The Hidden Leaf Village is the most important place in the world of Naruto. The protagonist of the series, Naruto Uzumaki, and the majority of the side characters, live in this village. What's more, this village is deeply rooted in Shinobi history as well, being the very first to have been established and a model for others to follow.
While the majority of characters from Konoha have been the heroes in the story, that certainly doesn't mean the village is free of any evil. In fact, Konoha has been responsible for several atrocities and is, in more ways than one, evil.
6 Uchiha Clan Massacre
Perhaps the most evil thing that the village has done in all its years of existence is the eradication of an entire clan. The Uchiha clan was was one of the most important parts of the village. In fact, they were one of the two founding clans of the village, yet, they were treated horribly as the story moved forward. The Uchiha barely held any power and all of it passed on to the Senju, simply because they were feared for their powers.
Instead of treating them with love and showing them that hatred is not the way to go forward, Konoha decided to eradicate the clan once and for all. Danzo ordered Itachi to murder every single member of the clan, including the children, in the name of the village. Itachi did it because he loved his village and, at the same time, wanted to protect his brother. The Uchiha Clan Massacre remains to be one of the worst tragedies to ever occur in the world of Naruto.
5 Conducting Human Experiments
Recreating powers is something that a lot of people have tried their hand at and Konoha is no different. Yet, for a village that goes on to preach love and harmony, conducting live human experiments is certainly not the way to go forward. When Hashirama Senju died, the village realized that they had lost a big asset. His Kekkei Genkai was incredibly powerful as it allowed him to control any Tailed Beast by restricting them. Konoha wanted this power and, to attain it, they went to extreme lengths. Children were signed up for this experimentation and, it resulted in the death of the vast majority of them, with Yamato being the sole survivor.
It isn't as though Orochimaru was conducting this experiment in secret. The Third Hokage was very well aware of what was happening and yet allowed it to happen anyway. For that, Konoha will have will always remain evil.
4 Ostracized Naruto
The main character of the story, Naruto Uzumaki started his journey as a young mischievous boy who appeared to be full of life. However, it wasn't long until fans found out that Naruto behaved the way he did simply because he craved affection and attention. Throughout his life, Naruto never received an ounce of parental love or something even remotely close to that. The village absolutely detested him simply for existing and carrying the Nine-tailed Fox within himself.
No children would talk to him, bar a few, and people would actively avoid him, going as far as telling their kids to avoid him as well. Naruto lived a very hard life and Konoha was primarily responsible for it. Knowing that he was a Jinchuriki meant that he needed to be taken care of properly, not given a room to live in and be forgotten about.
3 The Existence Of ANBU Root
The evils of Konoha run deep. While on the surface, they preached to be good and kind, they had a vast network of darkness beneath. This darkness manifested itself as the root ANBU. This faction of the ANBU was led by none other than Danzo. The Third Hokage was very well aware of its existence yet, once again, he did absolutely nothing to stop it. Simply put, the root ANBU was allowed to handle the dirty work of the village. Assassinations, cold-blooded murders, and all other crimes were permitted in this section of the ANBU.
What's even worse, every member of this organization was stripped of their emotions, Sai being a prime example of this. They were made to kill their own families to become capable of joining this order. To make things even worse, they had seals placed on their bodies which prevented them from revealing any key information to the enemy. Truly, Konoha was absolutely evil for this.
2 No Intervention In The Hyuga Affair
The Hyuga Affair was terrible from top to bottom. The Hidden Cloud Village once attempted to get their hands on the Kekkei Genkai of the Hyuga clan. To do this, they went on to attempt the kidnapping of Hinata Hyuga. This kidnapping eventually failed when the kidnapper was killed by Hiashi Hyuga.
Seeing this happen, the Hidden Cloud bizarrely went on to demand the head of the clan leader. Instead of questioning this demand or even intervening, Konoha did nothing and let Hizashi sacrifice himself for his brother. For a village that powerful, Konoha should have done better to prevent its citizens from falling prey to its politics. Yet, nothing was done.
1 Sending Children To War
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Konoha was built by Hashirama and Madara together as their village of dreams. They hoped to live in a land where peace prospered and most importantly, children did not have to go to war ever again. While this dream was very ambitious, it did not come to pass until much later in the story. Konoha did, in fact, send children to war on several occasions. Due to several wars breaking out in quick succession, the village was forced to send children to the battlefield to represent their village.
In fact, Shisui hadn't even hit double figures in age when he was representing the village in the Third Great Ninja War. Many just like him represented the village in the war as well and ended up losing their lives. Konoha was built on the promise of preventing children from ever going to war, yet, it failed to deliver on that and threw them to wolves with no remorse.