Disclaimer: I do not own Naruto.

Legacy of the Messiah

Chapter1: Awakening

Fire Country: Valley of the Dawn

People say that things always come in threes; bad things and good things no matter what they are always supposed to come in threes. The monstrous Mangekyo Sharingan for example had three sets of layers no matter which design you saw. Hell the Legendary Sannin was another example of this; they were all a team back when they were Genin under the Sandaime Hokage and they became some of the strongest fighters in the world.

Sadly no one wanted to inform Uzumaki Naruto of this little detail…

His current teacher was one of the Legendary Sannin; a man named Jiraiya and the two had come across each other during the one month break in the Chunin Exams. Since Jiraiya had knocked out the boy's original teacher for the exam he had to take the kid as his student and taught him the Kuchiyose no Jutsu. Sadly the boy's chakra network was so large it was nearly impossible to control; this was just made worse by the fact that Jiraiya discovered a suppression seal on him courtesy of his fellow Sannin Orochimaru.

It was removed however and Naruto's chakra control shot up to its normal level allowing him to master the water walking exercise. After many trials and errors at the Kuchiyose no Jutsu Jiraiya had enough and decided to have the boy try and draw out the monstrous chakra that was sealed in him by his own father.

'Forgive me Minato,' Jiraiya thought before he dropped her new student on the ground.

"W-where am I?" Naruto blinked and turned to him.

"Get up," Jiraiya ordered and Naruto shakily stood.

"W-what is it?" Naruto asked unsure.

"Your training ends here; if you value your life, you've got to figure things out for yourself," Jiraiya said simply.

"Huh?" Naruto asked confused before Jiraiya pushed him. The blond Genin reeled back and fell...straight into the large valley below, "oh crap!"

'Now...we'll find out whether the Kyuubi is pleasing or a curse,' Jiraiya mused as he saw his student fall.

Naruto tried to use chakra but every time he touched the wall he couldn't get any grip and kept on falling. 'If I can't grab onto something then I'll die; I'm really going to die...'

Naruto's Mindscape: Jinchuuriki Seal

Drip...

Drip...

Drip...

"Oh my aching head," Naruto groaned as he looked up. 'Where am I?' he thought as he looked around the sewer-like environment he found himself in.

A loud roar was heard as it echoed through the corridor...

'This feeling...it's that chakra,' Naruto narrowed his eyes as he made his way through the corridor and entered a large room. 'What the heck is this?' he asked in thought when he came across the large gate-like prison.

"Boy...come closer," a sinister voice said from the darkness beyond the gate.

"What the-" Naruto jumped back as four large claws attempted to catch him through the bars.

"I want to devour you but this gate...this seal prevents me from doing so...it won't open, how irritating," the voice growled out in frustration.

"Y-you are...Kyuubi no Yoko," Naruto breathed out.

"Child of my enemy, why have you come? Even those eyes of yours will not save you from me so tell me what you want or leave boy," the giant fox roared in fury.

Naruto gulped before he smirked up at the fox, "hey furball! I've been letting you live in my body all this time and you owe me rent! As payment I'll take you chakra."

Kyuubi's sinister laughter echoed through the chamber before he responded, "you've got some nerve brat. You are either very brave or very stupid...just like he was...very well boy, I will reward you for having such nerve but know that I am only doing this to help ensure my own survival."

Red liquid leaked through the bars and engulfed the blond where he stood...

Fire Country: Valley of the Dawn

"Kuchiyose no Jutsu!" Naruto called out as smoke exploded all around him.

Jiraiya smirked from his position above the valley, 'nicely done kid.' Just then Naruto shouted in pain, 'what's going on?'

The large toad, Gamabunta jumped out of the valley with Naruto who was covering his eyes and yelling in pain.

"Jiraiya! What's going on here?!" Gamabunta demanded as the Gama-Sennin jumped up onto his head and approached his student.

"This is Uzumaki Naruto...my new student and your new summoner...what's wrong kid?" Jiraiya asked concerned. Naruto looked up at him and Jiraiya had to stop himself from falling, "oh no."

His eyes...

"My eyes hurt Ero-Sennin; what's going on?" Naruto asked frantically as tears were falling down his face.

"Your eyes...you have the Rinnegan," Jiraiya gulped.

"He has the what?! Gamabunta demanded. "...No one has ridden on my head since the Yondaime Hokage...fine I will allow him to be a summoner but you had better make him into someone dependable Jiraiya," the giant toad disappeared in a poof of smoke allowing Jiraiya to catch Naruto as the two fell to the ground

"Naruto your channelling chakra to your eyes so stop channelling chakra and the pain should stop too," Jiraiya told him.

