Defiance
Summary: Uchiha Miki was a brave dutiful kunoichi. Her loyalty to Konohagakure was never in question. When her betrothed Uchiha Itachi confronted the Uchiha clan's betrayal, she spared him from a difficult scenario. Originally written before Itachi Shinden was released.
Warnings: This fanfiction is a retelling of the Uchiha clan massacre from an OC Uchiha's POV. As such, there is violence, gore, and related topics you would expect with the subject matter. There is also an on-screen suicide and a mentioned suicide (Uchiha Shisui's) in this work. If you feel you cannot stomach these topics, turn back now.
On a lighter note, there is a brief crossover with Harry Potter in a flashback. The flashback takes place right after the Battle of Hogwarts. Itachi's canon girlfriend and teammates do not exist in my story, as it was originally written years before the Naruto novels were a thing. Expect several original characters either on page or mentioned to take their place. Thank you.
Unrest had been stirring for years. It had started when she was a young girl. The Kyūbi attacked her village. Many of her clansmen had died protecting their home from the beast. Even so, several blamed her clan for its attack.
The Sharingan could control the Kyūbi, shinobi from the upper ranks muttered.
An Uchiha must have set it upon Konohagakure.
After the attack, the Uchiha clan were forced to live in a clan compound together. The proud ninja stared in dismay as their old properties either laid vacant, or were sold off with the new owners oblivious to why the houses were placed on the market in the first place.
They were constantly watched. ANBU stood guard just outside their clan's compound, as if imprisoning the Uchiha away from their outside connections. Several Konohagakure factions shunned the Uchiha.
Uchiha Miki was not as oblivious to the running of the Uchiha clan as she would like. The education she received as the clan heir's future wife peeled away her blissful ignorance a long time ago. She observed all kinds of political movements in her clan.
One particular movement recently gained a lot of attention. She hated it with all of her being. How could she not, when their goals involved overthrowing the current Konohagakure leadership?
The worst part was that her parents supported the movement. Many an occasion, the chunin kunoichi walked home after a mission, only to stop in the doorway. Her mother and father sat at the kitchen table, discussing rebellion against the village.
The first time it happened, she was completely floored. Her parents spoke about their plans as if they were planning a trip to the circus.
A thirteen year old Miki tiptoed into her house. She slid the wooden panel door behind her. She just returned from a mission. It was three o'clock in the morning, so she did not want to wake her parents.
The lithe pigtailed teenager headed for the kitchen. She really needed a bite to eat before falling asleep. Her late bite had been six hours ago, tearing into a ration bar while sprinting back towards Konohagakure's gates.
Voices sounding like her parents echoed from the kitchen area. She froze. She crept towards the doorway. She peered inside of the room from behind a wooden wall. A dim lamp illuminated the room.
What are they doing awake so late at night? Doesn't kaa-san have work tomorrow? Surely, tou-san has missions to worry about?
"So, we're going to the meeting Fugaku-sama is proposing, Kazuya-kun?"
Her mother's voice held a tone of excitement, something rare for the proper lady her daughter knew her to be. Her dark eyes had softened from their usual stern gaze. The chair she sat in squeaked.
"Yes we are, Asako-chan. In the Naka Shrine, we will discuss Operation Phoenix. Many have agreed to join it. In time, the Uchiha clan will be great again."
Her father's voice stayed level, but the black-haired girl detected a hint of seriousness. It was odd not seeing a wide smile on his fine-boned face. The girl found his somberness disconcerting.
"I wish I could assist more in the plan. It's bad luck that same border scuffle with Iwagakure that left me barren forced me to retire," Asako sighed.
She traced her right hip and upper thigh with a finger. The black-haired woman's long blue skirt hid the area from view.
Miki remembered hearing of how an Iwagakure ninja fractured her mother's pelvis in the last days of the Third Shinobi World War. Asako miraculously survived thanks to immediate treatment, but the nerves in her leg were left heavily damaged. On top of the nerve damage, the fracture tore her uterus. The injury ended the short woman's dream of a larger family.
Kazuya patted his wife's back. His hand brushed against her black hair restrained in a bun.
"It's not your fault, dear. Once Fugaku-sama assumes the Hokage position, he will search for the best medical ninja in the Hidden Countries so you can resume active duty. Assassinating the Sandaime should be easy at his age."
