Chronicles Of The Ancient Shinobi

Summary: When exploring the Hokage Mountain at the age of 5, Naruto makes an amazing discovery, an Ancient city ship with technology that seems only Uzumakis can use. Eleven years later, Naruto has just defeated Pein and makes a decision to relocate his people to somewhere where they well be safe from Madara.

Need to know: Sarutobi tells Naruto about his heritage and what he holds when he turns five feeling that he had a right to know but warns him to keep the knowledge to himself due to the danger that would come from his father's enemies from finding out about him. Naruto is also a lot more competent fighter than in the manga.

1. Finding A New Home

Story Start: Five Years After Kyubi Attack: October 10th: Hokage Monument

Naruto walked through the tunnels that the old Hokage had showed him and then told him to stay in if he was ever chased and during his birthday. By his side was a silver haired Anbu wearing a dog mask. According to the Hokage and the Anbu, the man had been his father's student and so was one of the few people that Sarutobi trusted to guard Naruto on this night.

As the two kept walking, Naruto looked up to his bodyguard and said "So the Fourth was really my dad and your teacher?"

Dog looked down and nodded as he said "He really was Naruto. And I can honestly say that I could not have asked for a better teacher."

Naruto looked down in thought as the two continued to explore the mountain.

An hour later, the two were looking at a dead end five feet in front of them. Naruto looked up to the Anbu and said "Hey Dog, do you know why there is a dead end here?"

Dog shook his head and said "No I don't. Although to be fair, I didn't even know this tunnel was down here. Maybe it's a false wall."

Naruto cocked his head in curiosity before walking closer to the wall and put a hand on the wall. As soon as he did, the wall glowed before shrinking into itself before it disappeared completely leaving another hallway.

"I think we better go get the Hokage." Dog said.

Naruto turned, but a light shining behind him drew their attention back to the hallway. Standing before them was a black haired woman who was looking at the two.

"Welcome descendant of the Altereans. Please continue down the hallway and everything shall be explained."

The two Leaf residents looked at each other before Naruto began walking down the hallway.

"Naruto wait! We should really tell the Hokage about this before going any further." Dog said.

Naruto stopped and looked back before nodding. The two then began walking back to find their leader.

Scene Change: Two Hours Later: Alterean City Ship Alzeaor Hologram Room

Naruto, Sarutobi and Dog were currently listening to a hologram that was explaining about the Alterean race's history. About how they were a race of advanced species that would travel across the galaxy seeding planets with life. They also learned about their enemies called the Wraith. All three of them were a bit freaked out when they learned that they survived by feeding off others life force. They also learned about Atlantis and how they had gone back to the Milky Way when the Wraith threat had become too much. The hologram then talked about how the Altereans left a city ship in the Land of Fire for unknown reasons and covered the city before leaving to the island region that would eventually become known as the Land of Whirlpools where they had integrated themselves with the natives there. Afterwards, it gave a brief description of the city itself.

As the hologram faded. Sarutobi turned to Dog and said "Dog, I am making everything that we have learned here an S-class secret." Once Dog had nodded showing that he understood, Sarutobi turned to Naruto and said "Naruto, if we go to this chair room, do you think you could use it?"

Naruto nodded and said "I'll try Old Man."

Sarutobi nodded and the three left to go find the chair room.

Seven Years Later: Chunnin Exams Final Exam

Naruto looked around as Leaf ninja clashed against the Sand and Sound. He suddenly spun around and slashed the throat of a Sound nin who had tried to sneak up on him before Kakashi landed next to him.

"Naruto! Three summons have just broken through the wall. And the Hokage is trapped with Orochimaru behind a barrier. We need your clone to fire those drones now!"

Naruto nodded and formed a shadow clone which quickly dispelled.

Underneath the mountain, another clone that was sitting in a chair received the message and leaned back in the chair causing it to tilt back and for the blue lights in it to turn on as it awaited its orders. The clone concentrated and saw in its mind the three summons as well as the purple box barrier. The clone sent an order through the chair and a hatch opened before twelve lights shot up a tunnel and into the air over the village.

The twelve lights separated into four groups before shooting off at high speeds to their targets. Explosions rocked the ground as they slammed into the snakes penetrating them before exploding sending gore and blood all over the place. The arena shook as well as the three lights hit the barrier which shattered like glass under the explosions allowing the Anbu surrounding the barrier to rush the Sound four and to aid their leader.

In the stands, Kakashi nodded to Naruto and said "Good job. Now go find Gaara and make sure he doesn't become a threat to the village. I'll summon one of my dogs to help."

