One possible motivation could be mind control. Maybe an enemy uses some powerful jutsu to take over Naruto's mind and make him do it against his will. However, this would be a very dark and extreme take on the Naruto universe.
In a really out - of - the - box fanfic scenario, there could be an alternate reality where Naruto has been corrupted by some dark power. This power could twist his values and make him see Kushina as an obstacle. But such a scenario is quite far - fetched and not in line with the Naruto we know, who values family and love above all else.
Perhaps in a very convoluted fanfic plot, Naruto could be tricked into believing that Kushina is a threat to the village. He has a strong sense of protecting the village, and if he's misled enough, he might think that killing her is the only way to save Konoha. But again, this goes against their established relationship in the original story.
One possible motivation could be power. Orochimaru is always seeking more power, and Naruto has the power of the Nine - Tails. He might think that by killing Naruto and somehow harnessing the Nine - Tails' power, he could become even stronger.
In some really complex fanfic plots, there could be a prophecy or some sort of ancient power play involved. Suppose there is a prophecy that Naruto will bring great destruction in the future, and Kushina is made aware of it through some dark magic or secret organization. She might think that betraying Naruto now is the only way to save the village and the world, even though it goes against her motherly instincts. This would be a very convoluted and interesting take on the idea of her betrayal.
Maybe in this fanfic, the author wants to create a unique and dark plot. Kushina might be made to hate Naruto due to some kind of misunderstanding. For example, she could be misled to believe that Naruto has some connection to a great evil that she is against.
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.
Maybe in this fanfic, there has been a misinformation spread about Naruto that makes Kushina believe he has done something unforgivable. For example, if false rumors say that Naruto is involved in something evil, Kushina might start to hate him without knowing the truth.
One possible reason could be for Naruto's safety. Maybe she has to go on a dangerous mission and believes Konoha is the safest place for him. Another reason might be that she is forced by some powerful enemies who threaten Naruto's life if she doesn't leave him in Konoha.
Another reason might be related to some external influence. Suppose an enemy of the village has the power to manipulate Kushina's mind or emotions. They could make her target Naruto by making her see him as a threat to her or the village. In the Naruto universe, there are many powerful jutsu that can control people's thoughts.
Maybe it's because she sees Naruto's strength and how he has overcome so many difficulties despite her absence. She realizes that if she had been there, she could have made his journey easier. Also, she might regret not being able to watch Naruto grow up, miss his first steps, first words, and all those precious moments that a mother should be a part of.
Another reason could be related to a prophecy. If there was a prophecy in the fanfiction that Naruto would bring great destruction in the future, and Kushina, being a self - sacrificing mother, might think that killing him is the only way to prevent that destruction, even though it goes against her natural love for her son.
One possible reason could be some sort of dark influence or curse that makes her lose her maternal instincts. Maybe a powerful enemy targets her and in order to protect Naruto from further danger related to her, she feels forced to abandon him. Another reason might be that she is made to believe false information about Naruto, such as that he will bring great disaster to the village in the future.