Before departing for his new adventure, Itachi had done his homework, having resolved the clan's financial issues for several years to come. However, there was one matter he hadn't been able to settle, mostly due to lack of time and more pressing priorities.
This unfinished business was left in the capable hands of Fugaku and Kakashi: their task was to deal with a certain small rat hiding in Konoha's shadows. This rat had been biding his time for years, accumulating power in reclusion. Root's clandestine ninjas were still carrying out their espionage with increasingly advanced stealth techniques. Danzō, on his part, had redoubled his efforts, training Root's members in all manner of forbidden jutsus and even performing genetic modifications on his most promising candidates.
Another hidden factor allowing Danzō to continue amassing power was his collaboration with Orochimaru, who had betrayed the village a few years earlier after Minato had discovered some of his human experiments and other illicit activities.
"What's the situation with the Uchiha? We must contact Akatsuki again to see if they can lend their support for a surprise attack to eliminate Fugaku and his most powerful ninjas," Danzō said in the darkness of his office, illuminated only by a desk lamp.
"We have uncovered new operations that Fugaku has carried out to oppress our Root, but we are unclear about the power of the rest of the clan. We estimate that to quickly eliminate Fugaku, we would need the collaboration of at least three Kage-level ninjas," reported Torune Aburame.
"Damn Fugaku! He's far more dangerous than we thought. His policy of secluding his clan has prevented us from killing more of his members," Danzō said, his face contorted in a mask of fury as he clenched his fist.
Meanwhile, Kakashi was resting in a tree, reading a small book, when a crow landed on a branch and looked at him for a few seconds before spitting a scroll from its interior. Kakashi looked at the scroll and smiled menacingly while covering his eyes with one hand. Anyone nearby would have seen a red glow emanating from both of his eyes. Unlike the original story, with Obito's death, both of his eyes had been transplanted—a small gift from the Uchiha clan.
It was two in the morning when twelve shadows emerged from the darkness. One of them took out a long scroll and began to make hand signs, touching different parts of the scroll as if it were a door with many locks. Little by little, different symbols spread across the ground. "It's almost done. This teleportation matrix will take us to Fū Yamanaka, whom we have implanted with Itachi's Flying Thunder God seal. Fū Yamanaka is Danzō's bodyguard, so they shouldn't be too far from each other," Fugaku said with a serious voice. "We chose this ninja because he is the best sensory type working with Danzō. If we eliminate him first, it will be very difficult for them to detect us."
"Kakashi and I will seek Danzō's chakra signature and fight him. Your job is to stop any flies that get close, but it would be better if we could avoid being found entirely."
Kakashi looked at Fugaku and said, "Let me fight him. My father would want me to settle this with my own hands."
Fugaku had his doubts, but this ninja by his side was very powerful. He possessed a powerful Mangekyō, and while he didn't have enough chakra, with the help of Itachi's chakra battery, he could last for a long time.
Fugaku nodded. "I agree, and you deserve this. But if you take too long, I will not hesitate to act. Remember, we must be fast."
Kakashi smiled again. It seemed sickeningly joyful, as he had been torturing himself day and night with training for this very day.
Fugaku gave a signal, and everyone gathered around him. In the next instant, they had vanished.
In the depths of a large cave, a ninja was meditating, surrounded by several scrolls. Suddenly, his senses screamed "danger," and he automatically performed a substitution, but unfortunately, the position where his real body shifted was exactly where a sword was plunging through him.
Fugaku plunged the sword, which came out of the ninja's chest. His speed in Sage Mode was unparalleled; only Minato with his jutsu and the Raikage could compete with him. Immediately after, a Uchiha ninja accompanying them sealed the body in a scroll, while Fugaku looked around, searching for a chakra signature he knew well—not just the signature, but the malevolent intent that radiated from Danzō's body, which he could see with his Sage Mode perception.
Without a word, he led the way through one of the mazes that branched off from Fū Yamanaka's cave. There were no other ninjas on the path, likely because Danzō had them all in training, with no time for idleness. In less than a minute, they arrived at Danzō's location, a large conical cave connected at the center by four bridges, with a hundred-meter precipice below.
Fugaku had a spatial seal that Itachi had left him to seal the place, preventing anyone from entering or sound from escaping. The ten ninjas stayed outside while Fugaku and Kakashi entered.
