Disclaimer: I don't own Naruto or any of its characters.
Chapter 01: Prologue.
Before there were any established Hidden Villages, there were the clans. Many prominent clans were smart enough to know not to stay in one place for very long, while others did not approve of a nomadic lifestyle and settled down in fortified areas. Nobody could trust someone from the outside. Many of these clans secured their futures by putting talented individuals from the family up for hire. Clashes and interaction between clans was minimal, but deadly, especially when the standing of your family was on the line when missions were assigned, but times were changing. People who refused to risk their own lives and led civilian lifestyles recognized that they could easily obtain power through the hire of the more powerful families.
Prominent clans had their own infrastructures consisting of Clan Heads, and a group of figureheads designed to keep the Clan Head in check, but motivated largely by their own greed, and not the welfare of the clan. As time passed, these clans developed their own signature styles, kept within the family, so that it could not be turned against them. Some of these signature styles were not usable by all members in a clan, and it was suspected that these styles were specific only to a specific ancestry within a clan. While some of these Bloodlines were useful, others were used mercilessly, and only for the advancement of one's own clan.
The Clan Head of the Senju Clan, for example, used his Mokuton to create his clan's home. Not having any Elders or a Council to counteract his decisions, his clan was dependant on his guidance and wisdom in order to survive. They didn't like to kill and reduce the value of a person to secure their economic future. They were content to sell the goods that the more proficient wielders of the Bloodline could grow. In contrast the Hyugas, for their own protection, separated the family to protect their bloodline, each faction having specific responsibilities to keep the clan stable. At first, both halves of the Hyuga family had equal standing, but after one of the weaker family members with a mutated, and non-functional bloodline ruined the reputation of one of the halves, the other stepped up, declaring themselves as the Main Branch of the family, and forcing the new Branch House into servitude, branding them with an experimental seal that would seal away their Bloodline when they died. When these radical changes took place, the now disgraced family member, one Madara Hyuga, was cut off from the clan, after having the seal forced onto his head instead of his back, like the other Branch House family members. Putting the seal in such a visible location was meant to act as an ultimate humiliation before sending him away. The clan was so wrapped up in trying to remove their "weakness" that they did not mind when Madera took his younger brother with him. Their parents were immediately killed by Main Branch family members. The other Branch House members were now fodder for the Main Branch and were used as soldiers, with little regard for their life.
But times were changing. The civilians who wanted more power realized that to get to power, they needed obstacles that impeded them removed. The missions offered to these specialized family members were becoming more sinister. Assassinations were becoming more common. Clashes between clans were becoming more common, as was the bloodshed associated with it, but the desired result was beginning to take form. Some of the more powerful civilians declared their own territories, just for the sake of being a person with political power. At first, there were five such territories: Fire Country, Wind Country, Water Country, Lighting Country, and Earth Country. These men likened themselves to the different Elemental Natures, because they believed themselves powerful, and there is no force more powerful than nature, or its different forms.
As the years passed, it became clearly obvious that to ensure the futures of the ninja families, they would need to band together. Word had spread that the more bloodthirsty clans had rebelled against the civilians who hired them, because they refused to pay their fee, after completion of an assignment. Using their Bloodline, various clans killed most of the civilians in those territories, tarnishing the reputation of Bloodline users. Most of the self-proclaimed Feudal Lords, demanded Bloodline clans to leave, for the sake of the safety of their followers. Public opinion meant a lot to the Lords, but even through the fear, they struck bargains with some Bloodline clans to stay, and suppress their power, to pass as normal. If they were to leave, they would strengthen some other territory, and that was unacceptable.
