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Leaf Village.

Somewhere in the leaf village deep underground, the construction of the Root's new base of operations was near its completion.

An elderly man with an eye bandaged and arm in a sling was walking the dimly lit hallway. He had much on his mind.

'It took a long time with Hiruzen keeping an eye on everything but at last it's done. The construction is completed and with the new added measures not even the Hyuga and their Byakugan would be able to see in here… Things are proceeding according to plan.'

The man Danzo Shimura, leader of the Root, soon reached his office. He saw a red scroll with the Insignia of the Hōzuki Castle on his desk.

Danzo opened the scroll and read its contents. 'So Isen has passed away huh. Serves right for that traitor. Because of Kensei, Hiruzen had been far too merciful with Isen's punishment. But now that's no longer a concern. He is now no longer a threat to me.'

At that moment the child he assigned to keep tabs on certain students in the academy appeared before him and knelt.

"Lord Danzo. I have an urgent update."

Without a word of acknowledgement, Danzo closed the scroll and placed it inside his desk. Only then did he turn towards the child Touma Asai.

"Report." The cold tone couldn't be mistaken for anything other than an order.

"Daichi has left the village."

Danzo's one visible eye slightly widened. It was the last thing he expected.

"Tell me everything you know." He needed to find out everything behind Daichi's departure.

—-

It has been a month since Isen regained his memories and freedom. He had learned that the Hokage was the one who convinced Danzo to spare his life. At Isen's insistence Kensei sent word to the Hokage and arranged a meeting.

Night Time - Hokage Residence.

Hiruzen was in his home waiting for the man to arrive. Because of the secrecy of the meeting he had dismissed his guards. Before long he sensed a foreign presence in his home.

He turned around and met Isen's eyes. After a few moments of silence Hiruzen spoke.

"You look better than I thought."

Isen was silent for a moment as he looked at the old kage. "Am I supposed to say thank you for saving my life…"

Hiruzen narrowed his eyes. "Yes. What you did was reckless, stupid and could have put a serious strain on our relationship with the Daimyo. Prison and the memory loss was a mercy compared to what Danzo would have done."

Isen let out a sigh as he heard those words.

"Thank you…"

Hiruzen looked at the man and then nodded his head.

At that moment Isen spoke again. "Just to be clear, I'm not thanking you for saving my life. I'm thanking you for what you did for my wife Binami. Kensei told me that you made sure she had a new identity, provided safe passage to the capital and gave her the sufficient funds needed for a new life."

"I remembered you telling me she was pregnant a few weeks before the whole mess. I didn't want her to get caught up in all that." Hiruzen took his wooden pipe and lit up the tobacco.

"I see you haven't quit that habit."

"Everyone has a vice. This is mine."

Isen was silent as he looked around the house. He noticed the absence of two important people in Hiruzen's life.

"I'm sorry about Biwako. Kensei told me what happened. She was a good woman."

The old kage merely nodded his head appreciating the sentiment.

"You know… After everything that's happened I thought you would be angrier with me…" The old kage said as he narrowed his eyes and looked at the man.

"Make no mistake. I'm angry about what happened. I spent 17 years in that place and I missed the first 17 years of my son's life… So yeah, when I learned everything, I was pissed… But I can also see the bigger picture. You did what you could. And it was my decision that landed me in that prison."

Hiruzen took the pipe from his mouth and let out some smoke. He asked a question that has been bugging him for some time. "That brings me to another question. What exactly did you find out about Danzo that he went through all that trouble just to get rid of you?"

"I was under your command in Anbu. But what you didn't know is that… I was also part of the Root."

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Hiruzen was startled at that admission. "Explain!"

"During one of the missions I discovered that Danzo had sent several spies to most of the villages disguised as Merchants, bandits or mercenaries."

"Yes. I know about them. After the loss of Lord Second, Danzo and I decided that it was imperative that we had an intelligence gathering network throughout the nations in place."

"Yeah well… What you don't know is that his network does a lot more than gather intelligence. He has created an extensive network that launders money, trafficking rare materials, weapons and people…"

"People?" Hiruzen's eyes narrowed.

Isen nodded. "Hm! More specifically those with special blood lines."

"Kekkei Genkai users."

"That's right. And that's not all… He's also interested in Tailed Beasts."

The old Kage's eyes narrowed. "Do you have any proof?"

"Just my memories."

"It still doesn't explain how you became part of Root or how you found out about these things… Danzo is a very careful man. He would have had safeguards in place for all his root members."

"I felt that something was wrong when I was on a mission in the Sand village. I found a merchant selling some of our secrets to the sand village. But the thing is, he was not from the Sand and he was keeping tabs on the One tails as well. At first I thought he was from another village but later I found out that he was from the Root. I felt that something was wrong and when Danzo came to recruit me I accepted. I joined the Root to see if someone had been compromised in Danzo's organization but what I found was that I was wrong. The man was under Danzo's orders to leak some intelligence to the sand village."