As soon as they stepped inside the cave, Fugaku unleashed the seal that enclosed the entire chamber. Danzō, on his part, felt the presences that had suddenly revealed themselves and instinctively placed his hand on his sword.
"Fugaku, you are very brave to do this behind the Hokage's back. Are you not afraid of becoming a traitor?" Danzō said as he sent an alert to Root's forces.
Fugaku didn't get a chance to respond when Kakashi disappeared into thin air and reappeared behind Danzō.
"For what you did to my father!" Kakashi roared as he executed a swift strike using his father's technique. A flash of white light illuminated the darkness of the cave. Danzō immediately drew his sword and unleashed a flurry of Shadow Clones that rushed toward Kakashi. The latter's red eyes widened, causing Danzō's expression to change.
At that moment, Kakashi increased his speed to a point that Danzō could not follow. He then executed one of his father's cutting techniques, and what Fugaku saw from the outside were many white lines forming an ordered, fractal-like pattern. Everything happened in a second, and all the clones vanished like shadows, but the real Danzō was smiling, blood dripping from his mouth.
Kakashi had given his all in that attack, using his father's most advanced technique, which, combined with the Sharingan, left no openings and gave the enemy no way to escape. As Kakashi was about to sheathe his sword, his Sharingan showed him an incoming attack. It was like a scythe's blade from above, and he was nothing but a frail stalk about to be cut. He tried to evade, but he realized that purple chakra chains had already wrapped around him, and even a substitution would be useless.
Danzō smiled, tasting victory, when suddenly, a celestial chakra exploded from Kakashi, breaking all the chains. The attack from above didn't connect with his flesh but with two skeletal arms. Before he could be surprised, another fist swung from the side.
"Summoning: Triple Rashōmon!" Danzō shouted, and different doors rose from the rock wall, stopping the incoming arm.
At that moment, the damage from the attacks caused the bridge-like platform to collapse. Everyone began to fall. Danzō, however, clung to the wall and used a Fire Style jutsu to create distance and buy time for the other Root ninjas to arrive. As Danzō fled, a shadow appeared from behind him: it was Kakashi, who had deactivated his Susanoo but kept his Mangekyō active. For a second, Danzō looked into those red eyes and fell into a Genjutsu. It was only a second, but when he managed to break free, a sword was already plunged into his chest.
Fugaku, who had remained silent until then, spoke again. "You must hurry! My ninjas are already fighting the ones Danzō alerted, and he still has a couple of Izanagi left. Try to cut off his arm and seal it."
Kakashi heard him and expanded his senses, seeing Danzō appear again with a confident smile. "I am immortal! You better give up!" Just as he finished speaking, he felt a part of his body disappear. What he saw next terrified him: his arm, which had several Sharingan he had collected over time, twisted into a spatial hole.
"Damn it, you bastard! I'll kill you!" Danzō yelled as blood came from his mouth and he vanished once more.
Just as Kakashi thought his vengeance was complete, Fugaku shouted, "Careful! He used Izanami with the implanted Sharingan in his eye!" As he said this, Danzō appeared again with a sinister gaze. The enemy knew about his power.
Itachi vanished into the Kamui space and reappeared next to Danzō. The latter tried to defend himself, but a white slash had already cut from his shoulder to his armpit. A white arm now rested in Kakashi's hand, who made it vanish into his Kamui space.
Danzō, losing hope, let himself fall, and as he did, he unleashed the Reverse Four Symbols Sealing Jutsu, intending to take Fugaku and Kakashi with him. But before the jutsu could take effect, Kakashi sensed the danger and instantly took Fugaku into his Kamui space. The two waited there for a few seconds to witness the destruction Danzō's final jutsu caused.
Thus, the Uchiha's secret enemy lived out his final moments without the possibility of escape, despite all his techniques.
Kakashi felt a bitterness in his throat and the melancholy of remembering his father. "You were magnificent. The White Fang would be so proud."
Aftermath
The news of Danzō's death spread like wildfire through Konoha's shadows, not through official channels, but through whispers and rumors. The shinobi community was in shock, with the once-unassailable figure of Root's leader mysteriously gone. Minato, with his Hokage's intuition, immediately understood the implications. He chose to leave the Root division in a state of suspended animation, without a clear successor. He knew that any hasty decision could lead to a power struggle. He would wait for the right time and the right person to take control of the organization, a person he could trust not to corrupt it from within.