Well, perhaps in this fanfiction, Naruto discovers a horrible truth about the ninja world. For example, he finds out that everyone around him has been lying to him all along and they are all part of some evil conspiracy. This betrayal drives him mad and he snaps, leading to him killing everyone. However, this would be a very dark and non - canonical take on the Naruto universe.
It could be that Naruto loses control of the Nine - Tails' power in a way that he can't be stopped. The Nine - Tails' influence over him becomes so strong that it turns him into a killing machine. He no longer sees the difference between friend and foe and just starts eliminating everyone in his path. This would be a tragic turn of events considering Naruto's usual nature of protecting his friends and the village.
One possible plot could be that Naruto is somehow corrupted. Maybe he's been influenced by a powerful dark force or a powerful enemy has tricked him into believing that everyone is a threat to the world he wants to protect. So, he decides to take extreme measures and kill everyone to 'create peace' in his warped sense.
In such a fanfiction, it could be that Harry Potter has been corrupted by a powerful and malevolent force. This force might have warped his sense of right and wrong. It could also be that the author wants to explore the extreme consequences of power and how it can turn a hero into a villain. For example, if Harry Potter was constantly taunted and mistreated by the wizarding community despite all he has done, he might reach a breaking point and lash out at everyone.
Well, it could be a dark AU (alternate universe) where Naruto is pushed to the brink. Maybe he discovers some great betrayal among his friends and village. So in his rage, he decides to take revenge and starts killing everyone. But this is a very extreme and uncharacteristic concept for the original Naruto character.
It could be that there is some sort of misinformation spread by an evil organization. They create false evidence that Batman is planning to destroy Naruto's village. Naruto, being the protector of his village, decides to take pre - emptive action. He tracks Batman down and in a fierce battle, kills him. But then as he starts to investigate further, he discovers the truth and has to live with the guilt of killing an innocent (in this case, Batman who was misrepresented).
For such a plot to be possible in the fanfiction, it could involve some major changes in the Naruto world. The Akatsuki could have some new secret weapons or techniques. Also, Naruto might be in a situation where he is not able to access his full power, like being poisoned or something. And perhaps the Akatsuki are more united and desperate than ever to achieve their goals, leading them to take out Naruto who is a major obstacle for them.
One possibility could be that Harry is under some dark magic influence. Maybe he's been corrupted by a powerful and evil spell or artifact that makes him lose his sense of right and wrong, leading him to turn on everyone. Another aspect could be that he's been betrayed so deeply by those he trusted that he snaps and decides to take revenge on everyone, believing they are all against him.
One possible plot could be that Naruto is forced into a situation where he has no choice but to kill Haku in self - defense. Maybe Haku is under some kind of mind control and attacks Naruto relentlessly.
It could start with a rift between them that becomes unbridgeable. Sasuke might side with a group that Naruto is sworn to oppose. Their ideological differences grow to such an extent that they end up in a final battle. Naruto, with a heavy heart, kills Sasuke perhaps because Sasuke refuses to back down and his actions are endangering too many lives. This would be a tragic departure from the original story where their relationship was centered around mutual understanding and redemption.
Well, one possibility could be that Naruto discovers that his friends have been secretly working against him in some way, like lying about their intentions or using him for their own gains. Maybe they've been making deals behind his back that go against what he believes in.
Yes, there might be such fanfictions. One possible plotline could be that Kami has been corrupted in some way and Naruto, in his sense of justice, has to take extreme measures. Maybe Kami starts to harm the village or its people, and Naruto, as the protector, has no other choice but to fight and end Kami's existence. Another could be that Naruto is tricked into believing Kami is a threat when in fact it's a misunderstanding created by an enemy.
One possible plotline could be a case of extreme misinformation. Maybe Naruto is tricked into believing that Raikage is about to launch a devastating attack on Konoha. So, in a moment of panic and believing he is protecting his village, he kills Raikage. Another could be a dark influence. For example, if Naruto is somehow possessed by a malevolent force that drives him to kill Raikage against his will.