One possible reason could be fear. If Naruto was 'godlike' in this fanfiction, his power might be uncontrollable and Minato, as Hokage, might feel it's a threat to the village. He could think that Naruto's power could attract too many dangerous enemies or cause destruction accidentally.
Maybe there was some sort of misunderstanding. Naruto's newfound 'godlike' abilities might have been misinterpreted. For example, some strange events might have occurred that made it seem like Naruto was using his powers for malicious purposes when in fact he wasn't. Minato, not fully understanding the situation, made the hasty decision to banish him.
One possible reason could be for Naruto's protection. Maybe Minato knew of some great danger that was coming for Naruto and he thought that banishing him would keep him out of harm's way. Another reason might be related to some prophecy or hidden power within Naruto that Minato feared could be misused if Naruto stayed in the village.
One possible reason could be for the protection of the village in a very extreme and controversial way. Minato might think that Naruto's presence is attracting too much danger and decides to banish him to keep the village safe.
One possible reason could be that Naruto discovers some long - hidden secrets about Minato that he feels betrayed by. For example, if he found out Minato had made a deal that affected Naruto's life negatively in some way, like with the Kyuubi. Maybe Naruto feels that Minato sacrificed him for the greater good of the village without really considering his future or feelings.
Naruto could also become determined. Since he is 'godlike' in this fanfiction, he might see this as an opportunity to grow even stronger away from the village. He might set out on a journey to master his powers fully and prove himself, with the intention of one day coming back to the village and showing everyone that he was wrongly banished.
One possible reason could be for Naruto's protection. Maybe she thought by banishing him from a certain place or situation, she could keep him away from a hidden danger that she knew about. For example, there might be a powerful enemy targeting Naruto specifically, and she believed that by making him leave, he would be harder to find.
It could be that Naruto is trying to prove himself. He wants to show that he can be as great a fighter as his father. Also, he might have received some training or knowledge transfer from someone who knew Minato well. This could have inspired him to adopt Minato's fighting style. He may also be in a situation where his normal fighting style isn't working, so he turns to Minato's as a last resort.
One reason could be guilt. Since Minato wasn't there for Naruto when he was growing up in the original story, in the fanfiction, he might be overcompensating for that lost time. He feels like he has to make up for all those years he wasn't around to protect his son.
One reason could be that Minato has some unfinished business with Naruto. Maybe he wants to pass on some crucial ninja skills or knowledge that only he can teach. Another reason might be the strong father - son bond. Despite being separated for so long, Minato's love for Naruto is still very deep.
Well, perhaps the writer wants to break the mold of the traditional Naruto story. In the original, Minato is a great father figure, but in this fanfiction concept, the writer might be aiming to show how an alternate reality could shape Naruto. Maybe they want to explore themes of trauma and how Naruto could overcome it. Or it could be a way to experiment with different character dynamics, seeing how Naruto would interact with a Minato who is not the loving father we expect. It could also be a form of creative exploration of the characters' personalities, pushing the boundaries of what we think we know about them.
Naruto might initially be very confused and hurt. He loves his father and the village, so being banished would be a huge shock to him.