Naruto did as he was told he sighed in relief as the pain disappeared, "w-what was that Ero-Sennin."

"Look at me," Jiraiya ordered and Naruto did so. "It seems that your Rinnegan is different from Nagato's; you can deactivate yours at will."

"Rinnegan?" Naruto asked confused.

"A Doujutsu said to be the most noble of the three; supposedly it originated with the Rikudō-Sennin, said to be the first Shinobi. He created the original forms of jutsu; Ninjutsu, Genjutsu, Taijutsu, Kenjutsu, Fuinjutsu and Kinjutsu. It's a very dangerous Doujutsu," Jiraiya explained.

"Who is Nagato?" Naruto asked him.

"Nagato was an old student of mine...I heard he died awhile back but he also had the Rinnegan. It's rumoured that the Rinnegan always appears when the world becomes corrupt; it's capable of being both a godlike force and an all-obliterating instrument of destruction. I never thought I would see one again...I never wanted to see one again," Jiraiya continued.

"What should I do?" Naruto asked hesitantly.

"...For now keep the fact that you have those eyes a secret...we don't want any of the other countries finding out yet...and we definitely don't need Orochimaru taking an interest in you," Jiraiya told the blond.

Naruto gulped but nodded, "sure thing Ero-Sennin."

Jiraiya paused for a moment before letting out a sigh, "aright let's see if we can get you some semblance of control over the Rinnegan...and maybe Kyuubi's chakra."

Fire Country: Konoha / Chunin Exam Arena

The day of the exam finals the entire village was abuzz with activity but none more than the arena itself. People from all over the elemental countries had come to watch the tournament where the strongest Genin from the various villages came to see if they could be promoted. Among them were the members of the infamous Konoha 12 as they were being called now.

The Hokage, Kazekage and surprising the Raikage had shown up to watch the tournament even though he didn't have anyone participating in the exam. When asked why he was there he just said that he came to watch the tournament. The participant soon arrived and stood in the middle of the field but…Uchiha Sasuke; the heir to the Uchiha Clan had yet to arrive.

Silently Sarutobi Hiruzen cursed Kakashi constant lateness; why did he have to be late now of all times?

"…Sasuke-kun's still not here…" Ino said as she looked down from the audience.

"…" Sakura remained silent beside her as she thought about her missing team-mate.

Ino nudged her, "hey. I know you're worried about Sasuke-kun but…Naruto's match is first so why don't you stop fretting and cheer him on?"

Sakura turned to look at her old friend and smiled, "yeah".

"The first match of the Chunin Exams will now begin. Will Hyuga Neji and Uzumaki Naruto step forward while the other competitors go the fighters box to wait until it is your turn," said the examiner: Genma.

As the other participants left the two Ino couldn't help but say, "…he's up against Neji…can he actually win against him?"

"I…I don't know," Sakura said honestly as she remembered their mission to Wave Country and their time in the Forest of Death. She smiled slightly, "but…he won't go down easy".

"The kid doesn't stand a chance; he's fighting a Hyuga," someone in the audience spoke up and several others agreed with him.

Kiba just grinned slightly at that, 'yeah that's what I thought too. Look at what happened though; I got my ass kicked'.

Up in the Kage Box the three assembled Kages looked down at the two fighters.

"So that's the Hyuga Progeny?" asked the Raikage.

Hiruzen nodded slightly, "yes he is. His father was the one that died during the incident with your predecessor Raikage-dono".

The Raikage nodded in understand, "I'm sure the boy must hold much animosity towards our village".

"The boy will have an easy win," spoke the Kazekage.

Hiruzen let a small smirk grace his lips, "we shall see".

The Raikage looked over at his bodyguard; a thirteen-year old Kumo Chunin by the name of Nii Yugito, "what is it Yugito-Chan?"

"Grandfather; that blond boy…I sense a great power within him," the blond girl whispered to him.

The Raikage nodded and whispered back, "yes…I feel it too".

Yugito nodded, "what should we do?"

The Raikage just smiled at his granddaughter, "just watch this tournament closely".

"I vow to win," Naruto spoke as he thrust out his hand towards Neji. He remembered his meeting with Hinata back in the training field before he came to stadium and silently swore that he would do everything within his power to defeat Neji.

"You appear to believe you can win," Neji chuckled in amusement. "You cannot change destiny though; fate has already decided the outcome of this match. I cannot wait to see your eyes when you realise the truth," he continued as he settled into his Jyuuken stance.

