Hiruzen placed his hand on the last chunin and easily removed the seal on his head. As a grandmaster in fuinjutsu just like Danzo, and already knowing the structure of the seal, breaking it forcefully was not difficult for him. However, if someone else had attempted this, the seal would have burned the chunin's brain and attacked the mind of the person trying to remove it.
After removing the seal, Hiruzen began reading the chunin's memories.
"You wanted them to bring him alive 'if possible,'" Hiruzen said, looking toward Danzo.
"I now declare that Danzo has committed grave crimes not only against the Uchiha clan but also against the village by trying to kill one of our youngsters, and will be punished for that," Hiruzen announced.
Shibi looked toward Fugaku and nodded. Hiruzen noticed this exchange and spread his chakra around the hall, but he was a second late. Fugaku had already sent the signal to Shisui to begin the plan.
The signal was sent using a simple seal developed by the previous grandmaster of the Uchiha clan. Its only function was to send a simple message across a distance of 10 km. While any seal master could create such a seal, what made this one special was its untraceability. Even if Hiruzen had deployed his chakra field earlier, he wouldn't have been able to detect the start or end of that signal.
'Please don't do anything stupid. I don't want to make this matter bigger than it should be,' Hiruzen thought. He was already planning to remove Danzo from his position, so there was no need for Fugaku and Shibi to blow up those bases. But after confirming what was inside those bases, both Fugaku and Shibi wanted nothing less than to kill Danzo in the most painful way possible.
They also knew how chaotic the village's condition would become if someone killed Danzo. Who knows what those hundreds of Root ninja would do to avenge their leader? Leaking sensitive information about the village was the least dangerous thing they could do, with going on a killing spree in the village and surrounding areas being among the worst possibilities.
Even though Hiruzen didn't sense anything from his chakra field, he was sure something was going to happen. Since there was nothing he could do, Hiruzen just went back to his seat and began speaking:
"The complaint raised by the Uchiha clan is valid. Danzo really tried to forcefully abduct and even attempted to kill one of the young geniuses of the clan. Due to committing this crime—"
Boom boooooom
Everyone in the room fell silent after hearing the sound of explosions coming from somewhere within the village. But before they could think further—
Boom Booom Booooom
Another set of explosions occurred. Fugaku and Shibi looked toward Danzo.
"Looks like there's a rat inside the village. We should go and find it before it does any more damage," Fugaku said, maintaining eye contact with Danzo as he and Shibi stood up, followed by all other clan heads. Only Danzo and Hiruzen remained seated in the hall.
Danzo looked toward Hiruzen, expecting him to stop them, because just by listening to the sound of the explosions, Danzo could tell that they came from somewhere around his base.
Though Hiruzen also understood what had happened, there was nothing he could do now. He decided to follow the clan heads and assess the damage caused by his negligence.
...
Shisui was present at the location of the Root base. Though from the surface no one could tell that there was anything remotely similar to an experimental facility present underground, they knew better. From an initial survey with the help of his Sharingan, Shisui was able to identify 20 Root ninja guarding the base in civilian disguise.
It was difficult to hide years of training and the killer instinct they had developed. Due to subtle clues in their movements, Shisui was able to guess who the Root ninjas were. But it was only because of the Sharingan that he was able to find them. If it were that easy to identify Root ninjas, there was no way they would have been able to complete the thousands of missions Danzo had given them.
After identifying these Root ninja, Shisui went back to the team following him. Fifteen veteran Uchiha jonin and three jonins from the Aburame clan were waiting for him. He went to the center of the group and started speaking:
"I have identified most of the Root ninjas in that area. Our job is to subdue them—don't kill them unless necessary. But if it's out of your hands to capture them alive, make sure to kill them in the most painful way possible. Fugaku and Shibi-sama have asked us not to kill unless necessary, but if it is, there is no order to give them a painless death."
Everyone present nodded. Since their faces were covered by masks like Kakashi's, with only their eyes visible, it was difficult to see their facial expressions. But Shisui could easily see the immense rage they were feeling just from their eyes. This feeling was shared by him too. Everyone present had been briefed about what was in the base so they would know why they were doing this and not lose their cool after seeing the contents of the base and do something foolish.
With a simple signal from Shisui, every jonin went into action. Shisui just pointed at the Root ninja, and a jonin would take care of them. Since most of the guards were of chunin rank, they were small fry for Uchiha jonin with the power of Sharingan. A simple genjutsu attack and they were out cold.
One jonin was unlucky enough to resist the genjutsu attack from a Uchiha jonin, though the reason for that was the Uchiha jonin intentionally used a weaker attack. As soon as the Root ninja came out of the genjutsu, his throat was slit by a kunai containing a poison that suppressed chakra flow in the area. The cut was made so precisely that the Root jonin would not die from respiratory failure and would be alive for quite a long time.
Just after slicing the throat, the Uchiha jonin took out some senbon coated in a special poison designed not to kill but to cause unbearable pain, and planted these senbon in various parts of the Root ninja's body. If his throat hadn't been sliced open, the Root ninja would have screamed until his throat burst. The pain was truly unbearable, but he could neither move nor scream. That ninja died a slow and painful death.
Shisui appeared next to that Uchiha jonin and said, "You can take some rest. We'll handle it from here."
That jonin was the father of one of the ninja who went missing during a simple escort mission. Knowing what had happened to his son, the rage he was feeling was like no other.
"Don't worry, boy. I won't make any rookie mistakes just because of anger," the jonin replied, his face calm.
Shisui just nodded and went back to his position. There were more important things to do than consoling a jonin, and if a ninja can't control his emotions, there's no way he would ever become a jonin. Well, not unless you're a person born with cheats like Asura and Indra reincarnation, Sharingan, and Uzumaki's absurd chakra reserves and a tailed beast inside your body.
Within a couple of minutes, all of the Root ninjas were either dead or unconscious. Shisui then once again gathered all the jonin.
"All of the Uchiha jonin will be in charge of civilian security. Move them away from this position and make sure no one comes near this area. All Aburame jonin will begin the task of planting explosion tags around the base. Make sure to accurately place them at pre-calculated locations. We don't want this base to collapse completely."
All of the jonin nodded their heads and went about their business.