Disclaimer: I do not own Naruto or 9. Let the story begin.

Prologue

This was not his intention when he began the organization Akatsuki; he wished to bring peace to this chaotic world. When he found out about Madara's plan, he faced Madara, and was able to put a stop to Madara's intentions, because after all, he had the eyes of the creator, and was one of the few immune to Madara's Mangekyō Sharingan eyes. When his organization had captured all nine of the Jinchuuriki, including the Hokage, Naruto Uzamaki Namikaze, and sealed all of the Bijuu, he succeeded in creating a Peace-Maker Jutsu, a Jutsu everyone was afraid of, and was forced into peace.

When the Hokage died from the extraction of the Kyuubi from his body, the elemental nations had met with dark and violent times. If a village was against the peace Nagato had offered, he would simply erase them from existence with the Peace-Maker Jutsu.

What he didn't count on, was man's thriving will for freedom, and the aspiration to overcome his powerful grip. What Nagato didn't see was the creation of a being that lacked a heart, a soul. What Nagato didn't see was the creation of man's supposed retaliation of his ruling of peace, and their imminent destruction. What Nagato didn't see coming was the creation of 'The Machine' and his own helping hand in the destruction and imprisonment of humanity, and the death of thousands.

Everyone was trapped under his iron thumb. But a small resistance group began to work on a way to oppose Nagato. The 'Machine,' they called it, for that was what it was. The main component that helped with its creation was that the Machine was made with chakra absorbing armor, and ran on the power of the Stone of Gelel, and with it, created armies of machines similar to it to fight against the Red Dawn group, Akatsuki. It was programmed to bring peace by ridding the world of evil.

It was man's last salvation against Nagato, but when he tried to use the Jutsu against it, the Machine was not destroyed, but malfunctioned, and soon, corrupted. As an act to shut it down, Nagato released the full power of the Jutsu to destroy the Stone of Gelel, but at the same time, destroyed himself. Without the stone, the Machine adapted, using the sun as its source of power, and began to wipe the world clean of the human race, now seeing man as the source of evil, believing that genocide was the way to peace.

In retaliation of the 'Machine', the Human race used a Jutsu to blot out the sun. Without the sun, the 'Machine' adapted again, this time using the chakra absorbing armor to convert chakra into energy. The human bodies generates more bio electricity then a 120 volt battery, add that to the human chakra network, could potentially power any machine for a long while. Now, instead of killing off the human race, it proceeded with capturing them, to use as a battery, and began integrating the human life forms into its components, placing the living into a state of hibernation, preserving them, and harvesting them.

This was not Nagato's intention when he began the organization Akatsuki; he wished to bring peace to this chaotic world, only to bring more chaos in a new form. What Nagato will never see, though, is the fate of the sealed Bijuu, and the nine souls they harbored.

A century and a half has passed since the fall the Hokage, Naruto Uzamaki Namikaze. Cities, Villages, and towns are now in ruins, the dead littering the ground. Plant life, with the lack of the sun, has all but withered, and the land has become a desolate wasteland. What is left of the human race now either remains in hiding, or has become part of the 'Machine.'

We see a young man running through a ghost town, keeping to the shadows. The man has orange hair tied in pony tail, and was wearing a white lab coat. In his hand is a small fragment of what's left of the Stone of Gelel. The young man finds a building, ducks out of the way of a searchlight from a machine floating in the air by a large balloon. He sighs in relief, and continues down the path, and approaches an old looking shack. He knocks on it a few times, and a small slit opens on the door revealing a man's eyes.

After the man confirms that the visitor is human, he opens the door quickly, allowing him in. Inside, many humans dressed and prepared for a fight stand guard. These humans wear the ninja Chuunin vests, ninja pouches containing a variety of weapons and ninja food pills, swords on their backs, and in their hands, the newest Chakra Launchers, a gun that was developed to focus ones chakra into the barrel clip, then fire Rasengan like balls of chakra at the target. This device was inspired by Rasen-Shuriken used by one of the Hokages. These men and women were the rebel forces against the 'Machine,' and were all that was left of the great Shinobi villages. As he journeyed deeper underground, the cavern grew larger, showing many makeshift tents and shelters, where the wounded and civilians resided.

