This is a rehaul of "My Name is Mina Shirito!" it'll probably follow the same basic storyline but many details are changing. Spoilers up to episode 329 in Shippuuden (and probably more depending on how close to cannon this ends up).

Disclaimer: This story is for entertainment purposes only. I do not own Naruto in any way. Original characters introduced are mine.

Prologue

The cold of winter loomed upon the horizon for Konoha, the wind bringing it ever closer on the mid-November night. The Third Hokage Hiruzen, despite the begging of his peers, was still up this late working. Many construction projects were still in need of approval after Kyuubi's attack the previous month, shortly followed by it being sealed within the only child of the Fourth Hokage: Naruto Uzumaki. Thankfully, most of the matters pertaining to the child were taken care of, so everyone's focus could be upon the village being rebuilt.

Hiruzen sighed, put his pen down, looked up slightly, and rubbed his eyes with a groan. It was about time for him to sleep. He looked down to stack the papers when he noticed a figure crouched before his desk. The figure was clad in unfamiliar clothes, holding a bundle of cloth in both arms. Within the darkness of the room, short, wind whipped, dark locks could be seen on top of the figure's head. Hiruzen stood up, knocking his chair back and getting into a battle position. Two jonin immediately jumped into the room and each put a kunai to the figure's neck. Once the kunai were put to the figure's neck, the whole room heard a cry come from the figure's bundle. Hiruzen and the jonin were put off guard as the figure spoke in the tone of a young man, "Please, do with me what you wish, but do not hurt her."
The figure gently moved a section of the cloth to reveal the source of the crying: an infant of pale skin and obsidian hair, eyes clothes due to crying. Hiruzen saw the child; eyes widened slightly, and then motioned for the jonin to relax. One of them spoke out, a woman, "But, sir…"

Hiruzen said nothing, gaze firmly upon the woman. She sighed and lowered her kunai, as did the other jonin. The figure sighed in relief, quickly comforting the infant, "There, there, it's fine, Lady Mina."

Hiruzen but his hands behind his back, "Who are you and what are you doing here?"
The figure looked towards Hiruzen, moonlight now peeking into the room. The figure stood tall, eyes silver, worry within his form, "My name is Keibi Sakushi"

Hiruzen furrowed his brow, "That name is impossible,"
Keibi frowned, "I don't have time to explain! Please,"
He looked down at the now calm infant, its gold eyes looking up at Keibi, "This is Mina Sakushi, and… we are the last of our clan."
The woman jonin spoke up, "Your clan was attacked?"

Keibi nodded, "I ask you, Third Hogake, please take our clan's head into your care. I'm leading any who've chased after me away from Konoha, but the illusion will not last for long."

Keibi held out the infant Mina, "There is a scroll in her bundle, her parents request she read it once she becomes of age."

The woman spoke quietly, "Lord Hokage, what will you do?"
Hiruzen closed his eyes and approached Keibi. Once he reached Keibi, a small smile grew upon Hiruzen's face. Hiruzen held out her arms under Mina, Keibi looked towards Hiruzen with tears in his eyes, "Thank you… Thank you Lord Hokage! Our clan… we will forever be in your debt."
Keibi gently placed Mina in Hiruzen's arms then stood back and bowed, "I must go, if anyone ever comes for her… then it is likely that I am dead. Trust no one but me."

Without another word, Keibi disappeared from sight, presumably leaving the village. Hiruzen and the two jonin relaxed, the other jonin, a male spoke, "We're just going to let him leave?"
Hiruzen spoke firmly, "He came here to ensure this child's safety, if he wanted to do something else, he would have done so."
The woman jonin spoke, "Lord Hokage, that name… you said it was impossible."
Hiruzen nodded, "It was rumored the clan had died out since they did not join any village, apparently that's what they wanted everyone to think."
He cradled Mina, "We'll talk more of this later in secret. For now, we'll add her to the list of orphans from Kyuubi's attack. Keep this secret, Kanaka, Nero."
The two jonin nodded and quietly exited, leaving Hiruzen cradling Mina.

Chapter 1: Enter: Mina Sarutobi!

Hiruzen had decided to adopt Mina Sakushi into his family, having her adopt his family name as his granddaughter. Twelve years had passed since Mina arrived at Konoha, and she had a peaceful life with her new family, not that she could remember her old one. She had a knack for being a shinobi, and passed into being a gennin on her first try. She was slightly saddened by it, as someone didn't pass even after some attempts.

