One main character could be a civilian engineer who devises new technologies that make the civilians less dependent on the ninja for protection. Naruto would be involved as he is always in the middle of any major change in the Naruto world. Additionally, a civilian diplomat who is able to negotiate with different ninja clans and villages on behalf of the civilians could be a main character. This diplomat would play a crucial role in getting the ninja to accept the idea of civilian rule.
One possible plot could be that civilians in the Naruto world get tired of being overshadowed by the ninja clans. They start a peaceful revolution, using their knowledge and skills in non - combat areas like trade and diplomacy. Naruto, being a ninja who has always valued the common people, could support their cause secretly, leading to a new world order where civilians have a more equal say in governance.
Well, perhaps the plot could start with the civilians in the Naruto world getting tired of being overshadowed by the shinobi. They might form some sort of organization or movement to assert their power. They could start making laws that restrict shinobi actions, like no more unregulated missions in civilian areas. And there would be a lot of conflict as the shinobi, who are used to being in control, resist this change. Naruto and his friends would be caught in the middle, having to decide whether to side with the civilians or their shinobi comrades.
Perhaps a scientist who has been studying Pokemon for years. When Pokemon start to rule the world, this scientist uses their knowledge to figure out how to live in this new situation. They might try to find a way to reverse the situation, or at least make sure that humans are treated fairly under Pokemon rule.
It could be a young and ambitious wizard. Wizards often have the power and knowledge to take over a world in fantasy stories.
I'm not sure about a specific 'Civilians Rule the World' Naruto fanfic. But you can try searching on fanfic websites like Fanfiction.net or Archive of Our Own. There might be some interesting ones there.
It could be a new Uchiha character created specifically for the fanfic. This character could be an outcast Uchiha who has been living in hiding, observing the village's problems from afar. He decides to come back and use his unique Uchiha abilities, combined with a new perspective on life, to rule the village and bring about change. He would be an unknown force that disrupts the status quo.
Perhaps the civilians have been influenced by some anti - Naruto propaganda. They might not understand the true nature of Naruto and the fact that he has no intention of harming them. Also, they could be in a state of panic after some events that they wrongly blame on Naruto. For instance, if there was some minor destruction in the village that was actually caused by other factors but they assume it was Naruto's doing because of his connection to the Nine - Tailed Fox. This could lead them to try and harm him until Kakashi steps in to rescue him.
Temari would also make a great main character. She's tough and has strong leadership qualities. In a female - only world, she could expand the influence of the Sand Village in new ways. She might form alliances with other female - led villages and use her wind - based jutsu to protect her people and the region. Her no - nonsense attitude would be a great asset in this new world.
In a Naruto fanfic where civilians rule, the whole concept of the ninja villages could change. For example, instead of being military - dominated, they could transform into more democratic entities. The decision - making process would involve civilians more, perhaps leading to different policies regarding training young ninjas. Instead of just focusing on combat skills, there could be a push for ninjas to learn other skills like farming or construction to contribute to the overall civilian - led society. This would also mean a change in the relationship between ninjas and their villages, with more civilian oversight and less autonomy for the ninja clans.
Since I haven't read it, I can't say for sure who the main characters are.