Disclaimer: I don't own Naruto. Copyrights owned by Masashi Kishimoto.
There are some who say that Minato Namikaze showed signs of evil even in his youth. Born to an abusive father and an alchoholic mother, he was initially shy and withdrawn.
At around six years of age, he started bullying the other children around him. He would frequently pickpocket, lie, cheat and steal. When his victims attempted to defend themselves, he would display prodigious skills in hand-to-hand combat.
By age eight, he was feared as a terrororiser of children. Justice did catch up with him though, as he foolishly attempted to bully a Hyuuga Main Household child. The clan leader saw this and arranged with Hiruzen Sarutobi, the Sandaime Hokage, to send Minato to a young offender's institution. This prison served as a recruting ground for the then newly established ROOT, a branch of the ANBU Black Ops that were loyal only to Danzo Shimura, a former team-mate and political rival of Sarutobi. The Hokage was unaware of this at the time.
Danzo read reports and sometimes personally watched the young boy. Minato showed talent, especially in decoding puzzles of a geometric design, and in learning old languages. These talents would later form the foundation of his prodigious skills in Fuuinjutsu.
After a few months, Minato's rebellious nature had calmed. He noticed that he was being watched and eventually deduced somewhat the purposes of his prison. He then set a goal for himself, to prove himself worthy of leaving the building and undergoing whatever training was bestowed upon those others who had proved worthwhile. In all, he spent only six months there, a remarkable feat given that the average ROOT candidate lived there on average for three or more years.
Danzo then brought Minato before the Hokage and pled his case. Sarutobi agreed that Minato showed a rare talent, and was therefore placed in an accelerated curriculum at the Academy, the training grounds for Leaf shinobi. By the time he was ten years old, the young boy had graduated as a Genin.
Danzo was faced with a dilemma after the graduation. Such a promising pupil as Minato couldn't be risked ending up with someone other than one of the old war hawk's allies. Jiraiya of the Densetsu no Sannin, a former disciple of the Sandaime Hokage, had expressed interest in teaching Minato. Danzo feared the consequences of such a possibility. He carefully arranged for a group of Jiraiya's informants in the Hidden Sand Village to be placed in danger, orchestrating events such that the only person able to rescue them was Jiraiya himself. Thus, did the Toad Sage miss the graduation ceremony and the naming of Jonin-sensei.
With Jiraiya absent, another former pupil of the Hokage stepped forth: Tsunade, grand-daughter of the Shodai Hokage and grand-niece of the Niidaime Hokage. She was hailed as the Slug Princess and renowned as the foremost medical ninja in the world. She had once been bright and cheerful, but the loss of both her younger brother, Nawaki, and her fiancé, Dan Kato, during the Second Shinobi World War had traumatised her. Danzo had found her at the point of committing suicide and had taken away her pain, by teaching her the meditation techniques he also taught to his ROOT agents, techniques designed to subdue emotion. From then on, Tsunade was Danzo's most prized student, a hidden ally in the camp of the Hokage.
Tsunade refused the traditional three man squad, insisting on training Minato alone. Eventually, the Hokage relented. From then on, she was Minato's Jonin-sensei.
Minato's training was harsh and often-times bloody. He was stuck to a strict regimen of rising early and settling in late. Tsunade revealed herself as a harsh task-master. She stuck to deviant methods. Whenever Minato failed, she would beat him repeatedly. If he accomplished something not particularly noteworthy, she would utter a short "Congratulations" and continue on with the next lesson. Whenever he performed a particularly difficult lesson flawlessly, she would give in to her desires and sleep with him, for she desired the flesh of young boys. This was a deviancy that Danzo had first awoken in her and then protected with some urgency: sometimes Tsunade's desires would get the better of her, and her secret mentor would have to cover up her crimes.
Minato's quick mind surprised even Tsunade, who was herself called a prodigy. By the time of his eleventh birthday, he was clearly the strongest Genin of his generation. The Hokage himself remarked that he hadn't seen such talent since his own tutelage at the feet of the Shodai Hokage. By age twelve, he was promoted, not to Chuunin, instead skipping that rank and being named Tokubetsu Jonin. He was placed on the fast track for promotion to the rank of full Jonin, which Sarutobi decreed that Minato would earn once he had at least another two years experience under his belt.
As a Tokubetsu Jonin, Minato saw to his own studies. Tsunade would often stop by and pass on what Lightning jutsu she knew, but more and more often, the young shinobi would study Wind elemental jutsu from Danzo, the Leaf's greatest master of that art. From the two, he also learned Fuuinjutsu. Eventually, his talents in that area outstripped his teacher's, entering a realm they couldn't hope to achieve themselves.
By the time of his promotion to Jonin, Minato was regarded as simply the greatest shinobi of his time. He had mastered over a dozen forms of Taijutsu, among them the chakra powered form Tsunade favoured, as well as both the Strong Fist and Gentle Fist. The Gentle Fist he had learned from a Hyuuga Jonin whom Danzo kept prisoner and drugged.