Miki forced her hand to her mouth, her black eyes wide. Surely, her parents couldn't be serious…
"Are you sure? He is called the 'Professor' for a reason!"
Kazuya cooed to her frazzled mother.
"He may have a large knowledge of ninjutsu, but age has left him a shadow of his former self. Being younger, Fugaku-sama would outlast him in a drawn out battle. The Sandaime Hokage's age has left him unfit to rule Konohagakure any longer. His counselors don't even respect him anymore. I've heard how they slip behind the Hokage's back."
Asako cupped her pale cheeks with her hands.
"I know. That hag Utatane Koharu passed a measure where no Uchiha may hold public office, unless the Hokage appointed them to it. That includes the Academy's PTA. The PTA, Kazuya-kun! A group that nearly every parent is expected to join and participate in when not on a mission. I couldn't even volunteer in our little girl's classroom before she graduated. Nearly everyone gave me the stink eye for not signing up, and the few knowing of why threatened our clan in case I ever went public."
Miki's pigtails flew back. She snuck out of the house. A figure with an ANBU owl mask flashed their mask behind her while she passed several quiet houses. She felt their presence tailing her as she exited the Uchiha clan complex gate.
She could not stand overhearing this talk of treason any longer.
What idiots! Overthrowing the Sandaime?! The topics they spoke of could end in their arrests and deaths!
Miki jogged to her friend Makuda Kinu's apartment. Her sleeveless blue kimono fluttered in the breeze. Surely, she could stay with her old friend for a few days. The blonde would understand.
Thankfully, Kinu's residence was on the first floor of her complex. The Uchiha girl knocked on the short-haired kunoichi's door as softly as she could.
In a few minutes' time, she was greeted by a teenage girl with bleary blue eyes and messed up blonde hair sticking up in several directions.
"Miki, what are you doing up so early? No, what are you doing back from your mission already? You told me it would take a week."
The black-haired kunoichi shook her head. She prepared a cover story.
"We caught the missing-nin just inside of Kaze no Kuni. They weren't as powerful as we expected. I had walked home, but my mom and I fought again. She didn't think I was acting 'proper' by not greeting her and tou-san when I entered the door. I mean, it was three in the morning. I was nearly asleep on my feet!It's obviously late, so can I stay with you for a bit?"
She was not telling her best friend what really occurred in her household. Miki had no intentions of dragging the kunoichi into her family's treason. She would deal with it herself. A few days away from her family would allow her space to mull over her options.
Kinu nodded her head after a few seconds.
"Sure. Let me go fetch the guest bed for you."
Even as she settled on to futon provided for her, it took a long time for Miki to succumb to sleep. She could not help but think about her clansmen wishing to overthrow the Sandaime Hokage, and the many people who would suffer because of them.
While staying at her friend's house, Miki weighed her options. She could turn her parents in for treason, join in their plans, pretend that the conversation didn't happen, or spy on them for the village.
In the end, the raven-haired kunoichi chose a fifth option. She wouldn't intervene at present, but refused to undertake her parents' betrayal, and would inform the Hokage if it became more serious. Though the small family often butted heads, her heart had grown heavy knowing her parents would likely die if they did not reverse course.
The owl-masked ANBU continued shadowing her after she returned home. In light of her parents' late night discussion, she wondered why she caught their attention. Was the ANBU aware she discovered her parents' treason, and protecting her until she mustered her courage? Or, were they considering her an accomplice? Was the ANBU assuring that she returned to the clan compound?
Miki noticed the Konohagakure higher-ups grew snippy when Uchiha clan members spent more than a few nights outside of the compound. She occasionally thought of moving into an outside apartment with Kinu as her roommate, but knew any attempt to spread her wings would be blocked. She heard of a rash of adolescent Uchiha being denied for apartments outside of the compound, while they attempted to place space between themselves and their parents. Permits to build apartment complexes inside the compound had also been denied.
The Hokage's advisors gave a civilian Uchiha woman a hard time when she fled the compound to escape her abusive husband. She lived with a friend for months, despite orders to return. The Sandaime Hokage Sarutobi Hiruzen eventually intervened with the matter; he relocated the Uchiha woman and her friend to an undisclosed location, while the Uchiha Military Police arrested her former husband. He was still imprisoned from what Miki recalled.
