Another idea could be that Naruto discovers some dark family secrets that he can't bear. This could include things like his family being involved in unethical experiments in the past. The shock and disappointment are so great that he loses control and ends up causing harm to his family, though it's a very tragic and complex situation.
He could realize his mistake later on. Maybe he has a moment of clarity where he remembers the true nature of his family and how much they love him. He then uses his strong willpower to fight against whatever was controlling him before and tries to make amends.
Perhaps in the fanfiction, there's an alternate universe scenario where Harry has a different personality. He might be more power - hungry and sees his family as obstacles to achieving greater power, so he takes actions to get rid of them. This could involve using his magic in cruel and calculated ways against his family members.
Another possibility is that there could be a new character introduced in the fanfiction, a mastermind who manipulates Harry into believing that his family is a threat. This new character could be the main antagonist.
One possible reason could be that his newfound 'godlike' powers make his family feel estranged. They might not understand his sudden transformation and the magnitude of his power, which creates a sense of fear or discomfort, leading them to ignore him.
He could also distance himself from them. Naruto might choose to avoid his family, not wanting to be around them as a way to show his anger. He could move out or stop participating in family activities.
Choji would be sad and also a bit scared. He has always been a loyal friend to Naruto. He might not be as aggressive in trying to stop Naruto as some of the others, but he would try to reason with him, talking about their friendship and how the village has also been a home to Naruto. And Ino would use her mind - related jutsu to try to break any possible mental influence on Naruto if there is one, while also trying to reach out to him emotionally.
It could be Sasuke. If he were to turn to the dark side in the fanfiction, his Rinnegan powers could be used to destroy Konoha. He has the potential to be extremely powerful and if he has some sort of vendetta or is influenced by some dark force, he might take his anger out on the village.
Maybe he has some personal grudges or misunderstandings within the family in the fanfiction. It could be that something happened in the past that made him feel betrayed or unappreciated, so he refuses to offer help.