"For what purpose?"

"The Root wanted the magnet bloodline of the Royal family. Rumor had it that the Kazekage was planning on starting a family. Danzo's plan was to plant a spy near the family and kidnap a child of the Kage or at least get enough experimental materials. He also had the spy send him regular updates on the Tailed beast of that village. Throughout my time in the Foundation, I learned that he has conducted several missions that I'm sure you wouldn't have approved of. He is invested in recruiting talented people and bolstering his forces. Near the last few years of the 3rd world war I learned that he planned to kidnap the 7 tails from the Waterfall village and assassinate the child of the Earth Daimyo and frame another village for it."

"What!?... Something like that could have had unimaginable consequences… The war would have gone on for much longer." The old kage was shocked. He never imagined that Danzo was so out of his control.

"Yes. It was a plan he hatched with a high ranking member in the Fire Daimyo court. During the chaos Danzo and his faction at the capital would convince the Fire Daimyo to make a move on the Earth country. There would have been plenty of chaos and death if this plan had moved forward. I had to stop it."

"If you learned all this then why didn't you come to me?"

"It was too late by the time I learned what was really happening. At that time Danzo found out about me spying on him. He had to move forward with the plan. He framed me and bought some time. So I had to make a commotion loud enough that would draw the Daimyo's attention to Danzo and the people under him in the capital."

The old kage had a realization. "That public attack on the minister… That wasn't the act of some rage filled fool. You did that on purpose didn't you, knowing full well the consequences…"

"Yeah. I knew if the Daimyo found out that we were interfering in the affairs of the royal court the village would lose his backing. And I also needed him to be vigilant of external influences... I had a contingency in place if I died so I knew you would learn the truth soon after my death. What I didn't expect was for me to lose my memories."

Hiruzen let out a puff of smoke as he took in the information. "There were many ways this could have been handled differently."

"I was out of time and options. I did what I could."

The old kage sighed. After a short silence he asked the man a question. "Are you willing to work under me again?"

"No… But if you want my help with Danzo then I can work with you."

Hiruzen looked into the man's eyes and relented. "I suppose that would have to do… I have a task for you."

—-

Leaf Village.

In an underground laboratory, 'Shigaraki' the researcher and scientist of the Root was performing experiments on a certain specimen using the genetic materials acquired from Orochimaru and Danzo.

At that moment Danzo walked into the laboratory and inspected the specimen. "How much progress have you made?" He asked the scientist.

"The sample Orochimaru provided is truly incredible. It can combine to any foreign DNA without rejection and can adapt its properties. Although the effects produced are not as powerful."

"What are the results of the merger with the blood sample of the first Hokage?"

"The DNA has adapted to the blood but there were some small mutations." With those words Shigaraki led Danzo to a certain area of the lab.

In a glass container filled with nutritional fluids a small child was kept suspended. There were several monitors connected to the child. Half his body was made of wood and the face of the first Hokage was present on the left side of his chest. But even with these mutations his vitals were reading normal.

"The first Hokage's blood contains too much power. More precisely Yang chakra. We need equally potent Yin chakra or something that requires the large reserves of chakra to keep the balance and the power of the first Hokage in check."

"I have something in mind. In a few months Orochimaru will be here with what I need. I need you to assist him with the surgery and graft the first Hokage's blood into my body when the time comes." Danzo told the man.

"I understand lord Danzo but…"

"What is it?"

"It's just… No matter how well the surgery goes, there will be some small mutation on your body. The power of the first Hokage is just too strong." Shigaraki bowed and spoke these words with slight fear.

Danzo was quiet for a few moments. "I'm aware of the risks. And your duty is to minimize the risks as much as you can when the time comes."

"Yes Lord Danzo!"

Danzo walked away from the lab and made his way to his home. 'If I had the best medic nin in the world then I could reduce the dangers of the operation down to Zero. But Tsunade would never perform the operation on me and if she learns that I've been using Lord Hashirama's blood for research like this, she'll be furious. She might make a rash move and bring Jiraiya and Hiruzen's attention to me and I don't want that right now. But then again, I don't necessarily need her. She has a new apprentice after all… Should I delay the surgery and wait for her to teach Daichi everything before I go after him?... No. That will take too long. This must be done as soon as possible.'

The moment Danzo learned of Daichi's departure from the village he used his contacts and found out what had happened.

He learned that Kensei wanted Daichi to learn about his business operations and took the boy to the capital. But Hiruzen, not wanting to let Daichi go, made a deal with Kensei. Danzo learned that the plan was for Daichi to come back by the time his class graduates and become a Genin with them.

A month later Danzo learned from his sources in the capital that Tsunade happened upon the child and took him as her student.

'The boy leaving the village is a perfect opportunity. Once she's done training him I'll make my move. Kensei won't be able to protect him. But the mission needs to be covert. I can't have anything connecting me to it.'

With that thought in mind he summoned a few of his people and gave them a certain mission.