The last several months had been taxing. Uchiha Shisui had died of apparent suicide. The death of the curly-haired young man sent the Uchiha clan into hysterics. None reacted worse than Miki's arranged fiancé, Uchiha Itachi.
Miki and her lover were sent on a far away S-rank mission merely months afterwards. It had been in a foreign land outside of the Hidden Countries.
The mission in question was top secret, and had been announced a year-and-a-half before it was activated. The around fifty or more young ninja chosen for it had to attend classes about the enemy and his subordinates, how the locals used chakra, organizations helping to undermine their target, the country's customs, and their language whenever they were off-duty.
While the mission was ultimately successful, many of their group perished. The foreign enemies' strange techniques caught those chosen off-guard, even with the classes they attended. One of the strange jutsu was a flash of light that killed someone instantly. Among the fatalities were Miki's longtime teammate Aburame Takuro, and her friends Saya and Hyata Toyoharu. Itachi lost his former teammate Nara Shiyoko as well.
Both teenagers were on mission leave. The Sandaime Hokage felt they needed at least a month of rest to process their losses. He shot a furrowed glance in Itachi's direction as they left his office. The village leader likely thought the young ANBU captain cast a lot of blame on himself for the high number of fatalities.
Miki slurped the last of her beef stew, trying to ignore the flashes of Takuro's last moments popping up in her head. How he fell to the ground once that green light connected with his off-white coat with a subtle violet butterfly pattern.
Her mother gave a reproving look, but she turned her head away.
"Miki-chan, such behavior is crude for the wife of the future clan leader. You should scoop up your stew with your spoon, not slurp it directly from the bowl."
In contrast to his wife, Miki's father gave a hearty laugh. His long black hair flowed freely behind him.
"Asako-chan, leave her be. You're too hard on her sometimes. Miki-chan is enjoying her food, just like her dad. At least she doesn't diet like some of the other crazy kunoichi."
Kazuya softened his eyes as he uttered the last of his statement. His lips quirked into the frown the kimono-clad kunoichi hated seeing. He patted her on the back.
The lithe teenager gathered the bowls around the table. She stacked the bowls on top of one another before bringing them to the sink. She turned on the water in the kitchen sink. Outside sounds caught her attention.
Objects collided with the clan compound buildings with a thunk. Miki realized the objects were kunai. People screamed outside. The screaming grew louder by the minute.
Odd. Outside of emergencies, kunai use is forbidden in the compound. What's going on?
A fist pounded furiously at their door. Miki's mother opened it, revealing an unkempt visitor.
Uchiha Yashiro of the Konoha Military Police Force breathed heavily, struggling to catch his breath. Sweat ran down his face like a rainstorm.
"Negotiations with the elders failed. Itachi betrayed us. He's killing members of the Uchiha clan as we speak!"
The kunoichi's parents glanced at each other with wide panicked eyes. The jaw of her usually jolly father set itself into a thin line.
"We'll assist our clansmen. Yashiro, wait a minute or two. Asako and I will join you. Honey, you and I need to suit up in our ninja attire."
Asako rose as fast as she could from the dining table. Her right hand clutched her elegant wooden cane. She leaned into the cane while limping towards hers and Kazuya's bedroom. Her pretty husband hurried in after her.
She emerged a few moments later decked in a dark blue kimono top with a breastplate over the top and a matching short skirt.
The skirt was much skimpier than what the black-haired woman usually wore. It bared the scars Asako usually concealed to the world. Miki could not look away from her mother's ruined upper thigh.
Kazuya rushed out from the bedroom, having traded his usual violet kimono for a dark violet long jacket bound with an obi, black pants, and a matching undershirt. He stared at his daughter with a somber expression.
"Miki, stay here."
The statement startled the pigtailed teenager. Surely, she would be of more use joining her parents outside.
"Stay at our house? Why?"
Her father frowned at her.
"We betrothed you to Itachi when you were young. It would be difficult for you to see him as an enemy. If he comes here, you might speak sense into him."
The blue-clad girl's mother bowed her head.
"Itachi is one of the village's most powerful shinobi. We might not make it back. We love you."
In a flash, Miki's parents and Yashiro were gone. The Konohagakure kunoichi switched off the sink. She ran to her room near the back of the house.