Genjutsu-wise, he was considered to be at the same level as the upper tier of the Uchiha clan's Genjutsu specialists.
Minato's Ninjutsu skills were nothing short of astounding. He had complete mastery over every Lightning and Wind jutsu to be taught in the Leaf village, and had even replicated some of the more prized elemental techniques favoured by the Hidden Sand and Hidden Cloud villages.
He invented many of his own techniques, two of which made him famous and feared.
The first was an A-class assassination technique, called the Rasengan, which was a spiralling sphere of pure chakra held in the palm of the wielder's hand. His inspiration for this technique came after a particularly dangerous encounter with the host of the Eight Tailed Demon. Minato used the Rasengan to assassinate targets, mainly because it acted like a drill, and so left quite a mess of its victim, a sight that Minato enjoyed.
The second famous technique was more feared than the Rasengan. This jutsu enabled him to wipe out entire armies. He called it the Hirashin no Jutsu. It involved him placing seals on objects or people, and then teleporting to that seal. He frequently wrapped a piece of paper inscribed with the seal around a kunai, which was then thrown towards an enemy. Even if the enemy dodged, Minato would simply appear next to the kunai just as the enemy was moving away.
By the time Minato was twenty, he had built up an impressive resumé. He had already served three years as a member of the ANBU Black Ops. During that time, he had risen to the rank of squad captain. His team was called in for the most dangerous of missions. He later, through Danzo's and Tsunade's influence, was transferred to the Missing-Nin Hunter unit, and rose to command said unit. He improved upon the techniques of the Hunter unit. He also converted the loyalties of many of the ANBU from Sarutobi to himself. To ensure his own safety, he had these converts pretend to be secretly loyal to Danzo, but they in fact served himself. Minato had learned the ways of infiltration and treachery well: he saw that one day soon, Danzo would make his move. Minato was already enacting his plans so that Danzo and Sarutobi would destroy each other.
After three years spent in the ANBU, he left the Black Ops, and was granted a sabbatical. He was now seventeen years old. He left the village, ostensibly to continue his Slug Sage training. In actuality, he left on a long-term mission assigned to him by Danzo.
Danzo had realised that Minato's talents in Fuuinjutsu outstripped his own. Realising the potential here, he ordered Minato to learn as much as he could about the seals used to tame the Tailed Demons, and to imprison them within hosts.
The first phase of this plan involved Minato tracking Jiraiya, who, after Minato, was the Leaf's greatest seal master. Jiraiya had studied Demon lore extensively and hidden his research in a series of scrolls he kept hidden. It took all of Minato's skill, and no small amount of luck, but eventually, he learned the location of the scrolls. He called upon agents of Danzo to distract Jiraiya, and stole them. To ensure no evidence of his crime was left, he copied the contents of the scrolls and placed the originals back where they belonged.
Minato was first glad and then stymied. Jiraiya's research at the time was incomplete. His own notes included a reminder to find the remains of the Hidden Whirlpool Village, whose shinobi were regarded as the greatest seal masters in the days before the Hokage.
Minato knew of only one Whirlpool survivor, a woman his own age named Kushina Uzumaki. She was fierce and skilled in Water jutsu, a talent that served her well in the ANBU Black Ops. Minato, as one of the highest ranking Leaf shinobi, knew of a secret: that she was the second host of the Nine Tailed Demon Fox. She knew little of Fuuinjutsu herself, but she did know of the location of the Hidden Whirlpool Village ruins. Minato then set out to charm and seduce her. Eventually, after two years, the two consummated their relationship. Kushina was eventually convinced to bring Minato to the ruins. It took him several weeks, but he found secret chambers that housed the Uzumaki clan scrolls on demon-related Fuuinjutsu. Taking a risk, he kept some of the knowledge for himself, giving to Danzo what he deemed would be enough to placate him.
During his twentieth year, Minato enacted a plan to ensure his future dominance over the village. He heard from his contacts that Orochimaru, the third and rumoured greatest of the former apprentices of the Sandaime Hokage, was negotiating to be married to the Uchiha clan heiress. Danzo feared such a move, as he and Orochimaru clashed politically almost as much as he did with Sarutobi. Danzo had his own plans for the clan, but could not act unless he had some hold over them. It was then that Minato suggested that he wed the heiress, one Mikoto Uchiha, instead. To ensure the clan elders were swayed to support of Minato over the Snake Nin, Danzo doctored evidence that implicated, but could not conclusively confirm, Orochimaru having abused several young boys who were in actuality victims of Tsunade.
Such a move almost ruined Orochimaru's reputation in the village. Sarutobi believed in his innocence and protected him as best he could, but the Uchiha clan elders eventually concluded that they could not risk a marriage with him. Minato was wed to Mikoto in a grand ceremony.