The man continued down the underground path way, until he made it to a large door covered with chakra seals. He opened the door, and inside were the rebel's brightest minds working tirelessly to invent new ways of combating the 'Machine.' He continued on further, until he came upon an even larger door littered with even more chakra seals then the last, and had one big blood seal on the door. He bit his thumb, and then spread the blood on the paper, opening the door. Inside was a large laboratory, where another man, this one much older looking, hard at work in the dark corner of the lab, sewing a needle through what looked like a rag doll.

"Professor, I found one!" said the man carrying the Stone. The old man stopped what he was doing to acknowledge the young man who walked, and then went back to sewing the doll.

"Good work, my assistant. Now put it with the other stones, I am almost finished with the last one!" The Professor stated while working on the doll. The Professor's flesh was riddled with wrinkles, giving him an ancient look. He wore a white lab coat, and black clothing underneath. His hair was pure white and spiked back, and his eyes were obsidian black that was faded having long lost its true black luster.

The assistant complied, and moved toward a large machine with eight other dolls strapped into it. The assistant stared for a moment at each of the dolls, taking in their detailed appearance. Each of the dolls resembled a human from the past, from the face to the hair, the eyes blank, but that was it, the rest of the features being made of components of machinery and fabric, which was currently open in the chest areas revealing machinery underneath, and a number on random spots of their bodies. From the elbow down, and from the knee down was not covered by fabric, thus revealing the metal armored arms and legs, the hand and feet were made of wood, but the fingers and toes were interconnected metal and were pointed at the end, resembling claws.

On tables were schematics for all the rag dolls, revealing that the fabric is made from a special chakra fabric made by Kirigakure for the purpose of hiding one's chakra. This fabric was originally created to help ninja stealth, especially when dealing with someone like the Hyuuga or someone able to sense chakra. It also could work as a Chakra container. The schematics also revealed that the robotic structure was similar to the structure used for Ninja Puppets in Sunagakure. Finally, the core of the devices revealed to be a core piece to chakra armor meant to contain large amounts of chakra, similar to the armor made in the Land of Snow.

"They are very well detailed, Professor. Were any of them someone you knew?" The assistant asked.

"No, I have seen the faces of them from pictures of their corpses. I have only known three of them, and I made their dolls from memory!" The Professor answered, while adding the finishing touches to the doll he was working on. When the man was done, he then took an ink quill, and then wrote on the stomach of the doll the number 9. He then rubbed his weary eyes, and then examined the doll. It was a 5 inch doll, with blonde spiky hair, whisker shaped stitches on its cheeks, and blank eyes. "I have finished the last one." The Professor stated, heading towards the machine with the other eight dolls.

"Professor, are you sure this is wise?" His assistant asks.

"Nothing I ever did was wise. All my life, I have done nothing for anyone else but myself, I even betrayed those close to me." He finishes hooking the doll up to the system, and then walks to another piece of machinery that resembles a mask with eye holes in it. "Everything I did was for my own selfish desires, and in the end, humanity paid for it. I wish to correct my mistakes, and make things right. It is time to repent for my past sins! Go prepare the others before I start. When the process starts, the 'Machine' will sense us, the rebels will need to be prepared for an attack, and the civilians will need to be evacuated. Besides, I need a moment alone."

The assistant wasted no time, and left the room to prepare the soldiers for an attack. The professor then took out a small wind up camera, with a recording device. He set it up to record a message of himself, taking a picture out of his pocket staring down at it, his eyes slightly tearing up. The photo was in horrible condition, the picture almost faded.

The Assistant reported that they would be starting the experiment in half an hour, and warned them of the coming of the 'Machine.' Instantly, the rebels began to evacuate the civilian to special shelters that should hide them from the machine's chakra sensors, and they prepared the defenses for their base.

When it was time, the Assistant ran back into the lab, prepared to aid the Professor, who had just finished his recording, adding the finishing touches. He walked up to the Professor, who placed the recorder on a scroll, and in a puff of smoke, it vanished inside the scroll. The Professor then picked the scroll up, and then handed it to his assistant.

"Make sure that they receive this." He said sternly, looking at his creations while saying it.

"Are you sure there is no other way, or that it will even work?" Assistant asked, fear and concern on his face.

The Professor responded by pulling a lever, lowering nine large glass containers hanging from the ceiling. Inside of each the containers, were violent streams of chakra, erratically swaying inside of the containers, almost taking the shapes of monsters and animals.

