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.
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.
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.
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.
There might be a very dark and twisted fanfiction like that. It could be that Naruto is tricked into believing that Minato and Kushina are some kind of threat to the village or to his friends. So in a moment of confusion and misinformation, he takes drastic action. But this goes completely against Naruto's character in the original series.
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.
There could be a 'catwoman kills batman fanfiction'. A possible plot could be that Catwoman is in a situation where she has to choose between saving the city and Batman. She might think that sacrificing Batman is the only way to stop a greater evil from destroying Gotham. For example, if there's a doomsday device that can only be deactivated by Batman's death and she decides to go through with it.
Maybe Draco discovers a powerful magical artifact that can defeat Voldemort and he decides to use it for the greater good, even if it means going against his family's past allegiances. He could then face many challenges and battles before finally being able to kill Voldemort.
There may be some fanfics out there with this disturbing concept, but it goes against the general nature of the Naruto series. One possible plotline could be that Naruto is somehow mind - controlled by an enemy and in that state, he attacks Hinata. But this is really a stretch as Naruto deeply cares for Hinata in the original series.
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.