'I will kill that meddling old bastard Danzo! I already have it all planned out.'
These last two years Shiki had already devised a plan to not only take out Danzo but to also take over the Root organization. He had successfully fused the Mind's Eye of the Kagura with his byakugan in a way that when he activated his byakugan it would have a greater range and all of the former's abilities, he called it the White Eye of the Kagura.
Using it, Shiki had mapped out Danzo's routine and, he realized that Danzo's official residence is not guarded! Probably because he doesn't keep anything suspicious there but the point is he still sleep in that residence.
Picking out a time during which Danzo's residence was vacant, Shiki infiltrated the main building and set up a hidden sealing barrier formation using specialized paper tags, in the room the old bastards likes to have his tea in. It was strong enough to restrain a tailed beast and focused on such a small area exponentially increased its binding power.
He also set a secondary formation covering the entire building in case the old cunt brought some bodyguards or in case someone else decided to barge in. In the first case it would restrain them long enough for Shiki to kill them while in the second it would give Shiki time to make himself scarce.
Quietly waiting using the Hiding in Surface Jutsu, Shiki watched in anticipation the approaching Danzo with his White Eye of the Kagura. He didn't even have bodyguards showing how confident he was in his grasp of the villages situation or perhaps because he wasn't willing to arouse the Hokage's suspicions. Whatever the case, it made Shiki's job even easier.
As Danzo entered his home after dark, he lit up a few candles and started to brew some tea. Shiki let him finish and just as he was about to pick up the cup, the boy activated the sealing barrier formation.
Danzo was immediately frozen in place. Not only were his physical movements restricted even his chakra was restrained thus preventing any form of resistance, he couldn't even speak.
Shiki calmly came out of hiding sat in seiza in front of danzo and cooly drank the tea that had just been prepared.
The mocking actions were getting on Danzo's nerves but even his expression was frozen, he couldn't even breathe his heart felt like it was being squashed by the barrier to stop it from beating, Shiki's actions just a final insult before his imminent death.
Soon even with is body juiced up by the Almighty Hashirama Cells, Danzo could no longer hold on and perished.
"Goodbye old bastard, I'm sure you won't be missed."
Shiki swiftly captured Danzo's soul and got to work. First he removed Danzo's right arm and eye and after placing them in special containers, he stored them in a scroll. Next, he extracted all the useful information he could find from the soul and it was bountiful indeed. following that he created a soul clone but this one was different from the normal ones.
To make a soul clone, a combination of a Yin Soul, a Yang Soul and an elemental soul of each of the five elements is used to make up the inner soul while a Pure soul his used to make a copy of the users outer soul and materialize a body. However this time Shiki made a perfect copy of Danzo's soul essentially making another Danzo but one under his control.
In hindsight he could have done this and let the Third Hokage bring in "Danzo" to be the hidden leader but no matter. Now the new Danzo would simple bring in the Reaper and set him up as the next leader of Root. The Reaper will also, in due time, upgrade the cursed seals on the Root members.
With the organization's resources and connections it would be far easier to infiltrate the other great hidden villages and obtain their secretes. He would soon have access to the cells of the First Hokage as well as extra sharingans the old bastard had in storage. The were also samples of other shinobis' DNA he had to investigate.
Disposing of the real Danzo's corpse with an amped up Body Elimination Jutsu, Shiki faded into the night leaving the fake Danzo behind.
The next day . . .
To benefit from Shisui's eye, Shiki devised a new seal from what he already learned from the legacy. If it worked then Shiki would have access to both his sharingan and Shisui's. The plan was to seal Shisui's sharingan into his sharingan in a similar as as to how a tailed beast is sealed inside a jinchuriki.
This was something he had been working on for a while in anticipation to when he obtained Shisui's eye. Naturally, this was a dangerous and untested procedure so first he used a random sharingan from Danzo's collection and attempted the procedure on one of his soul clones.
As soon as he tried it the subject's eye started to bleed and the soul clone communicated intense pain however, just as Shiki was about to determine it as a failure, the bleeding stopped the clone's natural healing abilities kicked in and repaired the damage.
Just to be sure Shiki tried it three more times and one one of them he used a criminal captured by one of his clones out in the world. The result was a success for the clones but the destruction of the criminal's eye.
'It looks like a resilient constitution and healing power is required for this procedure to work . . . In any case, it can be used on myself without any foreseeable problem.'
The sharingan used to perform the experiment on the criminal was lost but those used on the clones were retrieved. Shiki then performed the experiment on himself sealing half of the obtained sharingan into his right eye along with Shisui's and the other half into his left eye, this way they could be used as sacrifices for the Izanagi and Izanami int place of his true sharingan.
Expectedly Shiki began massively bleeding from both eyes as the clone did the procedure on him but compared to the pain of soul melsing, it was negligible so he endured it without any trouble.
As he stared at his reflection in a prepared mirror Shiki thought he was staring at some ghostly apparition. Alabaster skin, white hair and streaks of blood as if red tears, it was straight out of a horror movie but as Shisui's mangekyou manifested itself on his right eye, Shiki was left with the feeling of accomplishment.
Most if not all of his success could be attributed to the legacy so developing such a revolutionary jutsu with his own ability felt truly great.
Having recovered some of the fabled Hashirama Cells, Shiki used them to summon Hashirama's soul from the Pure Land and after extracting all the info he may have wanted, he refined the soul the main aims of this refinement were a Yang Soul for the powerful constitution and accelerated healing as well as Water and Earth Souls that contained the Wood Style.
Finally having access to an elemental kekkei genkai possessor's soul, Shiki was able to determine how the ability comes to be. As it appeared, Hashirama's Water and Earth Souls were interconnected as if yin and yang mixing together. A small change in the respective souls caused this intermingling, giving Shiki some ideas for later . . .
Leaving such matters aside Shiki melded all three souls at once thinking he was already used to the pain. Big mistake! As Shiki was made aware of an entirely new world of pain he had never before experienced, he could only curse his own stupidity in undestinaming the backlash of his actions. Melding three souls at once wasn't a problem, melding three extremely powerful souls at once however, was.
Still, after he was done pitying himself Shiki checked out his new Wood Style and further enhanced regeneration. Although he still couldn't regenerate lost limbs he was very, very hard to kill indeed.
'Well it kinda sucks i did such a reprehensible desecration of Tsuna-nee's grandfather's soul. It's for the good of the village and world though, he would be happy about it, no doubt!'
And so, like a true scumm of the world Shiki used all manner of faulty logic to justify his repulsive actions and moved on with his life. A few more days passed by and the Rookie Nine finally graduated.
'Now the going gets fun! Time to take advantage of my future knowledge before I mess up caon beyond all recognition!'