"My theory is that when a Bijuu is sealed in a person, they are attached to a piece of their soul. Thus creating the Jinchuuriki! But when Pain removed the Bijuu, I theorize that it tore a fragment of the respective human's soul." The Professor stated, staring at the nine containers holding the nine Bijuu. "Look at them, barely even a fraction of their former glory. Thanks to Pain's attempt to destroy the Machine, it had weakened them, not by much, but enough to reseal them into almost anything."

"But professor! Wouldn't the Bijuu take control instead if we attempt to seal them into these new vessels?" Assistant asked.

"Why do you think we have been toiling away to create these machines. The Bijuu are so weakened now, it will make the process easier to make sure the human soul is the dominant mind. Of course, we are leaving this up to chance for the future, but we will see what happens." The Professor stated. "A Jinchuuriki means the power of human sacrifice, meaning that in order to seal the Bijuu, a sacrifice must be made. The only difference to then and now is I am going to seal all of them for the price of one." He then took out of his pocket a small circular device, no bigger than a piece of yen, with three symbols on the top of it, and three power sockets on the back.

They both began to get to work setting up the equipment, the Professor placing the device on a spot in front of the dolls.

"When will they awaken?" the assistant asked.

"It will take time for the chakra to integrate into the systems, and maybe even longer for the soul to awaken. I have set the dolls to only activate when they are fully integrated. Could take hours, days, months, even years, and we still need to consider the chakra we are installing in them. We are indeed leaving this up to chance." The Professor then looked up at the containers again, mainly the container for the Kyuubi.

"Let us begin!" the professor then sat down behind the mask which was facing the dolls. "Have the soul transfer device on standby and open the first the container." The professor stated, setting his face inside the mask, the only visible part was his eyes and hair.

The assistant nodded, pulling a lever, lowering the first container containing the Ichibi closer to the small circular device, which was currently in front of the doll marked 1 on the left of its forehead. Dirt, dust and sand began to gather underneath the container. The assistant then pulled another lever, opening the container. The moment it opened, he was almost knocked down by the power and killing intent from the sentient chakra.

"Woo Yeah! I AM FREE BABY!" the chakra yelled out, beginning to take the form of a tanuki. "TIME TO LET THE BODIES HIT THE FLOOR! Oh YEAH!"

"I don't think so…" the Professor stated behind the mask. All of sudden, the eyes of the Professor had turned red, a black dot in the center and black lines intercrossing resembling a six sided star. "Sharingan!"

At that moment, a wave of energy leapt from the mask, taking hold of the Ichibi and restraining him. Ichibi tried to resist, but the eyes held a stronger hold over it. The Professor was looking for something within the Ichibi, something that would prove his theory right.

"There it is!" he yelled out, as he focused on the area around the beast's left forehead. The beast roared in pain, as something began to emerge from the forehead, a human shape, which was the color of a human's chakra.

"I have it! Activate the soul transfer device NOW!" He yelled out to his assistant. The assistant then pushed a button, and spherical device's symbols began to glow green, and then instantly the device opened up, beginning to suck in the tailed beast.

"OHH! BUT I JUST GOT HERE! I DIDN'T EVEN KILL ANNNYYythiiinnng…" he was completely sucked into the device, which was violently shaking, and the sand and dust settled. The Professor relaxed for moment, catching his breath, his eyes returned to normal, tears of blood beginning to trickle down his face. Wires connected to the device then surged, as energy left the device, and shot right into the first doll. The doll began to spasm, and ripping sound was being heard, as two raccoon ears and a tail ripped out of its body, and the number 1 began to glow a light green color.

"Professor! Don't strain yourself!" The assistant said in worry.

"I'll be fine; we still have eight to go. We must move on. Prepare the next one." Professor said, beginning to feel fatigue.

"Professor, you need time to rest." The assistant stated concern evident on his face.

Boom! The ground shook for a moment, the sound of a far off explosion sounding outside the lab.

"I said I am fine. We have to keep going. The machines are already here. We have to finish this before the 'Machine' gets here, or it will capture the Bijuu for energy that would last many lifetimes. WE MUST FINISH WHAT WE STARTED!" The Professor stated in a frustrated tone, and then sat behind the mask yet again. "Do it systematically! After I have finished sealing one, move on to the next! Do not hesitate for anything!"

"There must be another way other then killing yourself!" the assistant said, sorrow edged on his face. "I don't want you to die, Professor. You have been like a father to me!"

