Clear Skies

A Naruto universe fanfiction by FatefulGravy


Thousands of years ago, there existed a society founded on the way of the ninja. The people who lived in this society possessed skills and abilities unheard of, and their influence can still be felt today, long after they died out. We call them the ancients, their legacy lives on through our language, names, and legends. I am one of them. Blessed, no, cursed with eternal youth I have lived over two thousand years, wandering the planet making connections with few, if any, people. Now, at last, I have found something I can do, somewhere I belong. And, hopefully, a place where I can live without constant reminders of what I have lost.

Chapter 1: Gentle Winds

Kitada strolled down the hallway at a rapid pace. Under his arm he clutched a brown folder, stuffed full of sheets of papers. Although looking fairly innocent the folder contained a collection of top secret documents, a new set of orders for Kitada's team.

He had been mildly surprised when his superior had called him into her office and bumped him and his team off their previous mission. He had also been mildly annoyed when that mission had been assigned to a two man elite team, the members of which trailed him down the hallway. He rolled his eyes. As if the 'elite' pair could do the job any better than his team.

It wasn't his surprise or annoyance that were inspiring his rapid pace however. No, he was practically jogging to the briefing room because his new mission was damn important and potentially very dangerous.

He barged into the briefing room ahead of his two elite followers and was sorely tempted to slam the door in their smug, masked faces. Resisting the urge to inflict broken noses he noticed that his somewhat 'dramatic' entrance had caught the attention of all three members of his team. They had been lounging around while waiting, but snapped to attention and saluted, while glaring 'discreetly' at the masked duo.

"Something up Captain?" the shortest of the team members asked.

Kitada nodded and pulled out the folder. He decided to forgo the podium at the head of the table and took a seat in front of his team. The briefing room was rather large and addressing just three people from the podium would only make him feel stupid. He was a tall man, and the elevation would have left him towering over his team.

"Change of orders," he replied as the team sat as well, "We have a new A-ranked mission."

"But what about Operation Red Wheel?" the blond member asked, "We were just getting results."

Kitada sighed and gestured at the two masked men, who had turned their backs and were leaning against the podium.

"These two are taking over Red Wheel," he answered, "Chuck them the file Aki."

The short female team member who had spoken first pulled open her pack and pulled out a file considerably thicker than the one Kitada had been carrying. With a flick of her wrist Aki sent the file spinning towards the masked duo, who still had their backs turned.

Without turning, or indeed any motion at all other than lifting his arm, the man in the white tiger mask caught the file, quickly checked it was the correct one, and gestured to his wolf masked companion to follow. They left having never said a word.

"Damn EXEL squads," the dark skinned team member who had been quite up until now muttered, "We spend weeks getting that info and they take all the credit."

"Easy Yamanda," Kitada attempted to calm the man down, "They've earned their position."

Aki snorted, "We all know that you could kick the ass of any EXEL flunky Captain," she commented, while tying her dark hair in a pony tail.

"And yet you're still just a team leader," the blond pointed out, "Why's that?" he added with a cheeky grin.

Kitada leaned back in his chair and smirked, "Lets just say, Taiki, that I like where I am now and have no desire to move upwards."

Taiki chuckled and ran a hand through his hair, "Whatever you say Cap'n, but you have to admit its odd, sending the Execution Elite after a brat. Weren't he supposed to be brought in peacefully, not with a massive trail of destruction behind him."

Aki giggled, "Still upset you couldn't create a similar trail of destruction, hey Taiki."

"I could too," Taiki shot back.

"Highly unlikely," Yamanda put in, "previous trails of destruction have been rather limited in scale."

"I'll show you a trail of destruction!"

Kitada sighed and decided to execute 'argument ending plan no.3,' before the bickering got out of hand.

"Easy kids," all three stopped arguing, "I don't want to have to give you detention."

All three were now glaring at him, he smirked.

"Good, now that your quiet I can brief you on our new mission."

The glares vanished and his team settled into what he liked to call 'business mode'. The three of them could be childish at times but when it came doing to a life or death situation Kitada could not have asked for a better team.

"Last night," he began, in an official tone, "a team of two individuals infiltrated and destroyed one of the governments bio-tech research facilities. They managed to get in, plant explosives and escapes successfully despite the facility knowing they were coming and setting a trap."

He saw a couple of eyebrows rise in surprise. "Our mission is to locate and capture those two in order to find out who they are working for."

Yamanda raised a hand, "Are we dealing with mercenaries or one of those 'freedom fighter' groups?"

"Unknown," Kitada replied, "but the facility was classified top secret, so anyone who knew enough about it to want it destroyed wouldn't have needed mercs." Yamanda nodded in response.

