The antagonist could be a new, self - proclaimed ninja god who wants to rule over all the villages. He sees Naruto as the only threat to his power, so he used a powerful spell to take away Naruto's godlike abilities. Konoha wants Naruto back to stop this tyrant. This antagonist might have an army of brainwashed ninja at his command.
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.
Naruto would probably be conflicted. On one hand, he has a deep love for Konoha, his home. But on the other hand, he might have been hurt by the past events that led to his departure. He could initially be hesitant, but eventually be swayed by the thought of seeing his friends again.
One possibility is that Naruto would return with newfound strength and wisdom. He might have learned unique techniques during his time away. Konoha could welcome him with open arms and immediately put his skills to use in protecting the village. For example, he could train the new generation of ninja, sharing his experiences from his travels.
In a 'konoha wants naruto back fanfic', perhaps there's a prophecy that says only Naruto can save Konoha from an impending doom. The villagers, who once shunned Naruto, now understand his importance. They start a campaign to bring him back. Tsunade could be leading this effort, offering Naruto things like a proper apology for how he was treated in the past and a high - ranking position in 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.
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.
Definitely Naruto himself. He is the one Konoha wants back, after all. And then there would be his old friends like Sasuke. Sasuke might play an interesting role, either helping Konoha get Naruto back or being a bit hesitant because of his own complex relationship with Naruto. Also, characters like Iruka - sensei, who has always been like a father figure to Naruto, would be important. He could be the one who first realizes how much Konoha needs Naruto and starts the ball rolling to get him back.
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.