Only people who knew the full story remained now.
Hiruzen was the first to break the silence.
"Minato, regarding Orochimaru, I still recommend turning this matter over to Root. He's one of the Sannin. Dealing with him would damage Konoha's reputation."
"The thing that damages Konoha's reputation isn't punishing Orochimaru. It's protecting the people who covered for him." Minato replied with an unusually firm attitude. He leaned forward slightly, hands flat on the desk.
"According to the ANBU investigation, Orochimaru's experimental materials and funding were all provided by Root."
Danzō's face contorted with rage.
"Lies! Root has never participated in his experiments. This was all his doing alone. It has nothing to do with Root."
The conviction in his voice was almost impressive. If Kenji didn't know better, he might have believed the performance.
"That's right," Homura chimed in immediately, backing Danzō without hesitation. "Danzō has always been loyal to Konoha. How could he allow Root to do something as cruel as harming fellow ninjas? There must have been mistakes in the investigation."
Koharu nodded along. "Someone's clearly trying to frame Root, and sow discord between departments."
"Is that so?"
Minato reached under his desk and pulled out a sealed paper envelope, then threw it onto the table.
"Then explain these."
Both Danzō and Hiruzen's expressions changed slightly the moment they saw that envelope. Hiruzen reached out and picked up the envelope. He opened it and pulled out the documents inside.
Kenji couldn't see the specific contents from where he stood, but he could guess. This had to be the evidence Minato had arranged for Kakashi to gather by infiltrating Root. And the current Kakashi was far stronger than in the original timeline. In the canon story, Kakashi had become a jonin at twelve years old despite losing his teacher and father figure to tragedy. That version of Kakashi had been talented but directionless, grief-stricken and alone. He'd eventually stagnated. But this Kakashi was different. Minato was alive and trained him as a core member of his inner circle. The Fourth Hokage's resources and personal guidance were pushing Kakashi's development to frightening levels. Successfully infiltrating Root and obtaining incriminating evidence was well within his capabilities now.
The atmosphere in the office completely froze.
Minato and Kenji watched in silence as Danzō and the others finished reading through the envelope's contents. When they were done, Hiruzen placed the materials back on the desk. He looked at Minato, who sat there with an expression of quiet confidence, and understood the situation perfectly. If he wanted to protect Danzō and Orochimaru from complete destruction, he'd have to make major concessions. If he did nothing, Minato would use charges like "betraying the village" and "murdering Konoha ninjas" to thoroughly prosecute both of them. There would be no room for negotiation or possibility of mercy.
After a long moment of silence, he spoke, "Minato, I'd like to speak with you privately."
His voice had lost its earlier authority. Now it just sounded tired.
"Alright."
Minato stood. The two of them left the office one after the other, heading toward the rooftop of the Hokage Building.
Inside the office, Kenji turned to look out the window, his mind drifting to more pleasant thoughts. Maybe he'd take Honoka and Daiki shopping after this was over. She would probably enjoy that. And his son could use some new supplies too.
A voice interrupted his thoughts.
"Kenji."
Danzō's tone carried all the warmth of a corpse. Kenji didn't turn around.
"I want you to come work for Root. If you agree, the position of Root's future leader will be yours."
The arrogance in his voice was thick. In his mind, offering to elevate a jonin to command of Root was an irresistible temptation. What fool would turn down that kind of power?
"Thanks for the offer, but I'm not interested."
Kenji's response was flat. He still didn't bother turning around.
"Why?" Danzō's voice carried confusion mixed with rising anger. "Where there is light, there must be darkness. Root is the foundation of Konoha's great tree, silently delivering nutrients from below. Only by becoming its leader can you truly protect the village."
He was trying to sell his usual philosophy, completely missing the disdain in Kenji's eyes.
"I prefer staying in the sunlight," Kenji said. "I'm afraid of the dark."
In his view, Root was nothing but a tool Danzō used to consolidate power. And more importantly, it was a cancer that Minato would soon be cutting out. Why would he voluntarily join a department that was about to be downsized or dismantled entirely?