Mina waited on the swing near the academy, her obsidian hair grown just passed her shoulders, put into twin tails behind her head. She wore lightweight clothing, short-sleeved shirt dark blue in color with yellow filling the fitted lines. Her pants were fitted as well, mainly black in color but also with yellow along the fitted lines. She also wore simple shinobi shoes and her leaf headband normally.

Mina looked up, seeing whom she was waiting for, a smile dawned upon her face for only a moment before it descended into worry. The one she waited for approached her, disappointment and sadness in his eyes, goggles instead of the traditional headband upon his head. Mina spoke in worry, "Naruto?..."

The boy looked up at her, "I failed…"

Mina stood up and frowned, "Did you do your best?"

Naruto nodded, "I tried really hard but…."
Mina smiled, "Well, you tried your best, so you'll get there!"

Naruto started to go on a rant, but Mina only heard one word before she started to hear the words of the crowd. Malice towards Naruto; she hated it. Mina immediately rushed to the two girls talking about Naruto and punched them in the face. The whole crowd gasped at Mina's actions before Mina spoke feircly, "Anyone who bad-mouths Naruto's got to go through me! I'm not letting this pass by anymore!"
With a smile she turned back towards the swing to see Naruto gone, her eyes suddenly switched to concern, "Naruto?"

Mina then rushed off to try and find him, yelling his name into the distance. One of the two girls scoffed, "What's her deal? Why does she even hang out with that freak?"

Within the edge of the crowd, Hiruzen sighed, thinking he'd have to talk to Mina later. He turned his attention back to the person next to him, "Iruka, there's something we need to talk about."

Later that day, as night was upon the village, Mina gave up looking for Naruto and assumed he'd gone home. She was going to look for him there, but a jonin said that her grandfather wanted to see her. She grimaced, knowing he'd seen what she had done in front of the academy. Mina entered Hiruzen's office cautiously. Hiruzen immediately noticed her and spoke, "You know what you did was wrong."
Mina closed the door and argued, "They were insulting him right in front of his face! I had to do something!"
Hiruzen glanced over at Mina, "They were not directed at you,"

Mina frowned, "You told me not to act against the village when they spoke about Naruto like that. I have for years, and it's built up inside. I just can't take it anymore!"

Tears started forming in her eyes, "Sure he's done some pranks, but nothing to deserve this kind of hatred!"

Hiruzen spoke calmly, "You don't understand-"
Mina shouted, "Then explain it to me! I want to understand this stupid hatred!"

Hiruzen gently rubbed his ears and sighed, "I suppose its time you know."

Before he could begin to explain, a jonin opened the door in panic, "Lord Hokage, there's an emergency!"
Hiruzen stood up and started towards the exit of his office, Mina held onto his sleeve, "Grandpa-"
Hiruzen, "I'll tell you once this situation dies down."

Mina pouted as Hiruzen left with the jonin. Mina opened the door to find many jonin were rushing after Hiruzen. Something big must be going on, she thought. She listened to what the jonin were trying to say to each other, catching up on the situation. She wasn't able to decipher some of the whispers in full; she could only catch glimpses 'scroll' 'stolen' and 'Naruto'. Her eyes shot wide open and rushed out of the building. A male jonin stopped her by stepping in front of the exit. She grimaced, "Nero, get out of my way!"

The man with cropped black hair and matching eyes spoke, "Honorable Granddaughter, you don't know the situation."
Mina spoke up, "That they say Naruto stole a scroll, yes I do!"
Nero stood firm, "He stole the most valuable scroll! This is a serious charge! He must be brought in."
"There has to be some kind of mistake, Naruto would never do something like this! I'm going to find him and prove he's got nothing to do with this!"

Nero sighed, "You leave me no choice, I'm sorry for what I must do."
Within an instant, Nero appeared behind her and knocked her in the head; knocking her into a groggy state. She fell towards the ground, eyes unable to focus, and her body not responding to her desire to run. She nearly fell into unconsciousness before a rush of chakra filled her, keeping her awake. She landed on her hands and rushed out of the building at great speeds. Nero stood there, dumbfounded, "What… just happened?"