"Any more questions," no one asked anything so he continued, "Good. Okay, Aki, you and I are going to the site of the facility. Yamanda and Taiki, I want you two to check for any active mercs or terrorist groups in the area. Everyone got it?"

All three nodded.

"Then lets go."


It has been said that the wind has a soul, and that it screams through the streets of the city because it is dismayed at what it finds there. That it wailed at the corruption and cried at the poverty, that it mourned for the people cursed to live there.

It could also be noted, that the wind at the docks was a warm, gentle breeze. As if its anger at the city had been spent and it now longed only for the escape of the sea.

At least, thats what Naruto thought.

The gentle breeze that blew around him and Momo as they stepped onto the docks brought with it a barrage of smells. The underlying scent of damp wood, a hint of salt in the air and the overpowering scent of fish, fresh from the nets.

Naruto brushed his hair back from where it had blown in his eyes and took in the sight before him. Cargo was being unloaded from one of the large container ships while others awaited a new load, a pair of fishing boats were coming in to dock and all around him people went about their business.

Traders called out their prices. Business men in their snappy suits met with traders in greasy overalls. Shady people met with criminals in dark corners.

At the end of a row of container ships, at the cheapest and least well maintained mooring, as well as one of the only remaining wooden ones, sat a rusted, barley afloat cargo ship.

Naruto and Momo made their way towards said ship through the bustling crowd. They had exchanged their combat suits from the previous evening for standard street clothes, jeans and shirts, and now carried the suits in backpacks.

As they approached the ship more details became apparent. Rust covered much of the hull, and any remaining paint was flaking and begging to detach itself, barnacles and other shelled creatures hugged themselves to the hull around the water line. The name on the bow, though barley visible, read Ranmyaku.

"Home sweet home," quoted Naruto.

"Hn..." was Momo's simple response, as she entered the ship.

"You could be a little more happy about it," complained Naruto, following her in, "It's your home too."

He didn't get a response.

The interior of the ship was just as dilapidated as the outside. The flooring was a patchwork of differing colours and textures, and the doors were either about to fall off or so rusted that you needed all your strength to open them. The ceiling was also rather low, which was unfortunate, as few of the lights actually worked.

There was no doubt that the Ranmyaku was an old ship, but to the six members of the mercenary group Clear Skies, in was both a headquarters and a home.

"Go ahead and get some rest," Naruto suggested to Momo, "I'll tell the old man that we're back."

The red head simply nodded and moved off deeper into the ship, no doubt heading to her quarters.

Naruto sighed as he watched her go. In truth, Naruto had been told to never let her report again. The boss had said that trying to get a good report out of her was nigh impossible. 'Like getting blood out of a stone' he had said.

As Naruto headed towards the bridge at the stern of the ship he wondered about his anti-social partner. He hadn't known her that long, but in their missions together he had never heard the girl say more than two words at a time. He often thought about what had caused her to act that way. Was it some traumatic event in her childhood? Or was she just naturally odd? Heck, he had been able to get better conversations out of Sasuke, although, admittedly, it was rare.

At least Momo wasn't crazy and set on killing him though.

Naruto made his way through the deserted bridge towards the captains cabin at the rear. Although the Ranmyaku was quite a large ship the computer systems allowed the six people living aboard operate it well enough. Naruto was glad for that, more people would mean dividing his pay up more.

He reached up and knocked on the cabin door.

"Get in here!" was the shouted response from inside.

Naruto groaned at the shout and pushed the door open.

Furui Puramu looked like the ship he ran. Old and battered, his hair had turned gray decades ago and his skin cracked like dry earth. But his eyes still shone with life and, like his ship, he was still going strong. He also had an odd name, in Naruto's opinion. If only people knew what the ancient words they used for their names meant. Despite that, Naruto could have imagined him as a Hokage similar to the third, if it wasn't for one small detail.

"Uzumaki you bastard, what kept you!" he demanded from behind his desk.

"Geeze, sorry old man but it was a long way back."

Puramu snorted, "I've got no time for your excuses Uzumaki," Naruto muttered something about why he bothered asking then, "So give me your report."

Naruto outlined the events of the previous evening quickly. Getting in, getting separated, meeting up, escaping, blowing the place up. Puramu seemed pleased with the outcome, although he did sweat drop at Naruto's complaints over who got to do the blowing up.

"Good work, Momo too. And good work stopping her reporting, I half expected you to send her up here alone."

"Would I do a thing like that?" Naruto questioned.

Puramu didn't have to think about his response, "Yes."

"Hey," Naruto protested, "like I'd leave Momo alone with you!"

"Uzumaki you bastard!" Puramu was outraged, "I don't mean it like that! That girl freaks me out!" He picked up his wooden cane a started swinging a frantic combo at Naruto, who dodged each blow.

"Gah, take it easy old man I'm just kidding!"