Danzō was silent.
The power he'd spent his entire life pursuing, the organization he'd built from nothing, dismissed so easily. The rejection filled him with fury and a helpless frustration he couldn't quite express.
Kenji finally turned to face him. He walked over slowly and stopped beside Danzō.
"If I were you," Kenji said quietly, "I wouldn't do anything stupid. I hope for Konoha's sake you won't be narrow-minded about how this plays out. We both know how it will end, right?"
Then he smiled.
"Tell me... am I a puppet or the real Kenji?"
Danzō's visible eye widened slightly, and his hand moved instinctively to his chest. He didn't make a move against Kenji. Although Kenji wasn't famous in the broader shinobi world, he knew exactly how strong Kenji had become. Root had been closely monitoring Kenji. The gap between them had widened considerably.
Attacking Kenji would be suicide. And Danzō, for all his faults, wasn't suicidal.
"It would be a pity if Root needed a new leader," Kenji added calmly. "Don't you think?"
He turned away and went back to looking out the window, dismissing Danzō entirely. The old man stood there with a face like thunder, but he didn't move or speak. The office fell into silence.
---
Meanwhile, on the rooftop of the Hokage Building, Minato and Hiruzen stood side by side. Below them spread Konoha's streets, bustling with civilian life and off-duty ninjas going about their business. The view was peaceful.
Their moods were anything but.
"What would it take," Hiruzen asked, breaking the silence first, "for you to agree to hand Orochimaru over to Root?"
His tone carried compromise. He was no longer the Third Hokage who wielded absolute control. That era had ended.
"I know you're thinking of old bonds," Minato said. "You don't want him to die. I understand that. He was your student."
He turned to face Hiruzen directly.
"But to conduct his human experiments, he caused the deaths of many innocent people. Some of them were infants. Babies who'd barely been born before they were strapped to tables and cut open in the name of 'research.'"
"He did those things for the village." Hiruzen argued. "During the Second and Third Great Ninja Wars, he achieved countless victories for Konoha. He made great contributions to our strength."
"All Konoha ninjas risk their lives for the village," Minato countered. "Does having accomplishments mean he can ignore human life? Does it mean he gets to murder children without consequence?"
Hiruzen fell silent. He knew Minato was right, even if he didn't want to admit it. After a long pause, he made an offer.
"I can disband my personal ANBU unit and fold them into the regular ninja ranks. I won't interfere in village affairs again."
It was a significant concession. Those ANBU were his last direct power base, the final remnant of his authority as former Hokage. But Minato didn't relax his stance.
"Let Orochimaru leave Konoha as a missing-nin," he said, laying out specific conditions. "In addition, both Hokage advisors must step down. Homura and Koharu covered for Root and tolerated the experiments. They're no longer fit to remain in leadership positions."
"The advisors can't step down," Hiruzen said quickly. "You've only just taken office. You need their experience and guidance. Besides, they've worked tirelessly for Konoha for decades. Even if they lack major accomplishments, they've certainly earned their positions through service."
What he really meant was clear to both of them. If Homura and Koharu were removed, he would be completely cut off from Konoha's decision-making process. The old guard's influence would be broken entirely.
Minato thought about it for a moment, weighing his options. Then he made a concession.
"The advisor positions can be retained. But I want to add two new advisors to the council."
He knew that since Hiruzen had been forced to step down rather than dying in office, the old man still held some residual authority. Matters like appointing or removing Hokage advisors required approval from multiple sources, including the Fire Daimyō. Without Hiruzen's consent, getting that approval would be nearly impossible.
"Very well. Who did you have in mind?"
"Yamanaka Kenji and Nara Shikaku."
Minato answered without hesitation, the names clearly decided long before this conversation.
Kenji was his most trusted ally and one of his strongest combat assets. And among the Ino-Shika-Chō clans, the Nara had always served as Konoha's strategic thinkers. Having Shikaku involved would help balance the power structure at the top while also securing support from all three clans.
