Author's Note:

I decided to seperate the chapter into two, since they aren't really connected. Hopefully this makes it flow better.

So Double Post Today.

Danzo tightened his fist, as he was brought before the Hokage, like a common criminal. In chains and seals, suppressing his Chakra. "Everything I did," he spoke on his own defense. "Was too protect this Village."

"I decide how it is protected," Minato glared. "You're a middle man, the third may have allowed you to do as you please, but clearly he didn't ask enough questions. You took advantage of your childhood friendship, to do whatever the hell you wanted.

"Children stolen from their clans, from all over the continent. Tortured until there was nothing left, then reshaped how you saw fit.

"If not for the Wizards Mastery of memory altering Jutsus, these children would have been scarred for life." Instead they were living as carefree children, adopted by some of the clans throughout the village. Many of them even choosing to join the Shinobi Academy proper.

"We even uncovered plans for you to massacre the Uchiha clan, and hide away all it's children in Root's underground tunnels." Minato raged, "How is attacking our own clans, beneficial too our village!?!"

"I've recieved intel they plan to rebel," Danzo glared.

"I've heard nothing of this, and frankly, if genocide is your answer to civil unrest, then I don't blame them!!!" Although he would be having words with the clan elders. Any hint of a rebellion had to be rectified.

The Council, as they handled charges of treason directly, turned their eyes onto Lord Uchiha. Who looked stoic, and unreadable, as ever.

The head of each clan, sat on this council. Including the Village's new clans.

While the hidden villages, recieved 20,000 members of each clan they ordered. Konoha wasn't completely stupid about it. Giving themselves a small number of every clan they created. That was well over a thousand clans. But at only 500 members, per clan. This was just enough genetic diversity, within each clan, to prevent the effects of inbreeding.

The smaller numbers insured the clans couldn't be seen as too large a threat, to the other villages. While not putting the Leaf Village, at too large of a disadvantage.

From there, each of these tiny clans, were still given a "bigger on the inside," estate. As well as a seat on the council.

The original clans, were adjusting well to the pod borns.

The Hokage called for the Council to deliberate... then, once recieving a guilty verdict, sentenced the traitor to death.

Danzo was then escorted from the chambers, to be taken to the Shinobi prison. To await his sentence.

As the Council departed as well, Minato got Fugaku's attention. Requesting the Lord of the Uchiha Clan, accompany him to the Hokage offices.

Once they were alone, save for the ANBU that are always watching Minato, the Hokage began with, "This is off the books." He assured, "No actions will be taken against your clan. You've had a hard enough time as of late."

These passed few years, since word got out of an Uchiha being responsible for the Kyubi's attack... it had been difficult for the clan. The citizens lost respect for them, as the primary police force, as Shinobi, as a clan, even as people... Minato was ashamed of how the average villager was acting.

Originally, they were mad at Naruto, but Minato was able to nip that in the bud, by giving a press release, about what happened that Night. That Naruto was his son, not the fox reborn, and that the fox had been taken over, and not responsible for his actions that night. That Kurama was still the Village's champion...

Unfortunately, that meant accidentally throwing the Uchiha under the bus. He tried to stress, it was a Missing Nin that took over the fox... but that seemed to have fallen on death's ears. As the Civilians wanted someone to blame.

The various clans understood, a Missing Nin, a traitor to the village, who had gone free-lance, could come from anywhere. With one emerging, from every clan, at least once per Generation. It was an embarrassment, and a tragedy, whenever it happened... but it was understood not to be the clan's fault.

Fugaku... sighed, "I'm ashamed of my Clan's Elders, Hokage Sama."

"That's okay," Minato smiled. "I'm ashamed of this village's civilians."

Fugaku eyed his old friend. And they were indeed friends. They had gone to the Academy together. Played together as children. And now that they were grown, their own children played together.

Fugaku had no intention of following through with the Elders' suggestion... but the horror was, they had suggested it...

"The Elders have caused a splinter group, to emerge in my clan. Building up resources for an attack... I've been attempting to squash this little rebellion, on my own... I had hoped to do so, before you found out about it... this will do nothing to endear my clan, to the Civilians... and may even risk our standing with the other clans."

"Perhaps we can handle this silently," Minato thought on it.

"Hokage-Sama," The wolf suddenly appeared. Acting much calmer then the last time he had bad news. After all, he was an adult now. Regardless, the other ANBU often sent Kakashi to deliver ill news... given Minato's soft spot for his former student.

"Yes, Wolf-san?" Minato acknowledged, sparing a glance to Fugaku. Subtly telling his former apprentice, that the boy was interrupting an important meeting.

Kakashi bowed low, "Danzo's agents have moved against the Uchiha clan."

Obito, following his Sensei's orders, arrived at the new village's Clan District.

The Wizards had folded each of Konoha's original clans, into their own private "bigger on the inside" manors. Each having a single building, containing an entire continent inside. With all these manors, placed around the Twin Clans' Mountain.