"Don't call me that!" He finally landed a blow on Naruto, the cane hitting his head with a crack.

"Ow!" Naruto rubbed the lump on his head, "Fine I'm sorry."

"Good," Puramu put his cane away, "You're dismissed."

Naruto turned to go but hesitated, remembering something.

"Hey old man," Puramu rested his hand back on the cane, Naruto ignored it, "Whats the payment for the mission, and who was the client anyway? Not many people would be willing to wait months for us to finish a job."

Puramu looked mildly surprised for a second, then frowned. "There was no client Uzumaki, this was an internal mission."

"Eh? But that means-"

"Exactly, there is no payment."

"Correct me if I'm wrong," Naruto said, leaning over the desk, "but I thought we were mercenaries. Y'know, we do jobs and get paid for it."

Puramu sighed and lent back. "I realise you joined us relatively recently Uzumaki, but since you came to us and asked to join we all thought you knew."

"Knew what?"

"That we only do mercenary work to gather funds in order to complete our true objective."

"Yes, I know, but it would be real nice if you could tell me which missions are which!" Naruto complained.

"We're revolutionaries Uzumaki, freedom fighters if you will. We desire a return to the governments of old, before the corporations came into power. After the great floods-" Puramu continued, oblivious to Naruto's comment, "-when the world was in chaos and people had to scavenge for a bite to-"

Naruto interrupted before he could go any further. "I don't need a history lesson old man, I know what happened."

There was silence for several seconds.

"We would be pleased to tell you which missions are internal and which are not Uzumaki, but if you paid any attention we make a point of telling you so you can opt out if you wish." Puramu explained.

"What!" Naruto was exasperated, "No one told me!"

"Yes we did, we told you at the briefing, before we left to come here, before the first mission, after the first mission, before the second mission-"

"Gah! I get the point old man, I'll pay more attention from now on."

Puramu sighed and leaned back in his chair. "You know that your free to leave whenever you want, we don't force people to work for us."

"Why do you still want me here? Even though you know I joined not knowing what was really going on. That I just wanted some fun," Naruto countered.

Puramu smiled, "We would not have let you in if we didn't think you had a place here. And I do think you have a place here Uzumaki, I think that given the choice you would choose to fight as we do."

Naruto stared at him for a second, then sighed, "I don't know old man, It's not like I like the way thing are, but staying would mean me getting into a lot more than I intended." He stood and headed to the door, "I only came here for the pay, and for a laugh, what you're doing could get me into a lot of trouble." He snorted to himself, "Once upon a time..." he trailed off.

"Once upon a time what Uzumaki?"

Naruto stopped and turned back to the old man with a sad smile, "Once upon a time I wouldn't have thought twice about helping out."

"You're good at what you do Uzumaki," Puramu called out as Naruto left, "You could put your skills to good use, or you could go back to wondering around like you did before you got here."

Naruto turned and grinned, "Give me some time to think about it," he walked away and raised a hand in a half wave, "I'll see you later, old man."

"Team two should be back from their retrieval mission soon, at least wait until then."

"Yeah, yeah."

As he was leaving the bridge Naruto felt a twinge of guilt. He had lied to the old man. He hadn't joined up just for the money, in reality he had hoped that he would be able to recapture the old feeling of being on a team, going on missions together, having fun and saving the day with little thought about the consequences. He had been on his own far too long.


As Naruto headed away another man slipped into Puramu's cabin.

"So now he knows," the man asked.

"Yes."

"Will he stay?"

"We can hope."


The ringing of the school bell startled Hideki Kira out of his half asleep state. He looked around to see that everyone was heading out of the classroom, must be the end of class. Kira pushed some of his dark brown hair out of his eyes and started to pack his books away. How he had managed to get through the entire maths session practically asleep and without opening a book was beyond him.

He finished packing up and noticed that the rest of the class had left, no one had waited for him, but he wasn't surprised. It wasn't that the was an unlikeable person, he had some good friends, but he had a habit of staying quiet and avoiding confrontation. As such he was relatively unknown around the school.

Kira headed out of the school into the bustle of the street. Students were saying their goodbyes, making their way home. He ignored it all, better to go unnoticed.

Out of the corner of his eye he caught a glimpse of someone. What was here name? Moegi? She was a cute girl, he supposed, from his year. He thought he had seen her blushing while looking in his direction earlier. But not this time, now she looked scared, why was that? Ah, yes, now he realised. She was surrounded by a gang of older girls, bullying was such a widespread problem.

She looked around for help frantically, her eyes met his for a second, pleading for help. Kira dropped his head and hurried on, eyes firmly on the ground. There was no use in helping, not when he could do so little. Besides, it was better to avoid conflict.

He heard the shouts intensify as he rounded the corner.