"Reasonable choices," Hiruzen admitted after a moment's consideration.
He couldn't object even if he wanted to. Kenji's strength and alignment were obvious to everyone. Shikaku's intelligence was universally acknowledged throughout Konoha. Appointing them as advisors wouldn't provoke dissatisfaction among the other clans, and it would allow Minato to expand his influence within the leadership structure. It was a compromise both men could live with, even if neither was entirely satisfied.
"Now that we've settled the advisor matter," Minato said, his tone shifting back to business, "we need to discuss Root."
The brief moment of levity vanished. Hiruzen's expression didn't change outwardly, but he could sense the old man's attention sharpening.
"Intelligence shows Root was involved throughout Orochimaru's experiments. They provided materials, funding, and logistical support. How do you plan to handle that?"
Hiruzen remained silent. The situation was exhausting in ways that combat never had been. One was a friend of decades, someone who'd fought beside him through multiple wars. The other was his student, someone he'd trained personally and watched grow into one of the legendary Sannin. And now he was stuck cleaning up the mess both of them had created.
"Disband Root," Minato said bluntly. "Strip Danzō of all his positions and let him retire. In exchange, I won't pursue his involvement in the experiments. He keeps his life, and his reputation. That's the deal."
"No."
Hiruzen rejected the proposal at once.
"Root is ANBU's primary training facility. Many of Konoha's best operatives came through Root's program. Dismantling it would cripple our intelligence division's talent pipeline. We can't afford that kind of damage."
Minato's mouth twitched slightly. He knew perfectly well that Root had stopped being a legitimate ANBU training facility years ago. It had become Danzō's private army, operating parallel to official ANBU command structure and frequently pursuing objectives that directly contradicted village interests. It was a tumor that needed to be cut out. But he also understood that completely destroying Root overnight would destabilize too many things at once. The organization had embedded itself deep into Konoha's infrastructure. Pulling it out carelessly could cause more damage than leaving it partially intact.
"Root can be preserved, but under new conditions. All future operations must receive Hokage approval before execution. Any unauthorized action will be treated as treason and met with arrest. Additionally, all recruitment into Root must be vetted by the Hokage's office. Unauthorized expansion will be considered espionage."
The terms effectively neutered Root as an independent power base. Danzō would still have his organization on paper, but it would function as an extension of the Hokage's authority rather than as his personal instrument.
Hiruzen was quiet for a long moment, weighing his options. He understood what accepting these conditions meant. Root wouldn't be able to develop or expand under this level of oversight. Every operation, recruitment, or allocation of resources would require Minato's explicit approval. Danzō would hate it. The old war hawk had spent decades building Root into what it was. Reducing it to a glorified ANBU subdivision would feel like having his life's work dismantled piece by piece.
But refusing wasn't an option either. If the full scope of Root's involvement in the human experimentation became public knowledge, Danzō wouldn't just lose his position. He'd face execution. Hiruzen might be able to protect Orochimaru through backroom dealing and maneuvering, but protecting both of them from the consequences of something this severe was impossible.
"Fine," he said finally. "I'll inform Danzō of the new structure."
"Good."
Minato's expression relaxed slightly, though he kept his satisfaction muted. This was a negotiation, not a victory celebration.
"After this meeting, I'll have ANBU transfer Orochimaru and the experimental subjects from the captured facilities to Root's custody for processing. As for the civilians who were used as test subjects, I'll arrange medical-nin to examine them. Once we confirm they're healthy and stable, they'll be returned to normal life with appropriate compensation and support."
Hiruzen nodded once, then stood without further comment.
"Since everything's been discussed, I won't waste more of your time."
His tone was neutral. But the subtext was clear enough. This conversation was over, and continuing it would only make things worse for everyone involved.
Minato watched him leave, completely unbothered by the cold dismissal. Conflict with the Third Hokage had been inevitable from the moment he took office. This wasn't personal and it wasn't about the village's wellbeing. It was pure political reality. Two people with different visions for Konoha's future, competing for the authority to implement those visions.
