This kind of fanfiction could add a lot of depth to the Naruto universe. It could explore the darker side of Konoha that we may not have seen much in the original series. It could also show how far characters can be pushed until their loyalty breaks. And it might even lead to a redemption arc for Konoha if the story is written in such a way, where they have to change their ways to win back Naruto and Hinata's love for the village.
The overall Naruto universe would be turned upside down. Naruto's refusal to protect Konoha could lead to a breakdown in the relationships he has built. His former allies in Konoha might become his enemies, and those who were once his enemies outside of Konoha might try to use him for their own gain. The Akatsuki, for example, might try to recruit him or manipulate him to further their goals. This would create a whole new set of conflicts and alliances that we haven't seen in the original story.
The relationships within the village would be completely shattered. Naruto is a beloved character in the original, so if he kills Konoha ninjas, trust would be broken. Friends like Sasuke might turn against him even more, leading to a much darker and more divided ninja world.
The village would have to rely more on other ninjas. Younger generations like Boruto and his friends would have to step up earlier. This could lead to a different kind of character development for them, as they are forced to take on more responsibilities without Naruto and Hinata's guidance.
In fanfiction, Neji and Hinata's pregnancy would be a significant event in the Naruto universe. It could change the power dynamics within the Hyuga clan. With a new generation on the way, there might be rivalries or hopes for a stronger future for the clan. For the village as a whole, it could symbolize a new era of peace and growth. Hinata's pregnancy could also inspire other female ninjas, showing that they can balance family and their ninja lives. Neji, on the other hand, would become more of a protector not just for Hinata but for the future of the clan, and this could lead to him developing new skills or strategies.
This type of fanfiction can also affect how new fans perceive the Naruto world. If they stumble upon 'konoha hates naruto' fanfiction first, they might get a very different initial impression of the series compared to those who start with the original story. It can be both a source of new interest, as they might be curious to see how such a different take is developed, or a source of confusion if they are not aware that it is a non - canonical exploration.
The relationship between Konoha and the Uzumaki clan might be further strained. With Kushina leaving, Konoha would lose an important link to the Uzumaki. And other Uzumaki members might see this as a sign that Konoha is not a safe place for them.
It would be a huge blow to Konoha. Naruto is a hero in the village, and his departure would leave a big leadership void. The villagers would also lose a great source of inspiration. Hinata is from a respected clan, and her leaving would also have an impact on the clan's standing in the village. Morale among the ninjas might drop as they see two important figures leave.
The story would also change the perception of Naruto. Instead of being seen as the hero of Konoha, he would be considered a traitor by many. This would create a whole new set of relationships and conflicts. His friends might try to convince him to change his mind, leading to some very emotional and complex storylines. The shinobi world as a whole might start to question the values that Naruto has always represented, like loyalty and perseverance. And if Konoha does fall, it could inspire other villages to reevaluate their own security measures and relationships with their ninjas.
It would also create a power vacuum. Naruto was a strong force in Konoha. Without him, the village would be more vulnerable to attacks. Enemies might take advantage of the situation, leading to a whole new set of challenges for Konoha.
They could leave because of a prophecy. Some ancient prophecy might state that they need to leave Konoha to fulfill a greater destiny elsewhere. So they trust in this prophecy and leave their home.