The Professor then calmed, his face becoming serene. "And you have been like a grandson to me. But we do not have any other option at this time. Besides, I have lived longer than anyone ever should." He put his hand on the assistants shoulder, and then looked him straight in the eyes. "You remind me so much of your grandfather. He would have been proud to have seen what you have accomplished."

Boom! The ground shook again, another sound of a far off explosion sounding outside the lab.

"We do not have much time, begin the process!" The Professor then took his seat in front of the mask, his eyes turning red again. "Begin!"

The assistant repeated the process the same as last time, each time becoming more and more difficult for the old man, only some of the Bijuu being compliant. Blood was tearing out his eyes, his breathing becoming harder and harsher as each Bijuu was sealed into each doll. The process of bringing out the soul of the human was difficult, but he had succeeded for each one he did, making sure the human soul remain dominant. By the seventh Bijuu, he lost his eyesight, and was now completely blind, blood splurting from his eyes.

"I can't see! (Heavy breathing) You will have… to tell me… when… you released the beasts. I can still… see the chakra… but that's it!" the Professor said in absolute anguish, both physical and mental.

Boom! The ground shook again, another sound of a far off explosion sounding outside the lab, but this time, it sounded closer.

"It's almost here, we have to hurry!" the Professor desperately yelled.

They started up the process again, and, fortunately for the Professor, the Hachibi was the most compliant out of the others, making the task of finding the soul much simpler. Then came the hardest one of all, the Kyuubi, for the moment when they released it, the area was beginning to heat up, and the Professor was feeling immense pain, very fatigue from sealing the others.

"So, we meet again, Uchiha!" the demon roared out, looking the Professor in the eyes. "Time has not been kind to you!"

"You will be sealed Kyuubi, and he will be in control!" The Professor said unwavering, continuing to stare at the beast with his blind eyes, already beginning the process.

"HA! The kit in control, like I would let that happen! And it seems to me that you are pressed on time." The Kyuubi laughed, mocking the elderly Professor.

Bang! There was a banging at the door, the sound of metal hitting metal. The 'Machine' was coming for the Bijuu, sensing the near infinite amounts of chakra which it thrives on.

"You would choose the prison of the 'Machine' over the prison of a body?" The Professor asked no real concern in his voice.

"I couldn't care less where my prison is. But, oh how much joy it would bring me to see you dead, Uchiha." The Kyuubi then began to flail about, causing the Professor great pain.

The Professor pushed past the pain, continuing on with the procedure, hands gripping the table so tight his fingers were beginning to break. The sound outside continued, obviously the rebel's either retreated, or were all dead or captured.

"You… Will… Be… SEALED!" The Professor yelled, pushing one last time to seal the Kyuubi, giving every ounce of will and strength to seal it, his blind eyes now riddled with blood shots. He finally spotted what he was looking for, the fragment soul of Naruto Uzamaki Namikaze.

"Got you, seal it now!" he yelled to his assistant, who pressed the same button again, causing the device to absorb the Kyuubi's chakra.

"NOOOOO!" the Kyuubi was completely sucked into the device, the chakra recoiling towards the Professor, striking him down.

"Professor!" the assistant ran to the Professor, checking to see if he was alright, as the chakra made its way to the last doll, the number 9 glowing a light green color on its stomach, a fox tail and ears ripping out of its respective body parts.

"It…is…done…" the Professor stated, the color in his black eyes fading. "I hope… I've earned… your forgiveness…" a wet tear mixed with blood from his eyes, rolling down his cheek, falling on the photo in his hand. The picture was of four people, a silver-haired masked man with three twelve year old kids. Finally, the Professor breathed his last breath, and then stopped, finally letting death take him.

The assistant wept for the loss of his father figure, digging his head into the Professor's chest. He quickly snapped out of his depression when he heard the continuous banging sound. He realized that even with the chakra fabric, the 'Machine' would still be able to see them, and would still collect the dolls, and the Professor for parts.

The assistant quickly ran to the door, where a lever was, and quickly pulled it, revealing a large tarp made from the same Chakra concealing fabric as the dolls, covering half of the lab with the Professor's dead body and the dolls. He ran under the tarp, and then realized something.

"It already knows that a chakra signature is in here. If doesn't find anything, the tarp will not work. I guess I will have to be the bait." He then took out a kunai and a bunch of explosive tags out of his lab coat. "If I am going down, I will make sure it gets nothing from me, but I will attempt to take all that I can!" He then placed the scroll that the professor gave him right next to the professor's dead body. He then quickly prepared himself for the worst.

