One possible plot could be that Naruto, after being wronged in some extreme way by Konoha, like false accusations of a heinous crime. He then uses his godlike powers, perhaps newfound abilities he acquired during some hidden training. He might start by targeting the people who directly wronged him, like certain elders or ninja who were part of the conspiracy against him. He could use his powers to expose their misdeeds to the rest of the village before deciding on more extreme forms of revenge.
Well, it could be that Naruto discovers some dark secrets about Konoha that go against his beliefs. For example, Konoha might have been using some underhanded tactics against other villages and Naruto, being the moral character he is, feels betrayed. With his godlike status, he decides to take revenge. He may first cut off all of Konoha's alliances with other villages by revealing the truth. Then he could challenge the leadership of Konoha in a non - violent way, like a series of trials to expose their wrongdoings.
In the fanfiction, Naruto might have become godlike due to some powerful curse or blessing. If Konoha tries to take advantage of his new power for their own gain without his consent, he could seek revenge. He could start by isolating Konoha from the outside world, using his powers to create barriers. Then he might enter the village and start a revolution of sorts. He would face off against those in power, trying to make them understand the error of their ways through his actions, rather than just pure destruction.
Maybe the hidden organizations within Konoha that work in the shadows. They could have been involved in some plot against Naruto that led to his decision for revenge. They would be the ones trying to stop Naruto from exposing their secrets and exacting his revenge on the village as a whole.
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.
One possible plot could be that Naruto's incredible power makes the Konoha elders or some jealous shinobi feel threatened. They might spread false rumors about him being a danger, leading to the village turning against him. Maybe they frame him for a crime he didn't commit, like a powerful attack on the village that was actually the work of an enemy they secretly allied with. This would make Naruto, who has always been loyal to Konoha, feel extremely betrayed.
Sasuke could be an ally. He also has his own issues with Konoha and would understand Naruto's need for revenge. They could combine their powers, with Naruto's massive chakra reserves and Sasuke's unique Sharingan abilities.
One possible plot could be Naruto discovers a long - hidden conspiracy in Konoha that wronged his family, and he starts by using his influence outside the village to cut off Konoha's trade routes secretly. This slowly weakens Konoha's economy and forces the elders to come to him for negotiation.
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.
One possibility is that Naruto has left Konoha voluntarily after some great tragedy where his godlike powers were misused. Konoha, now in danger again, wants him back. They send out a team of shinobi, including some of his old friends like Sasuke and Sakura. The story could then focus on their journey to convince Naruto to return and help them fight off a group of rogue ninja who are causing chaos with powerful, dark jutsu.
One common theme is betrayal. Naruto might feel that Konoha has betrayed him in some way, like hiding important information or not standing up for him when he needed it. This sense of betrayal then drives his revenge.
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 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.