Well, perhaps Naruto comes back with some super - strong new jutsu that he learned during his absence. He might show off his new power to his old friends and foes alike, leaving everyone in awe.
Perhaps it's an old enemy who has somehow managed to come back stronger. Maybe someone from Orochimaru's old experiments that went wrong, but instead of dying, they gained some dark and powerful abilities. They see Naruto's return as a threat to their plans of world domination, so they target Konoha first. They might be able to control dark chakra in a way that no one has seen before, and use it to create chaos and destruction. They could also have some minions who are equally as powerful and loyal to them, making them a formidable foe for Naruto and Konoha.
In some fanfictions, Naruto might return to Konoha to a cold reception because the villagers still hold grudges from his past. Maybe they haven't fully accepted his power or the chaos he sometimes brought. For example, they could be afraid of his Nine - Tails power flaring up again and causing destruction.
One reason could be that Naruto has seen too much death and destruction in Konoha. His 'godlike' state might make him think that the only way to end all the suffering is to destroy the root cause, which is Konoha. He may believe that Konoha's system is so broken that it can't be fixed and needs to be completely eradicated.
Another reason might be that Naruto is seeking a greater purpose. In the fanfiction, his 'godlike' state could make him realize that there are threats out there that he can't face while being tied to Konoha. He may leave to protect the world on a larger scale, believing that he can be more effective away from the village.
One aspect of 'dark godlike Naruto Konoha bashing fanfiction' could be the exploration of Naruto's character in a much darker and more powerful way than in the original series. In these fanfictions, Naruto might turn against Konoha due to some past grievances. For example, if the village had treated him even worse than in the canon, he could develop a vengeful side. Maybe he discovers some dark secrets about Konoha's leadership and decides to take matters into his own hands, using his new 'godlike' powers to challenge the status quo.
One possible reason could be feeling betrayed by the village leaders. Maybe they made decisions that Naruto strongly disagreed with, like how they treated certain groups or individuals. If Naruto felt that Konoha was no longer the place that stood for justice and fairness as he once believed, he might abandon it.
It could be a rogue ninja who has been secretly building power while Naruto was away. This rogue ninja might have a vendetta against Konoha and sees Naruto's return as a challenge to his plans. So he directly confronts Naruto to prove his own strength.
Perhaps Naruto discovers some dark secrets about Konoha that go against his values. Like if the village has been involved in unethical practices that he can't overlook. This could be things like using underhanded tactics against other villages, which would make Naruto, with his strong sense of justice, turn against Konoha.
Well, it could be that Naruto, with his godlike powers, leaves Konoha because he feels misunderstood. Maybe the villagers still fear his power despite all he has done for them.