Her room was among the cleanest ones in the traditional-styled residence. Her bag and equipment sat by the entrance, ready to be grabbed for a mission at anytime. Her wooden desk was kept tidy, with her ninja-related textbooks stacked into a pile in the corner, and her pencils laid neatly into front of the chair. The bed had no sheets or pillows out of place. If there was one thing the black-haired girl could do right in her mother's eyes, it was cleaning.
Photos of her friends and family were arranged in a row on her desk. Miki's family photo was in the middle. Her mother's frown contrasted her and her father's beaming faces.
One to the right held her friends in the Uchiha clan, Hiroto, Kaori, and Seiji. Hiroto smiled, with his arms folded in front of his red shirt. Seiji waved to the camera as his spiky brown hair flew in the wind. Kaori held up one of her hands in a pumped fist, wearing a pale blue dress over a white undershirt.
To the left of her family photo was the official team photo for Team Kage. Her sensei Washiba Akahana's redheaded face beamed into the camera. Miki smiled as well. But, Takuro only quirked his lips slightly upwards; though he wore more colorful clothes than his clansmen, he shared their reserved nature. Their eldest teammate Komatsu Kanbe glared at the Uchiha girl, his pale blue eyes as hard as ice.
Kanbe's dislike of Miki stemmed from assumptions about her upper class upbringing. It had disappeared as they worked with each other. He learned quickly she wasn't some snobby upper class girl as he had first assumed.
They hugged at Takuro's funeral only a few days ago. The two young chunin cried as they placed flowers in his coffin, and then performed something unexpected.
The two teammates placed their pale brunette's dark sunglasses over his closed eyes. Their dark-haired comrade had wore his sunglasses at all times, even when he was asleep. Since death was the 'final sleep', Team Kage's membership thought that it was appropriate.
Her mother threw a fit about the hugging, but Miki did not care about the stern woman's complaints of 'acting improper with a boy'. She vanished to her bedroom after the funeral. She could not deal with Asako at that time.
The pale-skinned kunoichi gazed fondly at Itachi's photo. The longhaired teenager sat on a high ledge, lips in a light smile. Behind him was a field of bright grass.
He experienced a lot of grief in the last few months. His best friend killed himself, and he had been assigned a mission with a high body count. Among the deceased was one of his teammates from when he was a genin and chunin.
Wait! That mission. When we had finally dealt with the enemies, Itachi let slip that his father didn't approve of the Sandaime's reign. His father wanted to take over.
Itachi spoke with disapproval about his father's aspirations. The wording indicated the Uchiha clan head was part of the rebellion.
Miki ran to her lover. Itachi collapsed against the castle wall. His body shook with exhaustion.
"You overexerted yourself, didn't you?"
The teenagerraised his head in a brief nod. His shorter companion removed his blood-soaked shirt. Deep cuts littered Itachi's abdomen and chest.
The black-haired kunoichi brought her glowing hands over the wounds. She hadn't known medical jutsu would become such a useful skill for her. She mainly studied it to further her expertise with poisons.
The locals awed at the display, until Kanbe stood in front of the two Uchiha. He shooed them off.
"I'm sure you find Miki's skills amazing, but she needs room to work. If you want to help her, grab some water and food so she can keep her strength up. Maybe find a few towels, too. Otherwise, head back to the Great Hall."
The locals widened their eyes, shocked at being ordered around by a teenager, but did as he requested.
The tall shinobi left as well, calling behind his shoulder.
"I'll leave you here. Call for me if you need anything, Miki."
The cuts gradually faded. Sweat beating down her brow, Miki healed one last wound on Itachi's chest.
Her lover quivered as he attempting rising into a sitting position. She pinned him down with her hands.
"Itachi, listen to me. I healed these up, but the muscles need time to knit back together. You lost a lot of blood. You are only moving away from this spot if you agree to be carried, or are placed on a stretcher. Do you understand?"
After a moment of silence, the Uchiha clan heir nodded.
"I'm sorry I became injured like this. Those 'Death Eaters' took me by surprise. I do not want you blamed for my errors."
Miki grinned as broadly as she could under the circumstances.
"If it's about the clan blaming me for not protecting you, I don't care about their opinions. I'm used to my mom's nagging, and Hatsumi and Nori calling me an embarrassment. The people I care about are you, tou-san, Kanbe, Akahana-sensei, Hiroto, Kaori, Seiji, and Kinu."
