It was nighttime now as a shadow flickered silently through the trees. The shadow kept running for another 5 hours, before slipping into a hollowed out tree. Reaching down and pulling in a disguised handle, the figure went through it and locked a latch under the lid before descending underground. Travelling underground for another few hours, the figure eventually made it's way out of a concealed opening in another tree and then dashed towards the giant wall surrounding the village of Konoha.
Flashing through a few hand signs and flaring his chakra in a certain pattern, he waited a moment until he received a patterned chakra flare back. Quick as lightning, the figure flashed through a entrance that had been opened for him before stopping for air.
The figure stood at a height of 5'8 and was dressed in all black. He had a short sword across the small of his back and a long bow over his shoulder. A quiver of arrows was at his waist and he had 2 hip pouches on his belt. On each thigh was a holster that held kunai, shuriken and senbon. He had a black vest that held a few scrolls as well. On his head was a black cover and on his face was a demonic looking mask.
Nodding to the masked ANBU that opened the door for him, he made his way to the Hokage tower, roof hopping from shadow to shadow to remain unseen. Using his gloves hands, he scaled the wall and slipped through the open window to deliver his report.
The Hokage had been having a rough day. First thing that morning the Council had called a meeting where once again the civilian side had tried to order the death of one Naruto Uzumaki, which he had denied. Then his old teammate, Danzo Shimura, had tried to get him to allow him to turn the boy into an emotionless killing tool, which was again denied. After that waste of a meeting the old man had made his way back to his office to fight every Kages worst enemy, paperwork. He had battled it well into the night, and he had finally caught up for the day and was relaxing in his chair, reading a certain orange book while puffing on his pipe.
Feeling a breeze, without looking up, he signaled his ANBU to leave the room before flashing through a series of hand signs. After a moment the room glowed a blue color, signalling the room had been sealed. He turned and and started speaking, seemingly to nothing.
"Naruto my boy how did your latest mission go? And please, remove your mask, it freaks me out seeing you wear it." The boy just chuckled as he removed his mask and hood revealing a mop of blonde hair, blue eyes and a face with three whiskers marks on each cheek. "Jiji the mission was fine, I was in and out before anyone noticed anything was amiss. The target is dead and I even had time to get into his vault and help myself out a bit."
Stroking his beard and chuckling a bit, he just shook his head. Classic Naruto move, help himself while doing a mission and as long as the mission was completed, he would allow it. He then frowned a bit as he remembered why the boy had to help himself. The stupid villagers would only sell him a bright orange jumpsuit that screamed "here I am, kill me now!' Shops would only sell him expired goods and faulty equipment at premium prices so if he wanted to survive and live somewhat well, he had to resort to this while out on missions.
The old kage knew young Naruto had a rough childhood and because of that, he trusted very few people. He also knew he had multiple "safe houses" throughout the village and that his apartment was only used by a clone to keep the idiot villagers at bay.
He remembered one day when the boy before him had come to him, asking for a few empty storage scrolls and how to use them. When he had asked why, the boy had simply said he had found some things that he was sure that he needed to see. At the time he had laughed and given into the boys request, drawing up the scrolls himself and showing him how to use them. Thinking nothing of it, he had sent the boy on his way and figured that would be the end of it. Boy was he wrong.
A few days later young Naruto had came back looking like he had been roughed up by a mob and passed out in front of the man with the scrolls on his hand. The old kage had immediately dispatched an ANBU to bring the young man's doctor there and have him healed. When it was all said and done, he had totalled hundreds of cuts, dozens of punctures and quite a few burns from what looked like fire and lightning jutsu, which meant ninja had been involved in the mob. 2 days later the boy had woken up and when questioned, had informed the man that it hadn't been a mob that had done this to him, but a number of deadly traps, which were no longer operational.