Naruto nodded as Kakashi bit his thumb and made the necessary hand signs before Pakkun appeared in a smoke cloud.

"Yo Kakashi, what do you need me for?" Pakkun asked.

"Pakkun, I need you to lead Naruto here after another Jinchuriki that's fled the village. He's currently being chased by Sasuke so you should be able to follow them."

Pakkun nodded and he and the blond began making their way out of the village to find the Sand village's Jinchuriki.

Scene Change: Forest Outside Of The Village

Naruto stared at the huge form Gaara had taken from his spot in the tree and briefly considered summoning Gamabunta before dismissing that idea. It took the Kyubi's chakra to do so the first time and he had already gone past the limit of safely using the demon's chakra in this fight. Looks like he would have to use the drones again.

Crossing his hands, he called out "Shadow Clone Jutsu!"

Turning his head to the clone that appeared, he said "Tell the clone at Alzeaor to launch a couple of drones at him. Aim low so we don't kill him."

The clone nodded before dispersing.

Gaara turned the sand tanuki's head down to look at Naruto and laughed before he said "Now what will you do Uzumaki? You refuse to use your demon and you cannot hope to defeat me in your current condition!"

Naruto rose an eyebrow as both heard the sound of two drones coming in fast and Naruto said "I might not be able to, but I bet two drones will."

Gaara had just enough time to look confused before the two missiles slammed into the raccoon's lower body and exploded sending sand everywhere. Naruto saw a battered Gaara falling to the forest floor and quickly jumped over and caught the redhead before heading down to the ground in a way that wouldn't result in broken bones.

Time Skip: Three Years Later: Forest Outside Of The Village

Negato looked over at Naruto from his slumped over position and said "It is done. Everyone who has died in the Leaf's defense has been revived."

Naruto nodded and said "Thank you."

Negato nodded as well as he studied Naruto before he said "Naruto, while you were able to defeat me, the true leader of Akatsuki is still out there. His name is Madara Uchiha, and as you are you would have no chance against him."

Naruto looked down for a moment before he looked back up and said "What must I do?"

"Buried under the Leaf Village is a city built by our ancestors. One that can travel through the stars. I believe that as an Uzumaki, you should be able to access it."

Naruto smiled and said "Alzeaor."

Negato's eyes widened and Naruto chuckled before he became serious again.

"You wish for us to use its star drive and leave this planet? Just like that?"

Negato's eyes softened as he said "I know that it sounds like the actions of those of a coward Naruto. However, Madara's plan cannot be completed without all nine tailed beasts. Certainly not without the Kyubi. Leaving this world is your best option in keeping it safe."

Time Skip: One Day Later

Naruto was currently in the Alzeaor's chair room looking at the holographic map of the galaxy. Standing next to him were the current and former Hokages as well as the Kazekage who Naruto had a clone bring in one of the shuttles from the city's hanger. The map currently showed a planet that was mostly ocean with one continent and a small collection of islands.

"So this will be our new home?" Tsunade asked.

Naruto nodded and said "Yes. This is where Atlantis was sunk under the sea to keep it out of the hands of the Wraith. With any luck, it's still down there and in one piece. If we can raise it, we can dial back here with the extra stargate we have in storage that we plan on leaving in Sand and the people there can live in Atlantis."

The three kages nodded before the map shrunk and moved to the side before images of the people of the Leaf Village coming through the tunnel into the city and settling into quarters as Naruto's shadow clones directed them.

"Boarding seems to be going well." Sarutobi said.

The other three nodded and Naruto said "Yeah. We should be ready to go by tomorrow morning." He then frowned.

Seeing this, Gaara said "What is it Uzumaki?"

Naruto sighed and said "It's Danzo. I don't trust him. He has a group of Anbu under his command that didn't take part in defending the Village and he tried to make himself Hokage while Granny here was in a coma. Would have succeeded too if I didn't get her to the sick bay when I did. I don't think he should be coming with us. He claims to be doing what he does for the good of the village but when it's attacked he did absolutely nothing. How do we know he won't try anything on the way or when we get there?"

The other three also frowned before a hologram of a dark haired woman appeared.

"If I may Naruto?"

Naruto looked over at the hologram and said "What is it Rana?"

"It is obvious that this man does not truly care for the people of this village. As the descendant of the Altereans, you have the right to deny him and his people access to anywhere in this facility. We could keep them locked in their quarters if they do anything suspicious if you so desire."

Naruto nodded and said "I see. Let's just hope it doesn't come to that."

