Kakashi had been quite curious after his meeting with Kaida . He would lie if he said he wasn't curious about Kaida's claims. That little boy was so confident about everything, as if everything had happened right in front of him. Obviously, Kakashi wanted to check if what Kaida said was true or not, and whether Root was actually experimenting on Konoha ninjas. He also wanted to know if the second claim, that Danzo was behind the miserable condition of his sensei's son, was true.
He was near the base when the explosion happened since he was the one who gave the location to Kaida after confirming unusual activity there. Kakashi confirmed that something was going to happen at the base, and then it happened—a blast like every hell had broken loose. Due to Kakashi being in close proximity, he could feel the wave of the explosion hitting him.
"They made quite a show, and it will be almost a mortal blow to Uchiha if they don't have a solid reason for this," Kakashi thought. Then, at a second location, another blast occurred.
Kakashi went straight to the blast location even before Hiruzen and his company arrived. Even though there was a huge amount of dust in the surrounding area, Kakashi was able to see something inside the base, including the half-deteriorated bodies of some ninjas with their names written on the side to identify whose corpse it was. Some of them were ninjas who once worked with Kakashi. When Hiruzen removed the dust cloud, the whole truth came to light. This base alone contained so many bodies and body parts of ninjas that it became certain in Kakashi's mind that Kaida was correct about Danzo.
"If Danzo could do something this terrible to our own ninjas, doing something like that to Naruto is very easy for him. He may have done worse if not for Lord Third. What was I doing all this time not seeing the truth in front of me?" Kakashi thought. He knew about the disappearance of his former comrades, but he believed the official news that they died during a mission, even though his mind always told him that they were way too smart and talented to die during such missions.
While he was thinking all this, his Sharingan was uncovered, and the problem with Sharingan is that it sees everything, even if you want it to or not. Kakashi was able to see a vial of blood with a name: Sakumo Hatake. For a second, Kakashi didn't want to believe what he saw. Why was his father's blood in a Root base that was conducting human experimentation?
It is to be noted that Kakashi was still not completely sane. He had lost nearly everyone he ever cared for. When he saw that vial of blood, he remembered his father, the man who was once known as the White Fang of Konoha, the person who was stronger than all three Sannin combined. But he committed suicide because some useless people thought he was incompetent, just because he chose his teammates' lives over the mission.
Kakashi never came to terms with his father's suicide. He knew his father was not that weak that he would do something like that just because people said some bad things about him. He had survived and even made Konoha win the Second Great Ninja War. How can you say that he was weak? And now, seeing the vial of blood, Kakashi's suspicions once again arose.
When he saw that, he wanted nothing less than to go to Danzo, put his kunai on his neck and Chidori near his heart, and ask about the vial. But before he could even move, he saw Hiruzen attacking Danzo and taking him along with the other clan heads.
Kakashi could join the meeting if he wanted. He was a clan on his own, even though he was the last member of his clan. The Hatake clan had done so much for the village that they still held massive respect in the village. Kakashi could surely get a seat in the meeting if he wanted, but since there was literally nothing he wanted from the village for his clan, he never actually took part in any meeting. But today, he regretted his decision. He was dying to know the truth.
After that, some Anbu ninja came and took everyone to the Hokage building on Hiruzen's orders. Kakashi understood the higher-ups didn't want this news to spread, and he could understand why. This could very well make Danzo the biggest enemy of Konoha. Even other elders will have to answer many questions about how they didn't know about such a thing when it was happening right under their noses.
After waiting for some time, they simply got an explanation that Root was responsible for some crazy experiments and that an investigation was ongoing. No one was allowed to share what they saw with anyone. Since it was Hokage's order, everyone had to comply with those orders. Kakashi wanted to ask about the blood, but since he knew that asking Danzo would be pointless, he decided to ask Hiruzen about the matter.
Due to seeing all those things and the talk he had with Kaida Uchiha, Kakashi was already thinking of Danzo as some greedy and evil old man who would do anything for power. When he remembered his father, even though he didn't want to make any connection, his mind was not able to forget anything. That vial surely had his father's name on it. Kakashi was feeling a multitude of emotions at the moment, so he decided to take some rest and get an explanation before doing anything. Even though he kept telling himself that, a part of him surely did want to personally interrogate Danzo about the truth. Knowing his mental condition was nowhere good enough to meet Hokage, he went back to his house and locked himself inside his room, trying to calm his emotions.
After nearly an hour, Kakashi calmed down and decided to go to the Hokage office to ask about the situation. But when he was going toward the Hokage office, he was called by an Anbu guard.
"Kakashi Hatake, these are orders from Lord Third. You are given this A-rank mission. The team will be ready in an hour. Prepare for departure," Eagle said and then went back to his next task.
Kakashi remained standing there holding the scroll in his hand. After a couple of minutes, Eagle looked up and asked, "Do you have any doubts?"
"No, but I have something I want to ask Lord Third. Can you ask him to make some time for me?" Kakashi asked.
"Okay, I will ask for an appointment once you are back from the mission," Eagle said. Kakashi just nodded his head and went back. In truth, he just ran away from the truth. He was afraid to know the truth about his father.
…
After a week, Kakashi and the team came back from their mission. Since Kakashi was the leader of the team, he had to file the report. By then, more details had become clear about the situation with Danzo. Kakashi was now even more afraid to know the truth, but he steeled his resolve and went to the Hokage office.
...
"Oh! Come in, Kakashi. Well done on your mission. I expected nothing less from you," Hiruzen said with his grandfatherly smile.
"Lord Third, I want to ask you about something important," Kakashi said, completely serious.
"Go on."
"What are the chances that my father would have become Hokage if that incident hadn't happened?" Kakashi asked, maintaining constant eye contact with Hiruzen.
Hiruzen also kept looking toward Kakashi. His mind was working on finding the reason behind Kakashi's question, and the guesses were not good.
"Almost certain," Hiruzen said after some time.
"Do you know something about my father's death that I don't?" Kakashi continued.
"I know where you are going with these questions. I will ask Inoichi to read his mind. I will call you when I find something. But if your suspicions are true, then that fool has harmed Konoha much more than I initially thought," Hiruzen said.
Kakashi didn't say anything. He just left. Though this could be seen as a disrespect toward the Hokage, Hiruzen didn't care about formalities at the moment.