Ten years after these killings began, than the hidden villages began to form. Clans banding together and pledging their allegiance to the Feudal Lords, who were only too happy to be granted more strength and political power, was common place. Once strong clans like the Senju Clan were on the verge of disappearing. It was at this time when Madara Uchiha approached them. The current Senju Clan leader was a young man of twenty, thrust into the position if Clan Leader when his father was killed in an assassination mission. His name was Hashirama. Madara and his kin, a small group which currently consisted of his immediate family stepped out of the morning fog, and approached the encampment, Madara leading the others. The Senju guards that were posted at the entrance immediately reacted by going on the offensive. Clasping their hands together, focusing their energies, and whipping through hand-signs, they fired wooden posts with sharpened points at the intruders, while a defensive canopy of trees shot our of the ground exactly where the wooden projectiles were. Three more hand-signs and the fog thickened, making it difficult to see anything. As the guards relaxed, they saw red eyes flash through the mist.
Madara, having activated his new Doujutsu, went through his own hand-signs, stopping on Tiger. Tracking where the deadly projectiles were flying, he used a carefully aimed "Fire Release: Great Fireball." The flame shot out of his mouth, flying forward and intercepting the deadly wooden projectiles, burning them into ashes, and blowing the smoldering remnants away, as it continued to swell and burn through the trees that had just been grown to block their path. Hashirama's younger brother, Kenyu, having just gotten to the gate, and seeing the imminent danger from the large fireball bearing down on them took action. Not being that proficient with Mokuton, he made four hand-signs, and employed his preferred style. "Water Release: Water Wall." Pulling water right out of the air, he formed it into a large wall. The fireball was immediately extinguished when it made contact with the wall, creating a large amount of steam. Kenyu slowly approached his wall, making his hand-signs with the intent to kill. "Lightning Release: Lightning Strike." Thrusting his hand forward, Kenyu makes contact with the wall, electrifying it. Stepping back, still making hand-signs, "Air Release: Daitoppa." The resulting gust of wind blew through the wall resulting in chunks of electrified water to rain down on Madara, and his family.
Without warning, a figure broke out of the ground, in between Madara and his family, and with quick hand-signs, encased the family in a round wooden prison. With two steps, Hashirama was behind Madara, his left hand grabbing Madara gruffly, his right with a short sword at Madara's throat. "State your business."
"I'm not here to attack. I'm just here to talk."
"I find that rather hard to believe. Just last week, we were attacked by a clan, who wanted to know the secrets of our clan Jutsu."
"I'm not here for your Jutsu. Please just listen to me."
"Give me one good reason why we should let you live?"
"If I was here to kill you, would I have brought my family with me?"
Losing patience Hashirama dug his sword point a little bit deeper into the skin of Madara's neck, drawing a drop of blood. "That is not a reason. Storming our home with such pitiful numbers will only get you killed."
Madara, realizing that this was a bad time for what was left of the Senju clan decided to get straight to the point. "If you do not listen to me, what is left of your noble clan will no longer exist in the coming years. Perhaps you haven't noticed, but we are in the middle of a Bloodline War, right now. We need your strength."
Hashirama withdrew his sword from Madara's neck and turned him around, slowly. Putting the sword away, he quickly backhanded Madara, knocking him onto his back. "Do you wish to insult me? As a Bloodline user, I am well aware of the public opinion of me and my clan. But what do you propose we do about it? The best we can do right now, is to hold our own and stay with people we can trust."
"That course of action will only result in the extermination of all of the Bloodline Users," said Madara from his position on the ground. He quickly rubbed some of the blood off his lip from the punch. "We need to band together."
"We are together. My clan and my family stand together. I believe in my people, just as they believe in me."
"That is good. But we need to expand on it. The clans to the North and the East have already banded together, formed alliances, and secured their futures. By joining together and establishing Hidden Villages, they have ensured their futures, as we must do now."
"If I may, Brother," interrupted Kenyu. "What village or country would take in you, me, or any of us? Due to the acts of clans like the Kaguyas, we are feared, even if we would not stoop to lows such as them."