The other three nodded before the chair slid into an upright position as all of the holograms disappeared and everyone left the room.

Time Skip: Two Hours Later: Top Of Hokage Monument

"Danzo, we have been through this before. Leaving is our best option."

"And I am telling you Tsunade, that that is the path of cowards. We have advanced technology that no one else can use, and yet you wish to run."

"May I remind you that Naruto is the only one who can use said technology? The only thing everyone else can do is open the doors and turn on the lights. How do you plan on fighting a war with only one shuttle at a time?"

Naruto sighed from where he was looking out at what was once a proud village as the two kages argued with Danzo again over whether or not they should actually be leaving this planet. Truth be told, he still had his doubts himself but he would trust in Negato's judgment. Besides, it was pretty much a moot point seeing as how half of the Hidden Leaf Village's citizen's were already in the city.

"Do you actually believe that the Daimyo well allow his ninja to just leave like this?"

That got Naruto's attention and he looked over at the trio as Sarutobi said "He has the samurai and temple monks to defend this land. But if you feel so strongly about this, then you are welcome to stay here and rebuild Danzo."

Danzo's eye narrowed before he said in a dangerous tone of voice "Believe me Sarutobi, I plan to. You all are fools to even consider leaving."

As Danzo began walking away, Naruto stood up and said "Well, that went well."

Sarutobi sighed and said "Come on, we still have work to do."

Scene Change: Next Day Daybreak

If anyone had visited the Leaf Village a week ago and then come back now, they would have wondered if they had gotten lost. Earth style jutsu had been used to remove the mountain and dig out the city which now stood proudly ready to make it's trip through the stars.

In the chair room, Naruto was once again sitting in the chair leaning back with his eyes closed. Opening communications throughout the city, he said "Ladies and Gentlemen, this is your captain speaking. Please make sure all items are secure and enjoy the ride."

Right after he finished talking, Naruto sent a command to the city's engines and the city began vibrating as the ship began to rise off the ground. As it did that, the chair began to rotate while in Naruto's head 'screens' popped up showing different stats for not only the engines but also the shields that would need to be raised before they got too high in the atmosphere, life support systems, power levels in the Zero Point Modules, and various other systems.

Naruto held off from activating the shield to conserve energy in the three Zero Point Modules they had until they reached an altitude where it became necessary. When it did, the shield rose around the city visible as a slightly shimmering dome.

As the city broke away from the atmosphere, Naruto thought 'I really hope we're doing the right thing.'

Then he opened a hyperspace window and the city shot forward into hyperspace. Naruto sighed as the chair returned to its usual upright position and he reopened communications with the city.

"Ladies and Gentlemen, we have just entered hyperspace. ETA to the Alterean home planet: five days. Thank you for choosing air Alzeaor and enjoy your flight."

Scene Change: Alterean Home World Atlantis Control Room (Note, this is during the time just before Sheppard made his run in the puddle jumper.)

Tensions were running high in the ancient city of Atlantis as the Wraith fleet overhead prepared to send another wave of darts down to attack the city.

At his station, Doctor Redek Zelenka suddenly spotted something on his monitor causing his eyes to widen as he said "Uh, Doctor Weir, Rodney, you might want to see this."

Doctor Elizabeth Weir and Doctor Rodney McKay stepped over and Elizabeth said "What is it Redek?"

"I just picked up a hyperspace window opening, and if I'm not seeing things, a Ancient city ship that's exactly like Atlantis just came out of it."

Meanwhile, above the planet, Alzeaor had just dropped out of hyperspace and in the chair Naruto was cursing up a storm.

By his side Tsunade looked worried and said "What is it Naruto?"

A hologram showing the planet and a bunch of Wraith ships with Alzeaor practically right beside them popped up and Naruto pointed at it and said "That's what! A Wraith fleet is attacking Atlantis! Rana, I need you to show me where I can do the most damage on each of those ships!"

Rana appeared and nodded before a hologram for each class of ship appeared with the engines, hangars, and life support systems outlined in red.

Naruto nodded his thanks before closing his eyes and leaned back in the chair. Outside, the drone hangar hatches rotated open before dozens of drones shot out towards the Wraith ships which were just beginning to fire on the city causing the shield to flare.

Some of the Wraith's darts were able to intercept the drones but the rest plowed into the ships doing massive amounts of damage.

Atlantis Control Room

Rodney pumped his fist and shouted out "Yes!" as they all saw the three Wraith carriers and most of the cruisers explode while the rest of the badly damaged Wraith ships opened hyperspace windows and took off running.

