As everyone came into the Uchiha compound, the first thing they witnessed were the dead bodies of the Uchihas and also Root shinobis. Then they saw the Graffiti on the walls written with blood besides which a dead body without eyes was laid. When the other clans people read this, they had unbelievable look on their faces. They continued to venture and read more and more disturbing words all pointing to Danzo and the dead Root Shinobi were undeniable proof of his involvement.
Hiruzen and the oldies arrived and reading the words written everywhere, He opened his mouth wide and his eyes almost popped out. He ran fast and issued a command to his Anbus asking them to clear everyone from the Uchiha compound and its a restricted area for the time being. But the damage had been done. The people had already seen what should not have been seen. Especially other clans and also some clan leaders were here as well. Everything here related to Danzo and there was no denying it.
After seeing everything in place, Naruto left and went back to the Namikaze compound underground. Hiruzen didn't know what to do. He ordered the Anbus to clear the corpses and also erase the writing on the walls. The Anbu also found Sasuke unconscious and took him to the hospital. After a while, an Anbu reported to the Hokage "Hokage Sama, the bodies have been cleared and Sasuke uchiha was the only survivor and was sent to the hospital. All the root shinobis were killed by the same person. He used senbone needles and threw them at great speed and strength which pierced their heads and killed them".
Hiruzen nodded and thought 'Who was it that killed all the root Anbus and wrote the name of Danzo on the walls? It must not be the uchiha. Someone else is lurking in the shadows. I don't have the time to investigate now. I'll have to clear Danzo's name now. Many clan heads also saw what happened. I'll have to appease them. Sigh! I'm getting too old for this. Danzo is very careful all the time. How did he miss this?' As Hiruzen was thinking all this, at the underground root base, Danzo was clenching his fist gritting his teeth listening to the Root Anbu report which detailed everything including the death of many root Shinobi and also Danzo's name written on the walls.
Danzo then made his way to the Hokage's office and entered inside. He then looked at Hiruzen and asked "What's the meaning of this Hiruzen? Who did it?" Hiruzen shook his head "I also have no idea Danzo. They used senbone to pierce the heads of the ninjas. Someone lurking in the shadow. Atleast Jonin level or above. Otherwise with the strength, they cannot pierce the heads with senbone." Danzo also nodded and said "Must be a trick played by those damn Uchihas at the end of their lives. What will we do now regarding this?" Hiruzen thought for a moment and said "I'll try to appease the other clans first. You look into the attacker. If they are not satisfied, I'll make a gesture of disbanding the Root officially if it comes to that". Danzo nodded and left.
Next morning, there was a huge uproar in the whole village and Danzo's name started circulating among the villagers. How much ever Hiruzen tried, he couldn't suppress the matter fully. The other clan leaders were scared of the attacks and increased the security of their clan compounds. Hiruzen didn't have an answer to the question of why Danzo's root Anbu were at the scene of the uchiha massacre. To appease the people, he made a gesture of disbanding the Root and making Danzo retire, but the clan heads demanded Danzo to be punished. With no other way out, Danzo was arrested in front of all the clan heads for questioning.
The situation cooled down a little after Sasuke woke up and admitted in front of everyone that his brother Itachi Uchiha was the one who massacred the whole clan and he was a witness. Thus after Sasuke's testimony, everything started settling down a little and Itachi Uchiha was named as a rouge Shinobi. There was also a mourning ceremony for the Uchiha clan the next day. Finally, it took a whole month to settle everything without any major issues. Danzo was back to his root headquarters underground. He was fuming. He only managed to get three pairs of sharingan from the whole Uchiha clan massacre. All the other sharingans were stolen by the one who killed root Anbu and took it from them.
Danzo suspects many people. The akatsuki, who helped Itachi kill the uchiha, other village ninjas, the dead uchiha clan and also the snake Orochimaru. Finally he couldn't put his finger on who was responsible. He placed his bet on Orochimaru, but he had to confirm before he takes any action. He knew that only Orochi had knowledge of his involvement in the Uchiha massacre and also known his plans as he had told it himself as he wanted sharingan to be implanted in his arm from Orochimaru. So he doubted him and couldn't take action because he has no proof.
Thus the village started investigating any suspicious people who entered or left the village at the time. Understanding nothing was out of the ordinary, Hiruzen also came to the conclusion that it must have been the doing of Orochimaru. He's the only one capable of doing such things without the notice of anyone. During this whole month, Naruto just trained in the underground of the Namikaze compound and his blood clone also did its job as a normal student of the academy.