Another plotline might involve an alternate reality where Kushina has different values or has been misled about Naruto's true nature. In this 'fanfic', she could believe that Naruto is going to bring destruction in the future and decides to kill him to prevent it, not realizing she's been misinformed.
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 plotline might involve Naruto traveling back in time and meeting Kushina when she was young. They could start as friends and gradually fall in love. Or perhaps there's a prophecy that links them together, and they have to fulfill it, which leads to their mating. There could also be a situation where a powerful enemy forces them to work closely together, and that closeness turns into a deeper relationship.
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.
A plotline might involve Kushina being a 'psycho' due to some past trauma. This could lead to her having a hidden agenda within the Hidden Leaf Village. She could be secretly plotting against some of the village leaders while pretending to be a normal citizen. And Naruto, being her son, gets caught in the middle of her schemes and has to figure out how to deal with her and protect the village at the same time. It could also show how Naruto's friends react to this new, darker side of Kushina.
One possible plotline could be Kushina's daily life taking care of baby Naruto. She might be shown singing lullabies to him, or just watching him sleep with a loving look. Another could be about Naruto showing early signs of his ninja abilities as a baby, like accidentally using chakra in a cute way while Kushina tries to figure out what just happened.
A possible plotline is that Naruto gets adopted by a group outside the village. He grows up learning their ways and becomes a sort of outcast from Konoha. Then, he could return to the village with a different set of skills and a new perspective. Or, he might develop a vendetta against Konoha for allowing his abandonment and try to take revenge in some way.
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.
One possible plotline could be Naruto's struggle with abandonment issues. Since Kushina left, Naruto might have a harder time finding his place in the village. He could become more withdrawn and have to fight even harder to prove himself. Another could be the search for Kushina. Naruto might embark on a journey to find out why she left and try to bring her back.
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.