Once Mina knew she was a decent distance away from Nero, the rush she felt subsided. What was that, she thought, how did I do that? She shook away the thought, she had to find Naruto and prove he was innocent. She searched and searched, eventually hearing something in the forest. She followed it and kept her distance; she saw Iruka, Naruto, and someone in a nearby tree. Iruka was pinned to the wall of the wooden building, and Nartuo had a giant scroll on his back. Mina gasped, it was true that he stole the scroll. She wasn't able to focus until she heard Iruka scream out, "Don't tell him! It's forbidden!"
She then heard the person in the tree speak, "The decree is that no one can tell you that the Nine-tailed Fox in inside you!"
Mina's expression paralleled Naruto's, confusion, fright, and eyes widened. She had heard the story of Kyuubi attacking Konoha twelve years ago and how the fourth Hokage defeated it, but it being sealed inside Naruto? She continued listening to Mizuki in the middle of his speech, "Didn't you think it was strange how they treated you? Like dirt! Like they hated you for just being alive!"
She saw Naruto refusing to accept this as Mizuki continued, "That's why you will never be accepted in this village! Even your beloved sensei, even your beloved Mina hates your guts!"
That set her off, She screamed out, "YOU LIER!"
She then charged at Mizuki, before he deflected her attack and threw her down on the ground, "I'll deal with you later,"
Mizuki unhooked one of his giant shuriken, "DIE NARUTO!"

He threw it directly at Naruto, whom tripped and started to panic. Iruka shouted out, "NARUTO, GET DOWN!"

Naruto complied before seeing Iruka impaled by the giant shuriken. Mina tried to get up to help, but the pain in her back prevented her from moving, her body also still being affected by what Nero did earlier. All she could do was barely see what was going on, hearing Iruka's speech. She could do nothing as her only friend rushed away before everyone's eyes. Tears streamed down her face as Mizuki jumped down beside her, Iruka and Mizuki had their exchange before Mizuki declared, "As soon as I eliminate Naruto and get the scroll, I'll be back for you two."
He then jumped off to chase after Naruto. Iruka, still in pain spoke, "I'm sorry Mina, please stay here… while I stop him."
Mina groaned in pain, "Not like… I have a choice…"

Mina didn't know how long she was forced to wait there, she knew it had to have been a long time since by the time a jonin found her, the sun had been up for at least a couple of minutes. The jonin was Nero, "Honorable Granddaughter, are you ok?"

He helped her sit up then squatted his back in front of her, "Here, I'll take you to the hospital."
Mina sounded a stubborn noise, but accepted. Nero then made his way back towards the village, "You don't need to worry anymore, Naruto's been cleared of his charge."

Mina's eyes widened, "Really? How?"

Nero frowned, "Mizuki tried to use him to get the scroll, it seems. Oh, and there's something else you should know."
Mina blinked in confusion, "What?"
Nero smirked, "He's graduated to gennin."
Mina was silent for a moment, her eyes and mouth widening with joy. She let out a big laugh before she stopped and groaned in pain from her back.

Mina had no choice but to stay in the hospital for the day, allowing her back to heal from the impact. Naruto rushed in to see her, "Mina! Are you ok?"
Mina, laying down in her bed, nodded towards Naruto, "I'm fine, nothing's broken. It just hurts really bad when I move."

Naruto, still wearing Iruka's headband, sat down in a chair next to her bed, grinning from ear to ear with his eyes closed, "Don't worry, I gave Mizuki a couple extra punches just for that!"

Mina laughed lightly, "thanks, that does make me feel a bit better."
She saw his headband, "I hope we get put in the same team, now that we've both graduated."

Naruto scratched his head, "We're going to be put into teams?"

Mina nodded, "I don't know anything more than that about our orientation…"

Naruto groaned, "Guess we'll just have to wait until orientation to find out the rest."

Mina nodded, "I'll be out before then, don't worry about me."

Naruto smirked, "When you get out of here, I'm gonna treat you to some Ichiraku Ramen!"
Mina smiled, "I'll hold you to that."

Mina yawned, "Sorry Naruto, I gotta get some sleep and I'm sure you do to… it's been a long night for us."
Naruto stood up and yawned himself, "Yea, I'll see you later."
Mina closed her eyes and got comfortable, "see you later."