Both of them loved Konoha. That was never in question. But Hiruzen wanted to preserve the existing power structure, protect his allies, and maintain stability through continuity. Minato wanted to break the old guard's stranglehold on decision-making and rebuild the system from the ground up. Those goals were fundamentally incompatible.
Compromise was the best either of them could hope for.
---
Back in the Hokage's office, Hiruzen and Minato's return broke the silence that had settled over the room.
Minato walked to his desk and pulled a scroll from one of the drawers. He wrote out a formal transfer order in quick, signed his name with the Hokage's seal, and handed it to Hiruzen.
"The follow-up investigation into Orochimaru's experiments will be handled by Root under ANBU oversight. Make sure Danzō understands the new restrictions on his authority."
"Understood."
Hiruzen took the scroll, then turned to address Danzō, Homura, and Koharu.
"We're leaving."
The three of them understood immediately. Whatever had been negotiated behind closed doors, it had cost them significantly. Danzō's jaw was tight, but he didn't argue. Homura and Koharu exchanged brief glances but said nothing.
All three followed Hiruzen out of the office without another word. When the door closed behind them, only Minato and Kenji remained.
Kenji looked at his friend and couldn't help but smile slightly at the poorly concealed satisfaction on Minato's face.
"Looks like you came out of that negotiation pretty well."
"Better than expected, honestly," Minato admitted, leaning back in his chair. He recounted the terms he'd secured from Hiruzen, including the restrictions on Root, the preservation of Orochimaru's life in exchange for exile, and the agreement to expand the advisor council.
When he finished explaining, his expression turned more serious.
"I want you to serve as a Konoha advisor. For the other position, I'm planning to appoint Shikaku."
Kenji considered it for maybe three seconds before nodding.
"Sure. The Third Great Ninja War just ended. Things should be relatively quiet for a while. Being an advisor won't be too demanding."
And more importantly, it would let him influence village policy directly instead of working around the edges. That was worth the administrative headache.
"Thank you," Minato said sincerely. "Having you in that position will help balance power at the top levels. And it gives me someone I can trust in the room when decisions get made."
"Don't mention it," Kenji waved off the gratitude. "I've been annoyed with how those politicians run things for years anyway. At least this way I can do something about it."
Minato smiled at that. Then his expression shifted.
"We should move on this quickly. I don't want to give anyone time to organize opposition or start spreading rumors about the appointments being inappropriate."
---
That same day, Minato essentially dragged Kenji across the village to Shikaku's house.
The Nara compound was quiet and well-maintained, surrounded by forest. Shikaku answered the door himself, looking mildly surprised to see both the Hokage and Kenji standing on his doorstep in the middle of the afternoon.
"This is unexpected."
"We need to talk," Minato said. "Mind if we come in?"
Shikaku stepped aside and gestured them into his home. They settled in his study, and Minato explained the situation directly and without preamble.
When he finished, Shikaku was quiet for a moment, fingers steepled together as he thought.
"You're asking me to join the advisor council," he said finally. "Which means you're expanding it specifically to dilute Homura and Koharu's influence while giving yourself more reliable support in high-level meetings."
"That's correct."
"And you want Kenji because he's your strongest combat asset and most trusted ally. You want me because of my clan's strategic reputation and because the Ino-Shika-Chō alliance carries weight."
"Also correct."
Shikaku nodded slowly. "Having both of us there prevents accusations of nepotism or favoritism. It looks like you're building a broader coalition rather than just promoting friends."
"So you'll accept?"
"Obviously," Shikaku said dryly. "Refusing would be stupid. This is good for village stability, and honestly someone needs to help you navigate the minefield you just walked into. Might as well be me. Still, what a drag..."
Minato grinned. "I knew I could count on you."
"Just don't expect me to enjoy the paperwork."
