Perhaps the Organization 13 is somehow related to an ancient and forgotten ninja organization in the Naruto world. A young Naruto or other main characters discover this connection and have to figure out how to deal with the Organization 13, which has its own dark motives and plans for the ninja world.
One idea could be a crossover where members of Organization 13 end up in the Naruto world and have to adapt to its chakra - based powers. They might form alliances with some ninja clans while being in conflict with others.
One idea could be that Naruto is somehow transported to the world where Organization 13 exists. He might initially be seen as a threat but then prove his worth through his ninja skills and strong will. For example, he could help them in a battle against a common enemy.
One idea could be an OC who is a double agent within the Black Organization. They pretend to be loyal to Gin while secretly feeding information to the good guys. Another could be an OC with a special ability that makes Gin take a special interest in them, like an uncanny skill at forging documents that the Black Organization needs. A third idea is an OC who has a past connection with Gin that neither of them initially remembers, and as the story unfolds, this connection comes to light and changes their dynamic.
A plot idea could be that Naruto discovers a new, ancient form of chakra that has been lost for centuries. He then has to train to master this chakra while also dealing with the political implications within the Hidden Leaf Village. Some elders might be against him exploring this new power for fear of the unknown, but Naruto, being Naruto, is determined to master it for the good of the village.
One idea could be that the events of 9/11 somehow influence the Hidden Leaf Village. For example, they might tighten security and Naruto could be part of a new team in charge of protecting the village from potential outside threats inspired by the real - world event. Another plot could involve characters from Naruto trying to understand the concept of such a large - scale tragedy and how they can prevent similar things in their own world.
One idea could be a crossover where members of Organization 13 end up in the wizarding world of Harry Potter. They might be mistaken for dark wizards at first due to their strange appearance and powers. Another idea is that they form an alliance with certain Hogwarts houses to fight against a common enemy, like a new dark force emerging in both their worlds. A third idea could be that some members of Organization 13 attend Hogwarts as exchange students, leading to all sorts of chaos and new friendships.
One idea could be that Neji discovers a new hidden power within Naruto that he helps Naruto master. This could lead to them having to face a new, powerful enemy together.
One interesting plot idea could be a time - travel story. For example, Naruto is sent back in time to the era of the First Hokage. He could use his knowledge of future jutsu and events to change things for the better in the past. Another idea is a story where Naruto discovers a hidden clan within Konoha that has a unique and powerful Kekkei Genkai. He then has to help this clan gain acceptance in the village. A third idea might be a story where Naruto is turned into a different creature, like a cat or a fox, and has to find a way to turn back while still dealing with the normal threats to the village.
One idea could be a modern - day person suddenly being transported into the Naruto world and having to learn chakra control from scratch. They could struggle with the cultural differences and make friends with some of the original characters like Naruto or Sakura while trying to find a way back home.
A really interesting plot could be a time - travel one. Momiji somehow gets sent back in time to Naruto's early days in Konoha. She has to adapt to the past while also trying to help Naruto avoid some of the hardships he faced in his original timeline. It could be a story full of drama and interesting interactions as she tries to fit into the past world without changing too much.
One idea could be a story where Naruto is sent on a mission to the Soul Society and meets Soifon. They start off as rivals, with Soifon being distrustful of Naruto's brash and energetic ways. But as they face a common enemy, like a powerful Hollow that's immune to normal attacks, they have to work together. Naruto could teach Soifon about his never - give - up attitude and she could show him some of the more refined combat techniques of the Soul Reapers.