Well, the Naruto vs Pain fight in the original series is epic. Fanfiction allows fans to explore different scenarios and what - ifs. Maybe they want to see different character developments during that intense battle.
In the original Naruto vs Pain fight, there were many unanswered questions. Fanfiction tries to answer those. For example, what if Naruto had more help? Or what if Pain had different motives? This makes it appealing to fans who want to explore these ideas.
One consequence could be an imbalance in the world's population. There might be too many people for the existing resources, leading to shortages of food, water, and living space.
It could be that his new 'godlike' power has isolated him. People might be either in awe or afraid of him, and he may feel that he can't be close to others as before. So he acts coldly as a defense mechanism.
I think Hinata could be an ally. She has always been in love with Naruto and would not stand by while he is in danger from Dark Naruto. Additionally, Shikamaru is smart and strategic. He might see the threat of Dark Naruto to the village and decide to assist Naruto, using his intelligence to come up with battle plans.
Well, in some fanfictions, Naruto might use some super powerful jutsu that he either discovers or creates. Maybe it's a new form of the Rasengan combined with some sealing techniques. It could also be that he taps into some ancient power or makes a deal with some sort of god - like entity within the Naruto universe.
Maybe he got some kind of curse. In the Naruto universe, there are all sorts of dark magic and curses. If he was cursed, it could make him withdrawn and cause him to ignore everyone.
Maybe in that fanfiction, Naruto's over - eagerness to be recognized could be misconstrued. His loud and boisterous nature might annoy people. For example, if he constantly interrupted others or pushed his ideas too hard without considering others' feelings, it could lead to dislike.
Well, it could be about a dark version of Naruto having different goals and values from the original Naruto. Maybe the black Naruto wants to take over the Hidden Leaf Village by any means, while the real Naruto tries to stop him to protect his home and friends.
One possible reason could be a powerful genjutsu cast over the village. Maybe an enemy ninja with strong illusionary powers managed to make everyone forget Naruto. It could also be due to some sort of curse. For example, a dark curse was placed on Naruto that made people's memories of him fade away gradually.