In fanfiction, Naruto might be crying because he has reached a breaking point in his journey. He has faced so many challenges, and Minato's appearance and his embrace make Naruto realize how much he has missed having a father. It could also be that Naruto is crying out of sheer happiness to finally be in his father's arms, even if it's in a somewhat surreal or spiritual way.
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 reason could be extreme emotional pain. Maybe he witnesses the death of a very close friend or loved one in the fanfiction world. This overwhelming grief could cause such a physical manifestation as crying blood.
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.
It might be due to jealousy. If Minato was getting more attention or praise in the village for his achievements while Kushina felt overlooked, that could create resentment. Say, Minato was constantly being hailed as a hero for his speed and battle tactics, and Kushina, who also had great power, felt like she was in his shadow.
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.
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.
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.
One possible reason could be Naruto's pent - up anger towards Minato for leaving him as an orphan. He might feel that Minato sacrificed himself without fully considering the consequences for Naruto.