Naruto just grinned in response, "whatever. Let's go wild".

"Let the first match of the Chunin Exam Finals begin...now!" Genma called out as he jumped out of the way of the two.

Almost immediately Naruto made a hand-seal, "Taju Kage Bunshin on Jutsu". Twenty shadow clones popped into existence in front of Naruto and he called out, "charge!"

"The kid knows the Taju Kage Bunshin on Jutsu…that's a Jonin level Kinjutsu; where did he learn that and more importantly how can he use it so effortlessly?" Izumo asked as he observed the fight.

"I don't understand…he can't even pull off a simple Bunshin no Jutsu…how can he use a more powerful version of the technique?" asked Kotetsu in confusion.

'The fool…' Neji thought as the clones charged. He activated his Byakugan and smirked at the oncoming one-man army, 'his clones have an equal amount of chakra in them so I am unable to ascertain which one is the real one but…you cannot fool my eyes'. He dodged the attacks the clones sent at him and charged right at Naruto, "The one who hangs back while his clones fight is the real one". He lands a Jyuuken strike at Naruto's heart and sends him crashing into the nearby tree, "it's over". The 'Naruto' he hit however suddenly disappeared in a poof of smoke a moment later, 'what?!'

The ground below at his feet suddenly parted as Naruto emerged and landed a solid blow to the Hyuga's chin sending him flying back, "now good enough!"

Neji recovered however and shot the blond a glare, "you…"

"I came into this match knowing I'd probably lose…but I hate it when bastards like you say there is no hope at all so I won't take it lying down!" Naruto shouted at him.

"How did you do it? I always kept my eyes on your original body," Neji asked with a glare.

"Do you really think I was using those clones to fight you? I was just using them to find out what you were made of! Do you really think I'm stupid enough to fight a Hyuga in close-combat without an ace up my sleeve?" Naruto shot back with a grin.

'This ignorant little…' Neji trailed off as his eyes narrowed.

"The clones also served another purpose," Naruto stated.

"And what might that be?" asked the Hyuga Progeny.

"To find out if there was gap in your line of sight," the blond answered truthfully.

'What?!' Neji turned swiftly in surprise but was unprepared for one of Naruto's clones to land a rather powerful punch to his face. The blow sent him flying back with the clones in pursuit, 'he located the gap in my eyesight with his clones!'

"Finish him now!" Naruto shouted to his clones as they took out their weapons to finish the job.

'I have no choice; I must use that jutsu', Neji thought as he touched back down on solid ground and expelled chakra from all over his body. "Kaiten!" he called out as he spun and encased himself in a large ball of spinning chakra.

The clones were destroyed in moments…

"He's really pushing Neji into a corner," Ino said in disbelief.

"Go Naruto!" Sakura cheered at seeing her team-mate beating the Hyuga.

"I don't believe it," Izumo said not believing what he was seeing.

"This kid…" Kotetsu muttered under his breath as he watched Neji execute a Kaiten.

"That plan was worthy of a practical joke," Izumo said as he let a small grin form on his lips.

"Impressive," the Raikage commented as the Hokage smiled slightly. "The boy thought up a plan almost instantly to throw off his opponent," he continued.

Hiruzen nodded slightly at that, "the boy continues to surprise me as well".

"…" The Kazekage remained silent as he kept his calculating eyes on the arena below.

'This guy…' Yugito thought from the side as she watched the match.

"Do you see how you cannot change destiny? My fate is to win this match; you cannot stand against fate," Neji told him. Naruto remained silent so he continued, "I have had enough of your games; I shall end this now". He charged forward faster than Naruto could react, "Hakke Rokujuyon Shō!"

The blond Genin couldn't help but stand there as he was battered by Neji's barrage of strikes. Every strike felt like he had been hit by hundreds of needles at once and he soon found himself being sent flying back by Neji's final open palm strike to his chest. He coughed up some blood as his body hit the ground and Neji smirked at his handiwork.

"It's over," the Hyuga Progeny said in finality.

"He's done for," Izumo sighed at seeing the brutal attack.

"I guess I should have expected this outcome," Ino shook her head as she leaned back.

'Naruto…' Sakura thought as she remembered what he had done in the preliminaries.

"He is a very entertaining boy but he is still no match for a genius," the Kazekage spoke in slight amusement at seeing the blond Genin go down.

Hiruzen remained silent as he sent a sideways glance at his fellow Kage, 'it's almost like…he's referring to someone else'.

The Raikage didn't speak, instead opting to just watch, 'somehow I doubt it's over…that was too easy'.