Everyone else began cheering as well until a beeping sound drew Redek's attention back to his screen. "Oh that's not good."

"What?" Rodney asked.

"All the darts that are still in the area, they're headed straight for the city. They're going to ram us. And at the speeds they're traveling, there will be nothing left."

"Can you raise the shield?" Elizabeth asked Rodney.

"There's not enough power in the ZPM." Rodney said.

Back in the Alzeaor chair room, Naruto had just received the same information and was already taking care of it.

"Oh no you don't." Naruto growled out sending a command to the drone launching bays. Drones screamed from the hangars through the city's shield and into the atmosphere after the darts who were too intent on destroying the Ancient city below them to evade the missiles and so were easily destroyed by them before they reached their target.

Back in the Atlantis control room, everyone breathed a sigh or relief before Doctor Weir turned to the communications officer and said "See if you can contact them."

The officer nodded and began working his station. As he did, Redek rose his eyebrow as he said "I'm picking up a new signal. IFF reads as the Daedalus."

The communications officer looked up from his board and said "They are both hailing us."

Weir looked at him and said "Put them both on."

The officer nodded again and Atlantis heard "This is Colonel Steven Caldwell, commander of the Daedalus. Sorry we were late for the party. Looks like you guys had an ally though. May I ask who else is out here with us?"

"This is Naruto Uzumaki-Namikaze, Heir of the Altereans. Gotta say, I was expecting Atlantis to still be under the sea. Imagine my surprise when we get here to find it not only on the surface but also under attack by the Wraith. So mind telling me who you guys are? You're obviously not Altereans otherwise you wouldn't have had trouble with such a small fleet."

Elizabeth and Rodney traded looks before Elizabeth said "This is Doctor Elizabeth Weir, director of the Atlantis Expedition. We came from Earth in the Milky Way galaxy to explore the Pegasus galaxy."

"I see. Well then, I'm afraid that complicates things on my end. You see, we were hoping to use Atlantis as a new home for one of our allies. We had left a spare stargate that had been in storage on our home world for them to use when we got here so that they could come here quickly."

Elizabeth frowned and said "Yes, I see how that would complicate things. There is another group of people who are allies with us who have come to live on the mainland though. Maybe these allies of yours could live there as well."

Naruto looked over at Tsunade asking what she thought and she gave him a look that said "This is your show kid."

Naruto sighed and said "I cannot speak for them for certain, but I am pretty sure that will be acceptable. Do you mind if I bring the city down next to yours? I'd rather not drain our Zero Point Modules any more than necessary."

"Of course. And once again, thank you for your help." Elizabeth said before nodding to her communications officer who cut the line to Alzeaor.

"Well that went well." Caldwell said.

"Indeed it did." Elizabeth said.

"I'm sending down the ZPM with one of our technicians Doctor Weir. I'm sure Doctor McKay won't mind his help installing it."

"Understood, thanks."

"No problem. Caldwell out."

On board the Alzeaor, Naruto sighed as he said "Become Hokage, what was I thinking? I could barely handle that, and it wasn't even face to face. I think I'd rather fight Negato again. I don't know how Gaara does it."

Tsunade smirked and said "You'll do fine Naruto."

"If you say so." Naruto muttered. He took a moment to clear his thoughts before activating city wide communications.

"Ladies and Gentlemen, thank you for riding Air Alzeaor. We are currently preparing to enter the Alterean home planet's atmosphere. As such, please make sure all loose items are secure and get ready for one bumpy ride."

Tsunade smirked as Naruto positioned the city before it began descending. As it breached the atmosphere its shields began glowing as friction began to increase.

Rana did a quick calculation and said "Naruto, we are coming in too steep and fast, decrease your angle and put more thrust from the engines."

Naruto nodded and made the necessary corrections to their course causing the strain on the shield to lesson as they continued their course through the atmosphere.

Back in the Atlantis control room, everyone looked on as a fireball shot down through the sky towards them before flaring at its bottom once it reached the last thousand feet and seemed to hover before gently settling down the last few stories sending waves out that would leave any surfer in heaven if they were to ride them.

"Wow, that was some landing." Elizabeth said.

"I'll say." Sheppard said from Atlantis' own chair room where he had seen the whole thing with Atlantis' sensors.

"Yeah, yeah. The guy really knows how to fly his ship. I just want to know if he has any spare ZPMs in that thing." Rodney said.

On board the Alzeaor, Naruto took a deep breath before standing out of the chair and walking out of the room with Tsunade by his side. It was time to meet their new neighbors.