One possible plotline could be that Naruto is somehow mind - controlled. Maybe an enemy uses a powerful genjutsu on him, making him see the Konoha 12 as threats to the village instead of comrades. This would lead to a tragic situation where Naruto, in his altered state of mind, attacks them.
It could be that Naruto is tricked into believing that the Konoha 12 have been corrupted by an evil force. Some false evidence is presented to him, and in his haste to protect the village from what he thinks is a new threat, he attacks them. However, as he kills each one, he slowly realizes that he has been deceived but it's too late.
One possible plotline could be that Naruto is under some sort of dark magic or mind control. Maybe an enemy has found a way to manipulate his actions and make him turn on his friends. Another could be a situation where Naruto is tricked into believing his friends are actually enemies in disguise. For example, if there was a powerful genjutsu that made him see his friends as threats to the village.
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.
One possible plotline could be Naruto leaving Konoha due to feeling out of place because of the harem situation. Maybe he's overwhelmed by the attention of multiple characters interested in him romantically and decides to seek solitude or a new path outside the village.
One possible motive could be a deep misunderstanding. Maybe Naruto is framed for something he didn't do, and the Konoha ninjas turn against him. In his desperation to prove his innocence and defend himself, he might end up accidentally killing some of them.
There could be a 'naruto kills jiraiya fanfiction'. It could be based on a time - travel scenario. For example, if Naruto from the future travels back in time and somehow his actions cause a chain of events that lead to Jiraiya's death. Or perhaps there's a dark, alternate universe where Naruto's values are twisted and he sees Jiraiya as an obstacle to his new, malevolent goals and thus kills him.
One possible plotline could be that Naruto has to kill Momoshiki to protect the Hidden Leaf Village. Maybe Momoshiki has some new and extremely dangerous power that threatens the safety of the village and its people. Naruto, being the hero, steps up and in a fierce battle, manages to defeat and kill Momoshiki.
Perhaps in the fanfiction, Naruto is tricked into believing his clan is a threat to the village. So, in an attempt to protect Konoha, he takes drastic measures and kills them. It could also be that a powerful and evil entity takes over Naruto's body, and using his strength, murders the clan while Naruto is powerless to stop it from within.
Well, if there is a 'naruto kills kakashi fanfiction', it would be a very different take on the Naruto universe. It could be set in a world where Naruto has been corrupted by an evil force. This force could be manipulating Naruto's emotions and memories, making him think Kakashi is a threat. In the original series, they have a strong bond, so this would be a very controversial and unexpected plot.
One possible plotline could be that Naruto is somehow corrupted or misled. Maybe he discovers some dark secrets within Konoha that he believes can only be resolved by its destruction. As for the Alvarez Empire, they might see an opportunity to expand their influence in the chaos Naruto creates and form an uneasy alliance with him at first.