"Proctor; call the match. He's not getting up," Neji stated confidently.

Sadly reality didn't agree with him…

Naruto rose a moment later; he glowed red as an enormous amount of crimson chakra erupted from his body, "wanna bet?"

"H-how?" Neji asked as he took a step back at seeing the red chakra. He focused in on its source and his eyes widened further, 'was that a fox?!'

'Ero-Sennin told me not to use the Rinnegan unless I had too…I guess I'll just have to stick with the furball's chakra,' Naruto thought as the chakra encased his body in what looked like flames. He clenched his as he settled his gaze on his opponent, "now do you understand bastard?! I had you beat from the start! I just wanted you to show me your trump cards first so I knew what to expect!"

Neji's eyes widened at that, 'he had this planned from the start!'

"He's a Jinchuuriki," the Raikage spoke as he watched the match.

"Yes…I believe it's the Kyuubi," Yugito said barely above a whisper.

"This will be interesting," the Raikage smirked as he continued to watch.

'This chakra…when did he learn to control it in a stable form? Did Kakashi teach him this?' were the thoughts running through Hiruzen's head.

"…" The Kazekage continued to watch in silent anger.

Naruto cocked his fist back and then threw it out at Neji; a moment later the air around his fist rippled and was propelled towards where Neji stood. The Hyuga Progeny could barely dodge as the shockwave blew away the ground he had been standing on just moments ago. Just then Naruto shot forward faster than he had been before and Neji turned swiftly to intercept him. A moment later Naruto disappeared in a burst of speed surprising Neji and he couldn't turn in time to block the punch that connected with his face.

'He's faster than before! What's going on here?!' Neji thought as he recovered from the blow but couldn't stop the follow-up attacks that Naruto delivered one after another.

'I have to keep in close and not let him escape,' Naruto thought as he delivered yet another punch to the young Hyuga's face.

'It's no good,' Neji thought as he began to spin with chakra erupting from him. "Kaiten!" Naruto jumped away to avoid the boy's ultimate defence, "you cannot defeat me. Fate will not allow it," he told the blond.

"It maybe the Hyuga way to cave into destiny but it's not mine! If you believe that you can't change it then don't try; just stand there and take it!" Naruto shouted as he threw out a punch Neji which sent a shockwave at him.

"Kaiten!" the Hyuga Progeny spun as he released a large amount of chakra. The shockwave slammed into his chakra barrier and was harmlessly deflected, 'what a fool; direct assaults don't work on me'.

'Now!' Naruto shot forward faster than the average eye could see and just as Neji powered down his jutsu Naruto struck. "You shouldn't let your guard down!" the blond shouted as he cocked his fist back.

'There's not enough time to use the Kaiten again! He had this planned!' Neji's eyes widened as Naruto came within range.

There was an echoing slam as Naruto's fist connected with Neji's unprotected face. The Hyuga Progeny couldn't even register that he had been sent flying through the air before crashing hard into the stadium wall. He dropped out of the hole in the wall and collapsed on the ground a moment later.

'I am…defeated,' Neji thought as he tried to remain conscious. He looked up to see Naruto towering over his beaten form, "I was…careless".

"For the record; I failed the academy exam three times. Because unluckily for me there was always one jutsu on the exam; the Bunshin no Jutsu," Naruto told him making his eyes go wide. "My clones were pathetic…they still are," he continued.

Neji looked up at him surprised, "but you-".

"The reason I can't create regular clones is because I have too much chakra to make them; that's why I can create Jonin level shadow clones so easily. That's what you saw today…not my weaknesses but my strengths. Hinata is the same way; you always see her weaknesses but never her strengths…for someone who is supposed to be able to see everything; you sure are blind," Naruto told him. "Don't come to me with this destiny stuff…because unlike me you're not a failure," he finished with a grin and turned away.

"Winner: Uzumaki Naruto," the examiner declared as he gestured towards the orange-clad blond Genin.

Author's Notes:

Okay I've went back and rewritten this chapter because of the first part. I hope this makes up for the original sucking so much but in my defence I just couldn't think of a way to write it the first time around. Oh and I realise that I added a little line from Halo 3 in here; it seemed to fit with the Kyuubi and Naruto interaction (I don't own that either).

Translation

Kuchiyose no Jutsu = Summoning Technique

Taju Kage Bunshin on Jutsu = Multiple Shadow Clone Technique

Kaiten = Heavenly Spin

Hakke Rokujuyon Shō = Eight Trigrams Sixty-Four Palms
Rikudō-Sennin = Sage of Six Paths

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See Ya Later…