The first consequence could be a breakdown in the village's unity. Naruto is seen as a hero in Konoha, and if he turns against it, many of his supporters might be confused or even follow his lead. This could lead to internal strife within the village.
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.
Perhaps Naruto discovers some dark secrets about Konoha that go against his values. Like if the village has been involved in unethical practices that he can't overlook. This could be things like using underhanded tactics against other villages, which would make Naruto, with his strong sense of justice, turn against Konoha.
One possible reason could be for his safety. Konoha is a well - protected village with many skilled ninja. She might believe that leaving him there would ensure he has the best chance at survival and growth as a ninja. Also, she may have some mission or obligation that forces her to leave him behind, perhaps something related to the greater good of the village or the ninja world in general.
Perhaps he discovered some dark secrets about Konoha that made him lose faith in the village. For example, if he found out that the village leaders were involved in unethical or immoral activities that were against his values, it could make him hate Konoha. He might also feel betrayed if his so - called friends turned their backs on him for some reason.
One possible reason could be a sense of betrayal. Maybe he felt abandoned or mistreated by Konoha in some way. For example, if he was shunned because of the power within him that others feared.
One possible reason could be a misunderstanding. Maybe some false information was spread about Kushina that made Naruto believe she was a bad person. For example, if there were rumors that she abandoned him for some untrue reason, it might lead to his hatred.
Perhaps in this fanfiction, there is some sort of misinformation. For example, someone has spread false rumors about Naruto being a threat to the village, and Minato and Kushina believe it without proper investigation. This could lead to their hatred.
Maybe in this fanfiction, there was some sort of dark magic or mind - control involved. Kushina could have been unknowingly influenced to do something that deeply hurt Naruto. Like she was made to abandon Naruto at a crucial moment in his life, which then led to his hatred.
One possible reason could be a misinterpretation of Kushina's actions. Maybe some events were presented in a way that made Naruto think she was neglectful or had made bad decisions in the past.
One possible reason could be that Konoha has a history of dark secrets. Maybe Naruto and Kushina discovered some unethical practices within the village that made them lose faith in it. For example, the way the village treated the Uchiha clan was quite unjust. Kushina might have known about some of these underhanded dealings and passed on her concerns to Naruto.