That evening, Minato submitted the official appointment documents to the Fire Daimyō's office. The Daimyō's approval was technically required for high-level village appointments, but it was mostly a formality. As long as Hiruzen didn't object, which he wouldn't given their agreement, the approval would come through automatically.
---
Three days later, Kenji and Shikaku officially became Konoha's third and fourth advisors.
The announcement was low-key, just a formal notice posted in the administrative building and distributed to clan heads. But the news rippled through the village's power structure immediately. The old guard's monopoly on the advisor council was broken. Minato had his own people in positions of authority now.
As for Danzō, who still technically held the title of Hokage Assistant, Minato couldn't remove him completely without significant fallout. The position had too much institutional history, and Danzō still had enough allies scattered throughout the system to make his forcible removal messy.
When Kenji asked about it, he just shook his head.
"Not yet. Danzō will make a mistake eventually. Someone like him can't help himself. When he does, we'll have the justification we need to finish removing him from power. Until then, we watch and we wait."
Kenji thought about it and agreed. Patience was annoying, but it was also smart.
A few days later, Kenji was in the Hokage's office helping Minato work through a backlog of mission reports when Minato suddenly looked up.
"Just got word. Orochimaru escaped from Root's custody and defected from the village. I sent Kakashi with a pursuit team to track him."
Kenji paused in his reading, then set down the report he'd been reviewing.
"That was faster than I expected. I thought they'd try to hide him for at least another week."
Actually, this outcome wasn't surprising at all. On Kenji's second day as an advisor, he'd quietly suggested to Minato that they leak information about Orochimaru's human experimentation to the village population to create public pressure on Hiruzen and Danzō while simultaneously destroying their popularity and credibility.
Minato had implemented the suggestion immediately, having ANBU operatives spread carefully curated information through the civilian districts and lower-ranking ninja. The method wasn't exactly honorable, but the results had been spectacular.
Danzō had used similar public opinion manipulation to drive Sakumo to suicide years ago. Now karma had come full circle. The Third Hokage and his allies were being hounded by public outrage, forced to scramble for damage control. They'd had no choice but to arrange Orochimaru's escape as quickly as possible, even though he'd barely recovered from his injuries.
"If he'd waited any longer, he wouldn't have been able to leave at all," Minato said. "Public sentiment in the village is demanding execution. When Sakumo failed a mission, the outcry drove him to suicide. Orochimaru conducted human experiments on Konoha civilians and children. If he'd been captured and brought back for public trial, even I wouldn't be able to protect him from mob justice."
Kenji smiled slightly at that.
He found himself wondering if Hiruzen's effort to save Orochimaru's life would affect the man's future decisions. Would the Sannin still launch the Konoha Crush? Or would being saved by his former teacher change his trajectory?
Either way, Orochimaru had essentially been made into a scapegoat for Konoha's leadership. Now that the operation had been exposed, everyone else walked away relatively unscathed while Orochimaru alone faced exile. Even if he had used Root's resources to pursue his own forbidden research, he had to be furious at the men who'd thrown him to the wolves. Given his personality, revenge was inevitable.
Kenji finished the last document on his stack and stood up, stretching slightly.
"I'm heading out. Honoka's expecting me for dinner. And I promised I'd put Daiki to bed tonight"
"Go ahead," Minato said. "Thanks for the help."
Since becoming an advisor, Kenji's daily life hadn't changed much. He still took missions when appropriate, spent time with his family, and trained regularly. The main difference was that he now spent a few hours every week helping Minato with administrative work and attending the occasional high-level policy meeting.
It was pretty comfortable.
Minato really did live up to his reputation as the fastest Hokage, and not just because of the Flying Thunder God Technique. His work efficiency was incredible. Unlike Naruto in the original timeline, who'd been drowning in paperwork even with shadow clone assistance, Minato's desk was always organized and current.
When the workload increased, having Kenji and Shikaku available to help meant he could finish early and go home to spend time with Kushina and Naruto. The administrative records from successive Hokage administrations made it clear: during Minato's tenure, the backlog of pending documents was the smallest it had ever been.
---
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