He then had the old man privately look through the scrolls and what he found had shook him to his core. Dozens of dead bodies, hundreds of jars filled with random body parts, notes of genetic mutation and bloodline transference. Gasping, he realized that the young boy had stumbled across one of his old students deranged research labs. When asked where it was, the boy remained tight lipped, stating that he had cleaned it out of all the dangerous and scary things, and that he was going to use it as a safe haven from mobs and the like, since no one else knew where it was. After much back and forth, the old man agreed.
That had been when he was 5, he was 12 now and was "attending" the academy. Over the years, Naruto had studied every scroll in the hideout. From anatomy to chakra control, from food cultivation to jutsu theory, and he wouldn't have been able to do nearly as much as he had if he hadn't found the jutsu to end all jutsu, the Shadow Clone Jutsu.
After reading the entire scroll, it had taken him only 2 hours to learn it, and from there he would summon hundreds at a time to read and practice chakra control. Once he could tree and water walk, he started learning basic academy jutsu. His favorite by far was the Henge Jutsu, which thanks to his tenant that he had no clue about, made his Henge solid, and once he figured that out, he abused it with his shadow clones.
He would have some transform into birds and populate the training grounds and learn what they could, some would turn into various small rodents and sneak into the library so he could have basic knowledge such as mathematics, science and the like. He would even give some storage scrolls and have them sneak into shops before they closed and "acquire" what he needed to survive. During the chunin exams, he would do the same with clones disguised as birds and have them relocate the items from all the corpses in the forest of death for himself, after all the dead have no need of them.
One of the things he loved learning and practicing the most though was seals. He had read and learned everything he could from the sealing books that were in the library, both civilian and Shinobi sections. Because of that, he had made things like portable pocket dimensions, anti rape seals, anti pregnancy seals and many others, quite a few were VERY deadly.
He had informed the old kage of what he had been doing, and to say he was shocked would be like saying Jiraya wasn't a super pervert. He had tested a number of the seals and helped them get sold. A few of the seals hadn't been shown as Naruto was planning on keeping them as potential clan seals, if he ever got the chance to start a clan.
Things were going ok for the young man, especially with his seals helping him. He had a lush garden year round, multiple storage seals inked onto his skin, which were invisible, resistance and gravity seals, and a super secret seal.
Training had been going fantastic as well. Thanks to his shadow clones, he had mastered all 5 nature transformations and had a affinity for all 5, with wind being the strongest, followed by earth and water, and finally fire and lightning. He wasn't sure how he did it, but one day he had a clone tending his garden when one decided to goof off and "encourage" the plants to "grow faster". What had happened next shook him to his very core.
The entire garden, including the fruit trees he had recently planted, all grew to maturity in a matter of seconds. Dispelling the clone that was going bonkers about what he had just done, he tested it himself, and to his surprise, a sapling had burst out of the ground and grew to maturity in less than a minute. Quickly rushing to see his jiji, he cleared the room and informed the old man of what had happened, even making his plant grow right in front of him. The old kage had promptly passed out.
Upon waking up, he had informed Naruto he MUST keep this a secret or bad people would come to kill him, which Naruto agreed with. After asking how it happened, the kage theorized that because his affinities were so high with water and earth, he had gained the wood release. Soon after Naruto went back to his hideout and continued to train.
Not even a year later, the Hyuuga princess Hinata, was involved in an attempted kidnapping, which was stopped when the kidnapper had passed by where Naruto's base was. Using his few years of training in stealth and the Ninja arts, he had quickly and silently followed the man outside of Konoha, and when the man dropped the squirming sack down to rest for a moment, slit his throat with a kunai, killing the man.
Opening the sack, he saw a girl his age,l with dark blue hair and pale lavender eyes looking at him with tears in her eyes. He told her not to look at him for a moment as he turned and sealed the entire body into a scroll. Turning back, he scooped the girl up on his back and rushed back to Konoha, straight to the Hokage office, where he explained what happened and gave him the scroll holding the mans body. He then went over to the trash bin and emptied his stomach into it.