Already, a void filled the Konoha kunoichi's heart. There would be no more occasions where she and Saya would work together on joint missions. No more days in the library pouring over poison-related texts with Toyoharu. No more team meetings with Takuro present, with the older boy watching butterflies flutter over the trees.
A small smile graced Itachi's features. He chuckled softly.
"You know what, Miki-chan? I agree with you. I don't care what the clan thinks anymore. There are only a few persons' opinions I consider important nowadays. One of them is the Hokage's."
The fourteen year old gasped.
"The Hokage gives you his personal opinion? I feel jealous."
The younger teenager frowned.
"You shouldn't be. My father's been cooped up in the Military Police Force's Headquarters. Whenever he has been home, he avoids me and says strange things. He claims he wishes to become the Godaime Hokage."
It was Miki's turn to frown. She was quickly reminded of eavesdropping on her parents and hearing of Operation Phoenix.
"But, our leader is the Sandaime Hokage! It isn't Fugaku-sama's place to question his leadership!"
The black-haired girl thought she spotted a longhaired girl with pale lavender eyes spying on them from one of the entrances, but she didn't stop shouting. She was sick of the Uchiha clan's treason. If an outsider overheard, so be it.
Airi can keep a secret. She's managed keeping the truth of her father's death away from her little brother for years. We can trust her.
"I know," the longhaired ninja sighed.
From where he lay, Itachi cupped Miki's cheek.
"A lot of our clansmen do not look on Konohagakure favorably. Certain shops do not allow them inside, and there is an unofficial ban on Uchiha clan members entering politics, even on a local level. They don't view Sarutobi-sama as a leader who can protect them. They desire change. If a coup is what is required, they will overthrow the Sandaime in a heartbeat."
The pale-skinned girl gulped.
"What about you? Do you support a coup?"
Itachi shook his head, his body trembling from head to toe. His voice came out as a whisper.
"No. It would cause a civil war. Many lives would be lost. If Sarutobi-sama cannot lead anymore, he should pick his successor on his own accord, or the village should field candidates in a non-violent manner. I care for the village more than the clan I will inherit."
With the wedge between Konohagakure and the Uchiha clan, it was not surprising how the Uchiha clan heir chose. He was placing the village at large above his clansmen.
The longhaired boy must have reported the Uchiha clan's treason. The Sandaime or the elders must have ordered their murder. One of Konohagakure's founding clans suddenly turning rogue was an unforgivable event.
I won't be able to talk him out of it, Miki thought sadly.
She played out a number of scenarios in her head, where she pleaded for the clan's life. All of them ended in Itachi stabbing her with tears running down his young stressed face, even the one where she only asked for the lives of the youngest children and non-Operation Phoenix Uchiha like herself.
Itachi followed any orders from the village. So did the pigtailed kunoichi, for that matter. She would do anything for its sake.
That included carrying out her death.
The cheerful girl wished to spare Itachi the anguish of killing her himself. The idea of the black-haired teenager sobbing as he stabbed her with his tanto was unthinkable. He already blamed himself for what happened to Shiyoko.
She hated that events petered out as they had. Her life was heading to its close much faster than she anticipated. She would never have a chance to join ANBU, see Akahana and Kanbe again, or even develop hers and Itachi's relationship more to where they were heads over heels with one another instead of close friends. Her indecision stole that from her.
Stop, Miki. It's upsetting, but there's nothing you can do but carry it out. You'll be with Takuro, Saya, and Toyoharu soon.
From her bag, she slipped on a pair of gloves. With a morbid fascination, the black-haired girl fingered a square tin. A round phial found its way into her hand. The phial contained her most lethal poison.
Unlike many Uchiha, the kunoichi preferred using poisons instead of jutsu. Out on missions, Miki coated needles with toxins of her choosing and threw them at her enemies.
Opening up the phial and square tin, the kunoichi dipped a senbon needle in poison. Laying it to the side, she coated three more needles.
As she worked, Miki thought of the Uchihas out of the village. Of the clan members she was familiar with, her uncle Hiromitsu, Kaori, and Seiji were absent from Konohagakure at the moment.
Hiromitsu was on a joint mission in Takigakure. Seiji patrolled the border between Hi no Kuni and Kaze no Kuni. Kaori landed a fancy mission all the way in Tetsu no Kuni, where she and her team were working with samurai. Another uncle of hers, Yoritomo, left for Kusagakure just that morning. There were likely more.
How would Konoha deal with them?
