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The link is also in the synopsis
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In an underground facility under Hidden Leaf known only to a select few, Kinoto walked down a hallway lit with yellow light bulbs nailed to the walls with a line or jute rope where his footsteps trained to be silent still made echoing noise.
The facility was built deep underground, going further than any similar facility would generally be built. Because of that depth, the entire facility was reinforced against earthquakes to prevent cave-ins. The facility's purpose was secrecy, and because of the location, the whole base was covered in extremely complex fuinjutsu seals to prevent a particular white-eyed clan from peeking in from the surface.
Kinoto knocked on a door and waited in silence to get a response. He was a jonin of the Hidden Leaf, and not many places could make him wait, but the person behind the door could make him stay as long as the latter wanted.
After a moment, Kinoto entered upon getting the invitation. The room was an office without any adornments. Every room was furniture similarly in case they needed to abandon the facility, which required expedited destruction of 'evidence.'
Three people were waiting for Kinoto in the office.
Sitting in front of the desk was the Master Instructor, a chunin of the Hidden Leaf who was in charge of training the recruits inducted into the foundation. He raised the young orphans and molded them into operatives beyond their peers; he was the one to mold the older recruits into loyal operatives dedicated to the foundation's mission. The Master Instructor was an essential part of the foundation.
Kinoto remembered his own training days. He hated the Master Instructor with a passion.
The next was Kon, an operative, who was the reason behind their current situation. The foundation had a strict flow of information, and every piece of information was on a need-to-know basis. But from what Kinoto had learned recently, Kon was involved in the drug trade, which funded the foundation's expenses.
But right now, Kon had made the mistake that led to four trainees' deaths.
And finally, there was the Leader. The man had built the foundation from the ground up with his two hands. Shimura Danzo, the Hokage's Shadow, the Darkness of the Shinobi. The man who protected the Great Tree from anonymity, warding off the enemies who wanted to burn it down.
Kinoto knelt down in respect and waited to be addressed.
"Rise, Kinoto," said Danzo.
"Yes, sir."
"Progress report."
Kinoto started. "The bodies of the trainees along with their belongings are disposed of—cremated, and ashes flushed. We got to them before the Police Force could inspect them. The Police Force has mobilized a substantial amount of their resources for the investigation, but they don't have any leads that would lead them to us. The foundation is completely cut off from the situation."
Danzo hummed. "What about the target?"
"The target was lifted from the induced coma earlier today. From my conversation with him, he's upset about the missing bodies, but he doesn't seem to know any more than the Police Force already knows. The trainees were careful enough on that matter." Kinoto paused before asking, "Should I dispose of the target?"
"No need," said Danzo. "The matter has already attained widespread attention. If he dies now, the matter will be taken off the Police Force's hands and into ANBU's. It serves our interest that the investigation remains in the Police Force's hands."
Before Kinoto could reply, the Master Instructor spoke up, "The target caused the deaths of four trainees. We have to retaliate!"
Danzo glanced at the Master Instructor, who shut up. He gave the same look to Kon.
"Your decisions led to this situation. I do not blame you for going after the target, but you grossly misjudged the capability of the target, which led to us losing years of resources we put into developing four trainees. This mission was not a time-sensitive one, and you could have taken time to research your target and have assigned appropriate operatives—but you judged incorrectly, which led to heavy losses…. Both of you will be punished for this error."
The Master Instructor and Kon looked displeased.
"Kon, you are to leave for the Land of Frost. You will be keeping an eye on the situation there and protect and develop our war interests," Danzo ordered.
"… Yes, sir," said Kon.
The war between the Land of Hot Waters and the Land of Frost was ramping up, and it was a situation full of opportunity, but it wasn't somewhere people wanted to be. It was far from home, and the assignment there would mean working 24/7. It was a lot of tedious work of developing contacts, establishing presence in different circles, creating an information network, and other ground level tasks. And because Kon was a chunin, once he did all the work, a senior operative would eventually take his place once the grunt work was done.
No one liked that.
Danzo turned to the Master Instructor. "You are going on a scouting trip to replace the four trainees. You are to hand over the command of the training villa to Niko; she will be in charge until you return."
Kinoto felt a rush of joy upon hearing the punishment. Master Instructor's scouting days were past him and forcing him away from the "training villa," where Master Instructor's word was the law, where he was the King, was the ultimate punishment. Moreover, the Master Instructor hated Niko; their views on training were too different, and Danzo knew what handing over command to Niko meant.
"Understood, sir," said the Master Instructor. His face was impassive, but Kinoto could see the slight twitching on his face.
Danzo asked the Master Instructor and Kon to leave.
"Do you have any upcoming assignments that require you to leave the village?" asked Danzo.
"No, sir," said Kinoto.