Naruto entered his cabin, a small room with metal walls, a bed and a cupboard, and jammed the door closed with one of his daggers. The door would swing open and bang closed with every sway of the ship otherwise.

Naruto had come here with a purpose, and it wasn't to sleep. He opened the cupboard and pushed past the spare clothes and equipment until he reached a sturdy, wooden box. Carefully opening it he studied the objects inside.

The only remaining objects of his old life. His only reminders of his friends. A collection of metal plates, engraved with various symbols, one with a slash running through its swirling design. Other objects, a Shougi board and pieces. The game was no longer played, perhaps he could try and teach the old man? Several scrolls, pictures and other artifacts, things that would have no meaning to anyone but Naruto.

At the bottom of the box Naruto found what he was looking for, a bound book. This was not the original, none of the boxes written contents were. Over the years Naruto had made countless copies of his friends written works, unwilling to lose even the slightest thing.

This particular book was one of his most treasured. It was a journal, only two of his friends had bothered to keep one, and only this one had survived. And despite the fact that he was rarely in it, that it was from a female point of view and that it was full of pages and pages about Sasuke, Naruto had read in many times, and often turned to it for advice.


Kira was nearing home, and was feeling rather guilty about about abandoning Moegi. It wasn't like he didn't care, he would have loved to be the knight in shining armor. He was just far to practical, he knew that had he intervened he would have been targeted as well. He wouldn't have made a difference.

Looking around he noticed that the street was strangely empty, no cars on the road, very few people on the walkways. It was rather odd. The street was usually lined with beggars and vehicles tended to scream past with little consideration for the road laws, but today all was quite.

Kira wondered what had caused the change.

He was startled out of his thoughts when he heard a siren blare from behind him. He spun around, nearly tripping on the cracked and splintered paving, to catch sight of an emergency vehicle approach, scattering small debris in its wake.

Kira stepped back from the road to avoid being soaked as the vehicle hurtled through a puddle, the scattered water drops refracting the light and creating a brief rainbow effect. He wondered what the vehicle was for, no one policed the city, and no one would call in a medical team, not for a resident, the only possibility was fire.

He quickly scanned the skyline for signs of fire, and felt is stomach clench in fear. Rising into the air not far from him was a great column of black smoke, heading for the sky like a huge, dark wraith, marking death for those below.

But it wasn't this that had scared Kira, he was far to old to be scared by the shape of a cloud. His fear stemmed from the realisation that the smoke was rising from the direction of his home.

Kira ran.


Naruto set down Ino's journal with a sigh. It had been so long since he had seen his friends that his memories of them were blurred. Faces especially were hard to remember, and if it wasn't for the journal Naruto suspected that all he would remember of his friends would be their names.

His memories of events however were much clearer. Not battles, he had fought too many people over too many years and all the fights ran together into one big mess of blood and screams. No, his clearest memories of back then were of the saddest moments. The moment when Sakura's old and gray body gave up the ghost. The moment Sasuke was buried. The moment he was all alone.

Naruto deliberately put a stop to those thoughts. The past was the past and he couldn't change it, he had to live for the present!

He snorted to himself. He had told himself the same thing hundreds of times, but he had never actually done it. There was nothing for him to live for now, his time had passed long ago.

Absently Naruto let his mind wonder to the Old Man's offer. Stay with Clear Skies, fight for a cause, have a purpose.

Have a purpose.

There was something about it that deeply appealed to Naruto. Perhaps it was some long dead ideal calling out to him, pushing him to do the good thing, to help people.

Naruto chuckled, his ideals had died with his friends.

Have a purpose.

After a year on his own Naruto would have given anything to see one of his friends, after ten he would have given anything to see someone he knew. Heck, after a hundred he would have given the same to see an enemy. Through all of the years he had lived since then he had just been wondering, never having a purpose or a goal. Everything had come down to where his next meal was coming from, or when he would get some money. Recently everything he had done was just to try and have fun, which hadn't worked.

A purpose.

The old mans offer was enticing. It was an opportunity, a chance. And possibly a way for Naruto to gain a new purpose.

With a sudden thought Naruto started to dig through one of his drawers. He pulled out a small book similar to Ino's journal. Indeed he had planned to make a new copy using this very book soon. The old one was getting worn out.

He didn't, however, start copying Ino's words down. He had decided that this journal would be his, somewhere for him to right down his thoughts, something to help him remember. It was past time for a change after all.

He started to write;

'Thousands of years ago, there existed a society based on the way of the ninja...'


A/N: Few things; first I'm not sure whether to keep this a Naruto fic or make it an original. Second thanks to MoOn-ShInE-LorD for my best review ever, and third if you think the fic is good and should stay in the Naruto section I could do with a Beta reader. Thanks.