Itachi would have to be declared a missing-nin after his actions tonight. To acknowledge the Uchiha clan's issues with Konohagakure would place the government in a negative light. They killed children and citizens who had nothing to do with the coup. Whoever ordered the killing did not attempt a peaceful solution first, such as arranging a meeting with Fugaku about clan issues, or sorting out the guilty from the innocent.
Itachi could not stick around, lingering in wait for any returning Uchiha. The village would connect the dots if a mass murderer was allowed among them, striking down his clansmen as they reappeared. Kaori's team was scheduled to stay in their current location for three months.
Would a special ANBU squad track down and slaughter those out of the village? Would everyone that befriended the Uchiha be hunted down?
Miki faintly heard someone tearing away the house door. She grasped her senbon as carefully as she could.
It's time. I'm sorry for causing our team more pain, Takuro. Goodbye, Akahana-sensei, Kanbe, Kinu, Seiji, and Airi. Farewell, Itachi-kun.
The black-haired kunoichi aimed the four senbon at her chest, folding her knees under her in a kneeling position. With a quiet prayer, she flicked her wrist, releasing her coup de grace.
In seconds, the kunoichi's body collapsed to the floor. Every muscle burned, as if she were on fire.
The child felt no regret for her actions. She gave her life to protect the village. Her boyfriend would not shed her blood.
Miki believed she saw the spirits of her dead comrades by her side. Saya, as pretty as ever, shook her head. Toyoharu frowned. Hiroto lingered behind them, fainter than the others. Takuro knelt beside her.
"It's okay," he whispered.
"You will join us soon. Akahana-sensei and Kanbe will know the truth. They are assassin specialists, just like we were."
Her vision grew darker by the second. Itachi entered her room. Covered in the blood of their kinsmen, he halted upon seeing Miki's crumpled form.
"Miki-chan, what have you done to yourself?"
There was no anger in his voice. Just the sound of a boy trying to fight back shock and tears.
"For Konoha," the girl whispered.
A smile formed on Miki's bloody lips. Her spirit rose to reunite with her friends. The last words she heard in the living plane were Itachi's voice.
"Miki-chan, I'm sorry. I didn't mean to place you in the middle of this…"
A/N: Welcome to Defiance, a fanfiction about the Uchiha clan massacre I originally wrote way back in 2013, before the Naruto manga ended or the Naruto novels such as Itachi Shinden were released. I originally came up with it while trying to break free from writer's block, feeling inspired by the idea of Itachi's girlfriend he had to kill during the Uchiha clan massacre. A question popped into my head; what if she died that night like the other Uchiha, but not at Itachi's hands like several people believed? What if she also opposed the coup?
I came back and re-edited this story after hearing on various forums about the large possibility of shutting down and it not acting correctly for me around September 2022 (it showing I had no views for a week and a half on the viewing graph; it's since been restored to normal). I began a very large project to download chapters from all of my fanfiction stories, save them, and later re-post them on AO3. While I've since read that the website admins are migrating over the servers, this site is sadly very old, and I know it's only a matter of time.
When I downloaded and saved Defiance, I re-read it to see how I could improve spelling and grammar. I knew I had a few errors inside. Instead, I found several other areas lacking, such as a lack of description for Miki's parents or of specific instances of the Uchiha experiencing discrimination leading to the coup. I spent more time working on Defiance in light of this. I'm sure I bumped up the word count a bit.
As I rewrote Defiance, I added an element of deconstruction to the Uchiha clan discrimination and later massacre. There's only so much that can past muster before the regular Konohagakure citizens realize something is wrong, that the Uchiha are being treated differently than they should, and don't have the same rights or privileges as everyone else. Kinu and several others were cottoning on to there being a problem. Even if Itachi had not killed his clan when he did, the situation would have erupted a few months later at best.
I write my fanfiction in a multi-verse setting. I used to read Harry Potter/Naruto crossovers a lot years ago. There used to be a genre of the Konoha 11 deploying to assist the Order of the Phoenix against the Death Eaters. I turned several parts of the genre on its head for Defiance's storyline; it was Itachi and Miki's generation that were deployed on a so-called 'Hogwarts' mission, they were prepared for it extensively, and despite that last detail, many of those sent off died in the Battle of Hogwarts instead of having a happy ending. Konohagakure lost many skilled ninja from Itachi's age group from investing so heavily in it. Between that mission, the massacre, and something I will be expanding on for later works, Konohagakure's close to running out of young skilled ninja for a while.