It didn't take long for the 'Machine' to break through, accompanied by other machines that varied in appearance, bodies of the dead all around the area. The 'Machine' was a large creation of mechanical parts, its many arms covered in many tools and weapons, armor surrounding the core of it, and one big red optic eye that was currently peering down at the assistant.

"That's right, you see me. I am the one you want! But you won't get me, for I have other plans." He then jumped the 'Machine,' beginning to try and climb it. The smaller machines saw this, and began to fire sharp projectiles towards the assistant. Some of the sharp weapons embedded themselves into his back, but he kept going, ignoring the pain, for in his hand was a nice little ball made from paper bombs. All of sudden, one of the 'Machines' arms reached out and grabbed his leg, crushing it and breaking the bone.

"Ahh!" he yelled out in pain.

It then moved him to its optic sensor, seeing the paper bomb ball, grabbing it and tossing it aside, it then grabbed his other leg, and both of his arms, effortlessly breaking them. Sharp appendages began to move towards his body, ready to decapitate or dissect him.

'Professor, Grandpa, mother, father, I will be seeing all of you soon. And Grandpa, this one is for you!' he thought to himself.

All of sudden, the flesh on his face began to darken, the sclera in his eye turned black, his hair began to grow out and become wild, and finally, his right arm not only darkened in color, but his arm began to misshapen and to enlarge, breaking out of the clutches of the robotic appendage. He then brought his misshapen arm to his still restrain other arm, placing the palm on the mechanical appendage. A piston formed on his right elbow, coming out, then instantly receding back into his arm, causing a burst of chakra to explode out his hand, destroying the dainty claw.

Out of the assistant's back, the sharp objects and projectiles began to pop out, and then circular spikes began to form out of his back, ripping up the lab coat he had on. He then smashed the mechanical arms that held his legs, allowing him to free fall for moment, before the spikes released a burst of chakra, pushing him towards the optic of the 'Machine.' The piston formed again in his elbow, and he burst the chakra into the 'Machine,' pushing it back out of the lab. Due to the chakra armor, it sustained zero damage.

His legs instantly bulged, turning into monstrous appendages, healing his broken legs, allowing him to land on the ground safely. His right forehead had formed horn appendages, his mouth turning into maniacal toothy grin. He then looked towards the paper bomb ball, and then grabbed it, running towards his intended target.

The smaller machines began to fire sharp projectiles towards him, but he just shrugged it off, and pushed on, ignoring the pain. The man shaped machines tried to stop him, by launching chakra bullets towards him, but his arm simply changed again, and then elongated, grabbing one of the machines, and then flailing it like mace at the other machines.

The spikes on his back erupted with chakra, propelling him forward, towards the 'Machine,' paper bomb ball in his left hand. He smashed through the smaller machines like tinker a toy, ignoring the many sharp objects piercing his body. Using his misshapen arm, he propelled himself into the air, over the 'Machine,' free falling down towards it.

The smaller machines and the man size machines began to fire whatever long range weapon they had, but he continued to freefall, only some actually hitting him. The 'Machine' saw the threat, and began to try and use its multiple limbs to either knock him away, stab him, or cut him to pieces. To dodge these arms, the spikes on his back changed into a pair of webbed hand shaped wings. He swerved, and dodged, avoiding each appendage with agile vigor, until an appendage with a buzz saw attached came towards him. He narrowly ducked under the saw, so it was able to slice off one of his wings.

"AHHH!" He yelled in pain, but continued on, falling and landing on the top of the 'Machine.' Using his cursed arm, he took the paper bomb ball, and rammed it into the armor, greatly denting it.

"Good-Bye! Die!" he stated, setting the paper bombs off.

Boom! A great explosion filled the underground area, causing it to cave in. When the earth settled, almost everything was buried, except for the lab, thanks to the metal casing. We see the human arm of the assistant, buried, crushed, burned, and lifeless under the debris.

Little ways away, we see the ruble sifting and moving, revealing the 'Machine,' damaged, but not destroyed. It begins to move away from the area, the aid of the surviving machines aiding it.

Inside the lab, the dolls began to resonate, the numbers glowing even brighter than before.

I am sorry to say, but do not expect this to be updated often, I need time to gather my thoughts, and plan this out, makes some plots, etc. If you like this story, then please review.

Signed,

Mr. Nobody