least now Pervy Sage will believe why I'm late.'
He went onto a road that was nearby, lifting a rock and taking a bag from behind it. He slung it over his shoulder and began walking down the road toward the leaf Village.
…Hidden Leaf, Late at night
Lady Tsunade, Jiraiya, Shizune, Iruka and Kakashi were all waiting at the gate for Naruto who had yet to arrive. Tsunade was obviously angry, and Jiraiya was trying to keep his distance while wishing that Naruto would show up.
They continued to wait but saw no sign of Naruto, meanwhile Konohamaru was working hard cleaning Naruto's apartment making sure that there wasn't a speck of dust in the entire place. He had snuck out to do this expecting that Naruto would be home soon from the way he had seen Tsunade acting, he thought that Naruto was going to arrive the next day though.
Konohamaru's error seemed more accurate than the assessment of Jiraiya and the others though, as despite waiting Naruto didn't show up that night.
Lady Tsunade gave Jiraiya a stern look before returning to her office with Shizune.
…Hidden Sand Village
The council were all sitting around a table, Gaara at the head wearing his Kazekage robes.
This meeting is the same as the one in the anime, they talk about the Akatsuki and the defences that have been put in place to stop them should they attack.
…Hidden Sand Village
It was the next day, the sun was incredibly hot, as it always was in the Hidden Sand. Gaara was watching over his city from a small circular window. But he was unaware that at one of the Village's entrances two cloaked figures were approaching the team that was there to defend the village.
"Wait a sec… those cloaks… red clouds, they're Aka-!" the ninja was cut short when he was stabbed by the man beside him. The same man then proceeded to execute the others that were there guarding the village giving the two members of the Akatsuki an entry point that was free of distractions.
"Sasori my man, I think I'll be taking this one" Deidara removed his hat revealing his face, including a scar that Naruto made when he cut him. He made one of his clay birds and flew into the sky, high enough that he could see the village with his eyepiece and pick out the ninja that were watching the sky.
"Alright… six, hah, that's it. This should be easy." He noticed Gaara in the window. "That's cute, he's watching over them, can't believe this Kazekage is the Jinchuriki though hard to believe."
He slipped his hand into a bag that he had on his shoulder. Pulling out six small balls of clay he moulded them into small spiders which he dropped into the village one after another.
*BOOM*
Simultaneously the bombs exploded, sending the sand ninja into a frenzy. They desperately began to search for the attacker, but it was Gaara who spotted the enemy ninja.
Using his sand Gaara flew into the sky, sending a portion of his sand at Deidara for a surprise attack, but Deidara had already spotted the young Kazekage and was prepared for his attack.
A combination of explosions and constructs of sand filled the sky, the villagers' eyes drawn to the spectacular battle.
When the smoke from the explosions cleared Gaara was surrounded by a sphere of sand so thick that Deidara couldn't penetrate it.
"This might be a little more complicated then I thought, sorry but it looks like I'm gonna be late Sasori" he muttered to himself.
The distance between the two shrunk as Deidara flew toward Gaara's sand sphere. But when he got close a section of it shot from the main body and chased Deidara, wrapping around his arm and tearing it off when Deidara tried to fly away faster. "AH!" his cries echoed through the air as Deidara glared at his missing arm and then glared at the small hole that Gaara was peering through.
Ninja on the ground were readying weapons to aid Gaara in his fight, but seeing them Deidara gained some inspiration. "Haha, time for some more art I think" he laughed while mixing more clay, changing its shape into a strange looking bird.
It increased in size when Deidara dropped it, becoming dozens of metres high and when he dropped the clay figure Gaara's eyes widened as did Kankuro's as he watched from below.
*BOOOOOOOOOOM*
The massive explosion could be seen for miles, a giant ball of fire at the centre. Deidara looked down at the destructive blow with a cruel smile. "This is true art!" he cheered.
His expression changed when he realised that the village undamaged due to the sand which Gaara had amassed to block the explosion. The village people stared in amazement, unaware of how much chakra that the defence used, all but Kankuro whom knew what this meant for his little brother.
"No… G-Gaara" he mumbled.
"It's noble that you tried to protect them, a true Kazekage. But it now gives me the advantage. Using all that sand means you've used up almost all your chakra" Gaara began moving the sand so that it wasn't over the village anymore. "Hah! Depleting your chakra even more to save your people." He sighed. "Well it doesn't matter now" they were now hovering over an empty area of the desert.
A small bird flew near to the sand shell that was surrounding him and shattered his defence and knocked him unconscious.