A possible plot could be a Jugo Clan member going on a journey to find a way to control their clan's berserk state without relying on Orochimaru's methods. They could encounter various other clans and learn different techniques that help them in their quest. For example, they might study with the Nara Clan to gain better mental control.
One idea could be exploring a hidden sub - clan within the Uchiha clan that has a unique kekkei genkai. Another could be a story about a member of the Hyuga clan who rebels against the traditional ways of the clan and tries to create a new future for it. Maybe a story where a Naruto - like character is born into a minor, almost forgotten clan and rises to great prominence.
One idea could be a new clan that has the ability to control time in a limited way. For example, they can slow down time for a short period during battles, which gives them an edge. Another idea is a clan that has a special connection with animals, not like the Inuzuka clan, but they can communicate telepathically with all kinds of animals and use their skills in combat or for gathering information. A third idea could be a clan that has mastered a form of chakra that can create illusions so powerful that they seem real even to the Sharingan or Byakugan users.
One idea could be to explore the backstories of minor clans that are often overlooked in the original Naruto series. For example, how they might have been affected by the major clan wars in the past. Another plot could involve a young ninja from a small clan trying to unite different clans against a common enemy that threatens all of them. Or perhaps a story about a forbidden love between members of rival clans during the clan wars and how they struggle to balance their love and loyalty to their respective clans.
One idea could be a story about a young ninja from the snake clan who discovers a long - lost jutsu that can transform into a giant snake - dragon hybrid. This new power causes other clans to fear and target him.
One idea could be exploring Naruto's deeper connection to the Uzumaki clan's sealing jutsu. Maybe he discovers an ancient Uzumaki scroll that contains a powerful sealing technique that was lost over time. This could lead him on a journey to master it and in the process, he uncovers more about his clan's history and secrets.
One idea could be exploring the early days of the Sarutobi clan. Maybe show how they developed their unique jutsu. Another could be a story centered around a young Sarutobi clan member who has a rare ability and must prove themselves in the Hidden Leaf Village.
One interesting Naruto and Jugo fanfiction could be about their unlikely friendship outside of the main plot. For example, they meet in a forest and start to understand each other's powers better. Jugo's curse mark and Naruto's Nine - Tails chakra could have some sort of connection in this story.
Jugo himself is obviously a very important character. His struggle with his own powers and his connection to Orochimaru are key aspects. Then there's Kimimaro, another Jugo Clan member who was very loyal to Orochimaru. His backstory and his unique bone - related abilities are interesting to explore in fanfiction.
A possible plot could involve Naruto being transported to a parallel dimension where the Fox Clan rules. He has to prove his worth to them as they initially see him as an outsider. As he does so, he uncovers a conspiracy within the clan that could endanger both their world and his own original world.
The Mibu Clan could be involved in a prophecy that foretells either their rise to great power or their complete destruction. A Mibu Clan character might be the key to fulfilling or preventing this prophecy. They would have to overcome many obstacles, including rival clans who see them as a threat because of the prophecy. Along the way, they could form unexpected alliances with other outcast clans or characters in the Naruto world. Their journey could also lead them to discover long - lost secrets about the Ninja world as a whole, which could change the balance of power in the series.