"If any such assignments come up, you're to reject it. If there's something you can't refuse, you're to come to me, I will take care of it," said Danzo. "I want you in the village. You're to observe the Uchiha Clan, but that's a secondary priority."
Kinoto nodded. They already had people observing the Uchiha clan. Adding him would be a waste of resources.
"Your primary principle is Uchiha Shisui. You are to watch him, document his every move. I want to know everything there is to know about Uchiha Shisui.
"The full package?" asked Kinoto.
"The full package," Danzo nodded.
The full package not only included surveillance on the primary target but profile building on people with three degrees of separation from Shisui. They were going to piece together what the world looked like to the person called Uchiha Shisui. Some of the foundation's full package missions were so successful they could predict the primary target's future decision before they had made them.
"What resources will I have access to," asked Kinoto. Uchiha Shisui was a jonin of the Hidden Leaf, an ANBU, and a high-ranking Uchiha. He was a high-value target, which made the surveillance difficult.
"Anything you need."
Kinoto nodded.
"When constructing your team, I want you to be stricter than our standard requirement. Keep the team small, but choose the most skilled ones. You can't let Uchiha Shisui or anyone else get momentarily suspicious."
Kinoto was about to reply in affirmative when he noticed the look in Danzo's eyes. He straightened up. He knew the look meant that Danzo was asking him to listen very carefully and embed every word in his brain.
"Kinoto, if Uchiha Shisui finds you… Death is all but guaranteed. His eyes… are dangerous," said Danzo. "You and every member of your team will undergo the full juinjutsu (cursed seal) sealing. Anything less than that, and he will turn you into an open book. No amount of training you have will be able to prevent him from extracting information from you. Do you understand?"
"… I understand, sir. I will follow all the precautions," Kinoto replied.
He had his assignment. It was now time to work it.
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After Kinoto left, Danzo didn't immediately leave the underground facility. He was a busy man, and time was a precious commodity. Instead, Danzo took a moment to contemplate on his thoughts in silence.
Uchiha Shisui… He never thought an Uchiha would be able to attain the Mangekyo Sharingan during his lifetime. He had believed that Uchiha Madara was the last one to transcend the Uchiha dojutsu. But it seemed he was wrong, and someone had awakened those eyes again.
And with those eyes in the hands of an Uchiha, a danger now loomed over the Hidden Leaf village.
The person whom Danzo respected the most in this world was his teacher, Senju Tobirama, the Second Hokage. He had built his way of life, and his Nindo, from the wisdom his teacher had imparted before he passed away heroically while protecting the village.
Tobirama hated the Uchiha. He had shown Danzo the danger they represented. They couldn't handle their gifts; the stronger they became, the greater the threat they presented to the village. Unlike the others, Danzo saw the truth behind the cursed clan. They couldn't be trusted with their powers.
And he was in the right to think that.
Until very recently, the Uchiha were planning a coup against the village, and if not for the special circumstance, they would've gone forward with it.
Danzo had to give it to them. They had managed to keep the coup hidden for a time longer than he thought was possible. His ROOT had an impressive intelligence network in the Hidden Leaf village, and things of note rarely happened without him knowing it—but the Uchiha had managed to keep their intentions from him.
He had only become suspicious when Hiruzen had suddenly started peaceful diplomacy with the Uchiha. In his decades as the Hokage, the old fool hadn't extended the amounts of benefits to the Uchiha clan that he had done in the surprise move. When Danzo looked closer, he could see the cracks in the Uchiha's secrecy—something was simmering under the surface, and the Uchiha were ensuring it stayed that way.
His suspicions were verified when he approached Uchiha Itachi and got rebuffed. He might be ROOT's leader, and Uchiha Itachi might be an ANBU, but he was still an Elder and on the Leaf Council—it was insulting for Uchiha Itachi not to give him a proper meeting. That's when he knew that the Uchiha were hiding something.
But even then, he couldn't find out what they were hiding. His intelligence had failed him, which was worrisome, but more problematic was the source who finally revealed Uchiha's secret.
Uchiha Madara.
The orange masked figure with the Sharingan who claimed to be the Ghost of Uchiha, the legendary shinobi who had founded the Hidden Leaf with Senju Hashirama.
Danzo was naturally skeptical, but with the Nine-Tails incident from a few years back that had set back the village quite a bit, he couldn't help but wonder if the figure was telling the truth. The man did possess the skill—he could walk into a ROOT facility and put his operatives down without a peep just to meet with him.
It was an experience Danzo hadn't had since his hay days on the battlefield.
The so-called Uchiha Madara presented a gift to him in the form of information: The Uchiha clan was planning a coup. And even gave him a way to verify. When Danzo checked, he found it to be true—the Uchiha had improved their relationships with various powers within the clan and were even making moves in the Daimyo's court.