The marriage was strictly political. It took all of Minato's charm, but he eventually convinced Kushina to remain as his secret mistress. Kushina accepted on the basis that this was the only way for Minato to obtain the political support necessary to become Hokage. As a devout partner, she wished for her love to accomplish his dream by any means neccesary. She didn't like it, but she accepted the marriage.
The time was ripe for Minato's ascension. He had loyalists in both the ANBU Black Ops and ROOT. He had command of the Uchiha clan, through his wife, whom he dominated using mental jutsu learned from a ROOT member of the Yamanaka clan.
Using his agents, he played on the fears of both the Hokage and Danzo. The Hokage learned of several secret treaties concluded between Danzo and rogue elements of the nations. Danzo heard that the Hokage was preparing to raid his offices and arrest him.
This brought about a brief but bloody civil war. The Sandaime Hokage had the aid of two of his students, Jiraiya and Orochimaru, with Tsunade being away on a distant mission at the time. Danzo countered this with his many ruthless ROOT subordinates. Hundreds died in the conflict. Eventually, the battle ended with a final showdown outside the village. On one side was Sarutobi and Jiraiya. Orochimaru had been killed during the conflict. On the other, Danzo fought, alone at first, but towards the end, he pulled out his trump card: Minato. The golden haired man reinforced Danzo with dozens of well trained Uchiha. With this added support, even the Hokage and the Toad Sage were overwhelmed.
With his opponents dead, Danzo knelt down to pick up the tri-corner hat of the Hokage. However, he was surprised to find Minato's kunai in his gut. His last sight was of a particular seal underneath the hat, one placed there years before by Minato just for this moment.
Before anyone else could react, Minato used the Hirashin no Jutsu to wipe out those of ROOT who were fanatically loyal to Danzo. With this, his ascendancy was complete. No-one was left within the Leaf village with the skills to challenge him, or had the political clout. The Uchiha elders saw at once that they could gain everything if they promised wholehearted support.
Minato named himself as the Yondaime Hokage, the strongest of all Leaf ninja. He had lied, manipulated and murdered his way to power. However, he was not yet satisfied. He had eyes on more than the Leaf village.
By the time he was twenty-two years old, Minato had agents infiltrated throughout the court of the Daimyo of the Land of Fire. Before the year was out, the Daimyo was assassinated and replaced by a Leaf shinobi in disguise.
During his twenty-fourth year, the Third Shinobi World War began. The Hidden Cloud and Hidden Mist ninja feared the spread of Minato's influence, and took steps to curb his ambition. The Hidden Sand stood with the Leaf throughout this war, but bore the brunt of the fighting.
This war taxed even Minato's strategic mind. The leader of the Hidden Cloud ninja was an enigmatic ninja named A, the Yondaime Raikage. His skills were on par with Minato's own; he was rumoured to be strong enough to defeat the host of the Eight Tailed Demon and come out unscathed.
Many lives were lost, but eventually, after four years of constant fighting, a peace was reached. The Hidden Sand suffered the most, with their Sandaime Kazekage being killed in combat by the Yondaime Mizukage of the Hidden Mist.
After the war, Minato faced a new problem: the threat posed by his old sensei, Tsunade. The Slug Princess had remained neutral in the conflict between Sarutobi and Danzo, having purposefully removed herself from the scene beforehand. Tsunade was the one Leaf shinobi who could theoretically defeat Minato in combat.
Minato dug through old scrolls of the previous village leaders, eventually finding one written by the Niidaime Hokage, Tobirama Senju. It detailed a method to resurrect the dead, as minions of battle.
When Minato was twenty-eight, he played host to the Chuunin exams. There, Tsunade made her move to assassinate him and take his place. Instead, Minato countered her by sealing them both inside of the arena. He then proceeded to resurrect the Sandaime Hokage, Shodai Hokage and Dan Kato. He erased their minds and bent them to his will. Tsunade didn't stand a chance, as she refused to fight back against her old love. Within a matter of moments, the Shodai had speared her through the heart with a Wood Style Jutsu.
During his twenty-ninth year, Kushina Uzumaki became pregnant. She had consented to this only because Minato threatened violent retribution on a village of innocent civilians if she didn't. Minato wanted a child of the Uzumaki bloodline.
During the childbirth, Minato was almost killed. Despite the best security procedures he could think of, an enemy managed to infiltrate the birthing chamber. This enemy identified himself only as Tobi and stated he was here to take control of the Nine Tailed Fox. He was indeed able to draw the demon out of the seal that kept it imprisoned within Kushina.
However, it looked like this intruder had not been able to learn exactly what happened to Tsunade. Minato summoned the Shodai Hokage and ordered him to subdue the Fox. Tobi was surprised and angry to see an old foe.
The battle lasted for a few more minutes, until Minato cast a new Fuuinjutsu, one that had been invented by a certain older shinobi. The results were quite surprising. The intruder, Tobi, was nowhere to be found, and neither was the Fox. There were two dead bodies, that of Minato and Kushina. What survived was a newborn baby, one that strangely enough refused to cry...