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.
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.
One plotline could be that Naruto was mind - controlled by a powerful villain. He wakes up to find he has killed his clan and has to deal with the shock and guilt while also trying to clear his name.
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 that Kushina is somehow mind - controlled or influenced by an evil force to harm Naruto. Maybe she's under a powerful genjutsu that makes her see Naruto as a threat to the village instead of her son.
A possible plotline could be that Naruto and Hinata have a child who shows extraordinary abilities related to the Uzumaki clan. This leads to them having to protect the child from those who would want to use the child's power for evil. They seek the help of old friends and allies to keep their family safe.
One possible plotline could be that Harry is under the influence of a dark spell or dark magic artifact which makes him lose control and kill his relatives. Maybe it's a cursed object that he unknowingly comes into contact with, and it twists his mind, leading to this tragic event.
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.
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.