Kaori survived the massacre, but a ROOT team came along and killed her sensei and teammate in an attempt to eliminate her. She, her remaining teammate Inuzuka Taiki, and Taiki's ninken Kuromi never returned to Konohagakure. They stayed in Tetsu no Kuni and became samurai.
As for Hiromitsu and Seiji (along with any other Uchiha out on missions during the massacre), you can come up with your own theories. Just remember ROOT agents aren't unintelligent, and Danzō will soon face consequences for the Tetsu no Kuni-related mess. He will wash his hands of the massacre once that occurs.
Itachi has joined the Akatsuki, so he's too busy to try killing off the remainders of his clan. As skilled as he is, he cannot run off to all these far-off areas to pick off his remaining kin one by one. It would involve too much energy, and he will be listed as a missing-nin before long.
If a certain part of the second flashback wasn't noticed, there is another person who knows the truth of the Uchiha clan massacre. This OC is named Hyūga Airi. She is the much older sister of Neji. Her relationship with him is heavily strained because of their father's death (Airi knows her father willingly sacrificed himself, Neji does not until after Naruto defeats him in the Chunin Exams). Some ninja hunt after her as well for possibly knowing about the truth of the massacre among other things, so she will soon take a long-term mission back to the UK. She has some great magical defense skills even if she trained in it for under two years, and Hogwarts is looking for anyone that will take their formerly cursed defense post…
Hiruzen and his advisors could not halt the Uchihas from taking missions without suspicion. A big part of the massacre is that few know why it happened. The Hokage and his elders had to play it business as usual until the big date came.
I try to (mostly) stick to canon on subjects like this one. I only exclude The Last: Naruto the Movie, Boruto, Itachi Shinden, and several of the other Naruto novels, as I wrote my fanfiction and came up with the broad strokes of this universe before those materials were released. Very few know about the massacre's reasons until afterthe Fourth Shinobi World War in my fanfics.
Before that time, Danzo, Koharu, Homura, Hiruzen, Tobi/Obito, Itachi, and Airi are the only ones in the know. After Itachi's death, Sasuke, Mitsuki (Itachi's lover post-massacre that he meets during the Timeskip), and Naruto came into this knowledge. Our favorite blond hero tried to keep it a secret, but by the time of my New Gen crossover fic Whirlpools of Lightning, all of the Hidden Countries know the truth.
I would like to comment on Takuro's ghost speaking about their sensei and teammate. As assassins, Akahana and Kanbe are trained to be observant. They will notice the senbon punctures on Miki's corpse when they view her body. There is no reason for her teammates to be barred access to her corpse, even if a mass funeral for the Uchiha clan is planned later.
The Sharingan gives someone the ability to copy jutsu. Weapon use is not covered under that banner to my knowledge. Itachi used a sword during his ANBU days. He has not used senbon needles at all during his lifetime, and using them during the massacre for the first time would have been a poor choice. Needles are difficult to use. A long time is needed to train proficiently in such a delicate art.
Team Kage do not learn of the massacre's true purpose until after the war and/or their deaths, but they come to the conclusion that Miki killed herself. They realize that the Uchiha clan massacre is more complex than it seems. Danzō wants them eliminated for their suspicions, but is unable to do so because of committing his ROOT forces to taking out Uchiha clan members still on missions and Hiruzen coming down on him for his manhunt.
It would have been a bad move to kill Akahana and Kanbe at that time because of the mysterious causes of their teammates' demises (the massacre and their S-rank mission beforehand (the latter of which was classified). Miki and Takuro died within weeks of each other. Outside parties like Kinu or Takuro's family could claim that someone had it out for Team Kage. That would be bad for both Danzō and ROOT, wouldn't it?
As for Itachi's reaction at the end… he may have been ordered to kill the clan, but he didn't expect Miki to kill herself. Her actions brought him into shock.
There are several plot points dangling, so at some point when I don't have so many works in queue, I will write a second part called Defiance: Aftermath. It will go into the aftershocks of the massacre and Miki's actions. Among the featured characters will be Itachi, Hiruzen, Danzō, her surviving team, Kinu, Airi, Kaori, and even Miki herself postmortem.
Any comments on this dark fic?