In return, Uchiha Madara only wanted Danzo's friendship.
Danzo was no fool.
The Uchiha Madara of old hated the Hidden Leaf. Danzo's every instinct could sense that the man who claimed to be the Uchiha founder held the same malice against the village. He wanted to destroy the village.
Danzo couldn't let that happen.
And perhaps the masked man could sense that. The masked man knew how Danzo wished to be the Hokage—and extended his help. When the opportunity presented itself, he would help Danzo become the Hokage.
But Danzo could tell the darkness that lurked within the man.
This was the Devil's Offer. He was being invited to dance with the devil. Accepting it would be seeking destruction.
Danzo had wanted to laugh. He was usually the devil extending the favor—who knew that one day he would be on the other side of the table.
He accepted the offer. He had played this game before, so he knew how to beat it. He would become the Hokage and find out the true identity of the man and then ruin him. If the man was truly Uchiha Madara, the dead were better when cold. If it were just another Uchiha pretending to be someone else, he would eliminate them.
Danzo entertained the idea that if it was indeed Uchiha Madara, then that meant his eyes were the Mangekyo Sharingan. The Uchiha might be cursed, but the Sharingan was a powerful weapon—and it could be better utilized in capable hands—his hands.
"Mangekyo Sharingan," he whispered.
Another pair of those eyes were so near him in Uchiha Shisui's possession.
He couldn't believe it when Hiruzen told him about what Uchiha Shisui had done. The young Uchiha had crushed the coup by manipulating his clan with his eyes.
A shiver went down Danzo's back. Uchiha Shisui's eyes were powerful. It could twist minds to do his bidding, all the while making others think that it was what they wanted. What a terrifying weapon.
Wasn't that perfect for him?
Danzo wanted those eyes.
And maybe he would get them. After all, an Uchiha in possession of the Mangekyo Sharingan was a threat to the village. And it was his job to eliminate those threats.
However, it was a pity that the Uchiha clan were no longer on the warpath. If Uchiha Shisui hadn't manipulated his clan, Danzo would have had enough justification to wipe out the cursed clan from the face of the world.
Danzo blamed Hiruzen. The old fool had kept it hidden from him. Danzo wasn't worried Hiruzen kept something this grave from him for such a long time—the village would be in deep trouble if the Hokage wasn't able to keep a secret—and the fact that Hiruzen had shared Uchiha Shisui's actions with him meant that the Hokage still trusted him.
The Hokage's trust was a priceless commodity. It was nice to have it affirmed.
Now that he knew this information, Danzo could make suitable moves.
Maybe Uchiha Madara would be interested in knowing someone else had awakened the legendary eyes. Danzo wondered how the man would react.
Danzo stood up from his chair and was about to leave when he noticed the file on the table. He opened it to find that it was the file on the genin who had killed four trainees.
"Takuma…"
Where did he know that name from?
Danzo flipped through the file, and the memory became clear. It was the genin who had survived the Hidden Frost incident.
"Interesting," he muttered as he read the file.
The child was an orphan, a Ring fighter, a Police Force officer, Maruboshi Kosuke's protegee—which was more surprising than anything—he was even learning genjutsu from Uchiha Mikoto and had managed to dispatch three similarly aged ROOT trainees who had gone through intense for almost a decade.
This Takuma was a perfect candidate for a ROOT operative.
Someone who had access to the Uchiha patriarch's family and even had an indirect connection to the Hokage through Maruboshi Kosuke would be a massive asset for the ROOT.
Alas, it was already too late.
Turning loyalties through mental conditioning took time. Even if ROOT tried to convert Takuma, it would be a long and risky process with multiple points of failure due to Takuma's activeness in his career. It would've been optimal if they had somehow gotten to Takuma while he was in the Genin Corp and then injected him into the Police Force—which they had done, but their spy wasn't as successful as Takuma.
Danzo closed the file.
The Master Instructor was right. Someone had caused the death of trainees; they needed to retaliate. But not in the way the Master Instructor would have suggested.
He had other ideas.
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AN:
To clarify because it was a bit confusing to the Patrons. Danzo didn't personally order the hit on Takuma. It was Kon who was part of managing the drug trade who ordered the hit. Kon went to the Master Instructor who provided him with four trainees to go against Takuma (a genin). The assassination went wrong, and Kinoto had to clean up.
Danzo is the leader of the ROOT, but that doesn't mean everything has to go through him. There's a level of autonomy and ROOT operatives take their own decisions. Danzo of course knows what is happening all the time, but he doesn't order everything that ROOT does.
He was aware of an assassination but wasn't the one to order it (but he also wasn't against it.)
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The link is in the synopsis!