"Fire Country. We must go to Fire Country. The Feudal Lord there is not as corrupt as the others and he would allow Bloodline Users to settle down." Madara slowly got back to his feet and faced the two brothers. "Now, time should not be wasted, what say you?"
One of the guards who had seen Madara's Doujutsu when it was activated decided to give his own opinion. "We cannot trust them. Whatever trick he used on his eyes is not normal. I feet it's been tampered with. It almost felt demonic."
"It is as you said. I was born with a deficiency in my eyes which was cured shortly before I found my wife. I am most appreciative of the fox demon that helped me. It is a shame that my brother is no longer here with me. These eyes were the fruits of both our labor."
Hashirama looked at Madara in shock. "The Kyubi no Yoko gave you those eyes? That such a powerful demon would even think of helping you." Hashirama turned to look at the small group of gathered people. "We will need to discuss your offer," he declared as he started walking away.
"But there isn't time. And my family is still in. . . ." Madara quickly dodged all of the projectiles that were thrown at him.
"We will find you when we are ready. You would do well not to return here," announced Kenyu, leaving Madara with the round wooden prison that encased his family. Madara sighed activating the perfected form of his Doujutsu. He would have to thank his brother for his eyes if he ever met him in the afterlife. He proceeded to free his family from their prison.
After deliberating, the Senju clan agreed to relocate and settle down with the Uchiha clan in a remote area of Fire Country. The Feudal Lord accepted their proposal to establish a Hidden Village in his lands, and over the next few years, the village was slowly taking shape. Clans from nearby areas made their way to this new village, which seemed to be accepting of clans with Bloodlines. The Senju clan and the Uchiha clan were prominent during construction time. They hadn't decided on how the village would be ruled yet, but Hashirama and Madara were both highly looked up to, and there was little doubt that the village would be ruled by one of the two. Unfortunately, there were some tense moments during the construction, one of which almost destroyed the village which was still not completed.
The Hyuga clan had heard of the development of the new village and was heading towards Fire Country to relocate there. Hashirama, who was a lot more open now that his "family" had increased in size, was willing to allow them entry, but Madara, who still harbored a grudge, would not. Neither could persuade the other to see their way. Mere days before the Hyuga were to arrive, Madara left the village to give them a piece of his mind, but he was cornered by Hashirama. In the resulting fight, the earth was torn asunder, and people could feel the chakra signatures of the two men for a long ways off. The two fighters were evenly matched, but things took a turn for the worse, when Madara used his Doujutsu to possess the Kyubi no Yoko, who was attracted to the battlegrounds by the chakra signatures to help in his attack. This was not enough to beat Hashirama who was strong enough to suppress the Kyubi's chakra, and when Madara lost, Hashirama told Madara never to come back. To think that a person would go so far for revenge, he had no place in a village which was supposed to be a haven to those Bloodline clans who had harbored anger and resentment that they had not earned. Hopefully his taint had not been passed on to his family, who would be allowed to stay. Madara was not heard from for a very long time.
When the new village was completed, the Feudal Lord came to christen the village. They named it Konoha, the Village Hidden in the Leaves. It was named this in honor of the Mokuton ability which shaped the village and provided the raw material for the construction of the village. Hashirama was declared the founding Hokage. As time passed, the other Hidden Villages would wage war with others to establish their power over the other villages. In later years Hashirama found it ironic that he hadn't accepted Madara's offer readily. Even if there were deaths at war, the combined forces were enough to keep an entire clan from dying out.
In later years, the remaining members of the founding Senju clan were assassinated just like Hashirama and Kenyu's dad were leaving only Hashirama's daughter, who married out of the family, and was not proficient with Mokuton. With the death of the First and Second, the village flourished under the Third and Fourth Hokages and further established Konoha as the strongest Hidden Village when they won the Third Great Shinobi War. On one fateful night, the Fourth gave his life to seal away the Kyubi no Yoko who stormed the village one cold night in October. The Third still being alive, he rallied his village and they would press forward.