Naruto- Secret Sage

"In that case we will call a meeting to discuss "future plans for the village" that Danzo will need to be a part of at the end of the week. At that time we will reveal his crimes and try him for them there if he doesn't put up a fight but be prepared should he choose to try and escape." Tsunade said sternly and everyone here nodded in agreement before leaving.

'That ability is such a nightmare to plan around. To subvert someone's mind without them knowing or direct eye contact can simply cause too much devastation.' the blonde thought seriously.

[Kotoamatsukami], the mangekyou sharingan ability of the deceased Shisui Uchiha. It allowed the user to subvert the mind of anyone it was used on without eye contact or any signs at all like a extremely well hidden and distanced form of brainwashing. One moment you could wish to kill the user and the next you would consider them your best friend without you ever realizing this change had occurred. It was capable of doing extreme good in the right hands as it could point influential people in a way that was for the greater good but in the wrong hands it could prove disastrous.-

Danzo Shimura was DEFINITELY the wrong hands for the ability to sit in. He was too selfish and greedy to use it properly. A question that could then be asked was if he had used the ability in secret all this time and if not why? He could have easily utilized the ability to take the position of Hokage or even take control of the geniuses that show up in the village like Kenzo and yet there was no signs he had done so.-

'I'll need to search my granduncles notes on the mangekyou as well as any information I can find on the regular sharingan.' Tsunade thought as she realized the strangeness of the situation.

Over the next three days a silent tension built up as the clans prepared to spring the trap on Danzo. Meanwhile Tsunade Senju had trespassed the study of Tobirama Senju to look over his knowledge of the sharingan and was astounded by what she found. The use of a mangekyou sharingan came with some heavy downsides such as blindness over time, heavy chakra drain and massively increased costs to the sharingan if the user wasn't an Uchiha.-

It turns out that this was the reason no one tried to steal the eyes of the clan most of the time other than the retaliation they would receive. The cost to use them rendered them more of a burden than a help and all but crippled the users future growth.

'I knew Kakashi was having some extra strain on his chakra because of that eye but I had no idea it was this bad and he has still reached the edge of S rank? Truly a genius and worthy of being that mans son. At least now I know why Danzo hasn't used that eye this entire time, the cost is too high.' Tsunade thought as she closed the scroll.

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(Last day of the week, Council chamber.)

"What is the meaning of this!?" Danzo roared angrily as he was surrounded by armed shinobi all poised to take his life in an instant.

"Yes we would also like to know what is going on?" Homura said with the other elder who had been left out of the loop agreeing.

"I have a list compiled by the third Hokage with evidence of Danzo's many transgressions and crimes. Feel free to look for yourself." Tsunade tossed out a copy of the evidence with a serious look.

The two elders that were old friends of Danzo's read through the evidence in horror before looking at Danzo and shaking their heads sadly. "The evidence is overwhelming, we can not stand up for you this time." Homura said tiredly while throwing the evidence at Danzo's feet where he could read it.

The look on his face grew darker and darker as he read but he didn't apologize or even speak.

"Have you nothing to say in your defense?" Tsunade asked with a cold expression.

"This farce ends here!" he roared as vacuum jutsu tore apart the shinobi near him and blasted open the nearby wall where he tried to flee out of.

"Kill him, he cannot be allowed to escape!" Tsunade ordered while chasing the man and the other clan leaders moved into action as well.

A barrier was formed immediately sealing Danzo inside and he growled in fury before turning to those that were coming after him.

"You forced me to do this!" he roared as he unwrapped his head to reveal the sharingan in his right eye socket "Kotoamatsukami!" he roared and the eye bled as the pupil rotated and transformed into a pinwheel shape staring right at his pursuers.

The council members froze with glazed looks for a moment which made Danzo sigh in relief until the sound of glass shattering rang out and he suddenly realized that the genjutsu had been forcefully interrupted cutting his eyes ability off even as the vision in it dimmed to blindness. The council members all shook as they snapped out of it and glared at the old man who was now drained and down his trump card.-

The following fight was too one sides to even be considered as such as the combined prowess of Tsunade and the clan leaders immediately overwhelmed him and he drowned in a barrage of high rank jutsu that he was unable to dodge. Like this his soul was sent howling at the unfairness of the world into the void. 

"We all need to be checked for any lingering remnants of that genjutsu but this matter ends here." Tsunade said with a relieved expression.

'Nawaki, Dan, everyone justice has been served for you.' she thought as her mind seemed lighter now that she had gotten closure for all of those wronged by Danzo.

Over the next few days the Root was taken apart and all the foul experiments that the third Hokage didn't know about or mentioned came to light and were destroyed without hesitation or integrated into advancing the village properly. While much of the research was forbidden and useless to others not on those paths a good deal of the data was able to push medical knowledge and cellular development forward by leaps. The word had been sent through the root's channels to those hunting Kenzo to cease and return to the village immediately.-

Kenzo was of course not aware of this as Tsunade quickly discovered that she couldn't reach him at all. Whether it be by messager hawk, other shinobi or even his summons that she could find no message could reach him. This caused her quite the amount of distress as for all intents and purposes he had vanished from the face of the world save the three remaining shadow clones that were still hunting bandits. When asked about it the clones had remained tight lipped and refused to say anything even if it meant they risked getting dispelled.