Obito knew what was happening, as Madera had planned for this inevitability. And had sent the young man to insure it succeeded.

Itachi slaughtered the traitors, sparing no one. While the children were taken to the emergency safe house. The Estate, upon an attack, was enchanted to teleport every Uchiha, under 30, whom wasn't wearing a Shinobi headband, to the underground base, at the center of the continent.

Root had moved against the Uchiha, and while Itachi understood this was a distraction... he couldn't stand by and do nothing.

Itachi turned against Root, to protect his clan. While most of Root remained loyal to Danzo, not the Village... they were traitors... and Itachi despised traitors.

Yes, there were unsavory elements in the Uchiha Clan, but they should be rooted out, not just slaughter the whole clan!

Thank Kami, Sasuke had chosen to go to the Jinchuriki Dojo, after school.

The most powerful, and loyal, Root operatives met Danzo's police carriage. Killing the Guards, and unchaining their leader. Danzo smiled, although the grin still looked like a frown.

"How does 'Plan B' progress?" Danzo asked the lead operative.

The root agent bowed low, before speaking, his eyes not meeting Danzo's. There were upsides to being centuries old, when it came to training Shinobi. This man had been in Danzo's "care" for 40 years, since he was a small baby... he knew no other life, nor wondered on them. Thanks to his training, he was completely obedient, and extremely powerful. "Most of the Village's forces, are focused on our raid against the Uchiha clan."

The operatives each pulled out a pencil, before handing one to Danzo. They were Port Keys, allowing for long range Teleportation.

While most villages had wards against ports, as head of a division of ANBU, Danzo had the authority to create bypasses. Even though his authority had been stripped, when he was arrested, that just meant he couldn't make new ones. All of the, thousands, of ports he already made were still active.

Unfortunately, the village would likely take the upcoming weeks, to ward against his ports, specifically. So they would be useless, after today. So might as well use them.

Danzo wasted no more time, and snapped his pencil in half, thereby activating the one off emergency port. Taking him to his secret base, far outside the village.

Itachi was panting. As he struggled against the new player. The young man was only a little older, then himself. But he was much more powerful.

He was able to force Itachi into a corner, unable to defend his clansmen... as root slaughtered them all.

Suddenly, there was a flare in the sky, and the fighting stopped. The Root Operatives began stuffing all the corpses they could, into storage scrolls.

This was not camaraderie, as they didn't bother retrieving their own fallen teammates. They wanted the Uchiha's Bloodlimit.

Itachi growled, not able to stop them, as his own opponent was not letting up. Not until Root got away, with ALL the Fallen Uchiha. Itachi tried to follow them out of the Estate... but he saw no sign of them... only the trace signature of thousands of portkeys.

The Wards, of each clan, were too great, and personalized, to allow even a village approved port's use... but unfortunately, Itachi hadn't managed to stop the traitors... his clan had been massacred... but what of the children?

Fugaku returned home... to find only his immediate family.

His wife had managed to guide the Genin to the safe house. So she was safe...

But Itachi was badly injured... and resting in Konoha's primary hospital... He had both an arm and a leg, damaged beyond repair... they needed to be amputated. But thankfully, the Supers' Clan healers, were fitting him for cybernetic prosthetics...

Then Itachi's eyes, the most treasured part of an Uchiha, had been badly damaged. He had tried using his mental illusions, but had been countered, to the point he burst blood vessels, in both his eyes. He was practically blind now... and his eyesight would only worsen.

To an Uchiha, this was a fate worse then death. Other clans might be able to survive, without their eyes... even thrive, but not an Uchiha.

The Magicals had prosthetic eyes, with enchantments to rival an Uchiha's own... but Itachi refused... not wanting to lose the symbol of his clan. He would rather be blind, then replace his eyes... and Fugaku could understand the sentiment entirely.

All Itachi saw, was vague shapes, and blobs of color. Yet he insisted he could still use his Sharingan. Which let him see perfectly fine. At a constant Chakra drain.

Sasuke hadn't been present, during the massacre, to which Fugaku was eternally grateful.

A cause of great relief, was the Estates wards had worked, and the clan's children had all survived the raid... but only one hundred adults still lived... where there had been tens of thousands.

Only some were confirmed dead, as most were listed as missing... as Root had taken all the bodies... no doubt mutating, and experimenting, on their lost family.

For the first time, since he was a child... Fugaku openly wept, over all his losses.

Danzo appeared in his safe house, with his private army... with Madera waiting for him, along with his young apprentice.

Madera smiled, "Konoha didn't seem to value all your contributions. You're just a Missing Nin, in their eyes." Danzo clenched his fist in anger, at the mere thought. They were probably writing his name, in their bingo book, as they spoke. Danzo didn't question how Madera knew any of this. With the plant Zombies ability, to travel through plants, they were quite the impressive spies. Even knowing the location of Danzo's safe house, wasn't a surprise. They likely new what was happening, in every unwarded inch of the continent.

Madera, smiled, not trying to hide his hand, at all. "I have an offer for you."