Perhaps it's a plot device to introduce a new power or ability. With his chakra sealed, Naruto has to find a new way to be strong. This could lead to him discovering a hidden power within himself that was overshadowed by his original chakra, or it could even be a way for him to bond with other characters in the fanfiction who help him in this new power - seeking journey.
One reason could be for protection. Maybe in the fanfiction, there are powerful enemies targeting Naruto's chakra specifically. Minato, as his father, seals it away to keep Naruto safe from those who would misuse his power.
It might be related to Naruto's training. In some fanfictions, sealing Naruto's chakra could be a part of a unique training method. By restricting his access to his chakra, it forces Naruto to develop other skills and better understand the nature of chakra control, kind of like how in the original series he had to learn to use the Nine - Tails' chakra in a controlled way.
Perhaps Minato has been corrupted by power. In the fanfiction world, he might have come across some source of power that has twisted his mind. By sealing Naruto's chakra, he could be trying to take that power for himself. It could also be related to some prophecy that he misinterprets. He thinks sealing Naruto's chakra is the key to saving the world, but in reality, it's the opposite.
Naruto would likely be extremely confused at first. He has always idolized his father, and to have Minato do such a thing would shatter his perception. He'd probably try to talk to Minato, ask him why he's doing it.
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 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.
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.
It could make his friends more protective. Since Naruto is in a weakened state without his full chakra, his friends might be more concerned about him and try to keep him out of dangerous situations.
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 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.
Well, it could be that they find out some 'dark secret' about Naruto. Maybe they think he has some sort of uncontrollable power within him that they fear. Or perhaps they are forced to disown him due to political pressure in the village. There could be a group of elders or powerful clans that demand it in order to protect their own interests or maintain the so - called 'balance' in the village.
One possible reason could be a misunderstanding. Maybe some false information was spread about his parents that made Naruto believe they were bad. For example, if there were rumors that Minato sacrificed the village for some other purpose rather than to save it, Naruto might be angry at him.